AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_bsub_mtub_300.orf -o255_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 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #2 ynbA 220 similar to GTP-binding protein protease modulator #3 ynbB 187 similar to hypothetical proteins #4 glnR 110 transcriptional regulator #5 dnaJ 199 heat-shock protein #6 dnaK 23 class I heat-shock protein (chaperonin) #7 grpE 71 heat-shock protein #8 hrcA 119 transcriptional regulator #9 hemN 52 coproporphyrinogen III oxidase #10 lepA 133 GTP-binding protein #11 spoIIP 62 spoIIP #12 gpr 203 spore protease #13 Rv0347 300 hypothetical protein Rv0347 #14 dnaK 226 dnaK #15 dnaJ 35 dnaJ #16 dnaJ2 74 dnaJ2 #17 hrcA 171 hrcA Motif number 1 TTATTGTATTCACGGACATGGGGTGGACAAACCAT 1 142 0 CACGGCGGGG 0.952405 -159 CGTCTTTTGAAGCACATGTGCCGGCAAGTGAAG 3 9 1 GAAGCCGGCG 0.976145 -179 CAAGTGAAGGGAAGCTCCTTTCCAGAATCAAATCG 3 35 1 GAAGCCTCCG 0.680597 -153 TTTTCGGTCAGCTCCGGAAGCGGGGCTGACACTAA 5 18 0 GCTCCGGGGG 0.736346 -182 AGTGTAAGGAGAAGGACAGGTGCTGCCCTTCGATA 7 29 0 GAAGGCGGCG 0.94584 -43 AAGCCGCCGCAGTCTTGTACTGCGGCT 9 3 1 GCCGCGGCTG 0.860769 -50 TGAATCCCTCCAGCGCTTGTCTAGTAATTACTCT 11 39 0 CCAGCCGCTG 0.576348 -24 TCCTAAGATACAACCTGTAGCACAGTGTCTTAAGG 12 21 1 CAACCGGACG 0.505898 -183 CAGGCTATCCCACGCGGCTGCGAGGTGCCGCTTGG 13 40 1 CACGCGGGAG 0.708588 -261 TTGTCGTGCCGACCGTCGCGGGTGGCCGCGTTGAC 13 114 1 GACCGCGGTG 0.827515 -187 GTCACAGGCTGACGCGCCTGGCCAGCCAGACGCTC 13 162 1 GACGCCGCCG 0.989846 -139 TGGCCAGCCAGACGCTCGCGAAGTGCGGGTCCGTC 13 180 1 GACGCCGAGG 0.980448 -121 GCGGCTACGACACCCTCGCGGCCAGGACGGACCCG 13 205 0 CACCCCGCCG 0.942629 -96 GGGTGTCGTAGCCGCGGTCGTAGTGTGAGACTCCG 13 225 1 GCCGCGGAGG 0.946105 -76 TCCGACACCTGATCCGCCAGCGCAGAGATGTGAGA 13 256 1 GATCCCGGCG 0.879862 -45 TGGGAGAGGCCCCGGTCAAGCCCGGAGAGCAGTGC 14 11 0 CCCGGCGCCG 0.924606 -216 GTCGGCAGGGCACACGCTCGGGGCGTAGCTGGGAG 14 40 0 CACACCGGGG 0.850306 -187 GCGGGAACAAGACCCGCACGACCAGCGTTAGCATG 14 77 1 GACCCCGCCG 0.974704 -150 AGCTTGCCTCGACGGCGGTGTGCTGTCAATTCAGA 14 141 0 GACGGGGGCG 0.971343 -86 GCCGTCGAGGCAAGCTTGAGCGGGGTGCACTCATC 14 160 1 CAAGCTGGGG 0.703871 -67 ACGCGCACCTGCTGCAGGGTTTGTGGATA 16 5 1 GCACCGGAGG 0.643939 -70 TTTGTGGATAGCCGCTTGAGAAGCGGCATAAAGAC 16 30 1 GCCGCTGAGG 0.813027 -45 GCGGCATAAAGACGCGGCATAGGAGAATCAAGC 16 52 1 GACGCGTGGG 0.878874 -23 GATCATGCTGGACACGTTAGTCGGGGCACACGCCC 17 49 1 GACACTGCGG 0.508778 -123 GGCGTCTGCCGATGGTCAGGGGGCGTGTGCCCCGA 17 69 0 GATGGCGGGG 0.895987 -103 CCTGCTAGATGACGGTCAGTGGCCGCCGAGAACGT 17 102 1 GACGGCTGCG 0.848928 -70 GTAAAATGAAGCCGGTCAGGCAGCGTAAGAAGTGA 17 135 1 GCCGGCGAGG 0.93675 -37 ***** * * ** * Masking position 15 Map Score: 34.0407 Number of sites scoring better than the average of aligned sites = 1770 Number in coding regions = 1611 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 TAGAGAGAACAGAGAGGTGAAG 1 289 1 AGAGAGGGAA 0.905407 -12 TGTGCCGGCAAGTGAAGGGAAGCTCCTTTCC 3 27 1 AGTGAAGGAA 0.932156 -161 TAAGAAAAGGAGGAAATTGAG 4 100 1 AGGAAATGAG 0.83553 -11 CCCGGGATAAAAGGAATTGAAAAATCATAAT 5 128 1 AAGGAATGAA 0.699123 -72 AATTCGGGAGAGTGAAGCGAG 5 189 1 AGTGAAGGAG 0.925909 -11 TCCCTCAAAGTGTAAGGAGAAGGACAGGTGC 7 41 0 TGTAAGGGAA 0.819387 -31 TTACACTTTGAGGGAGGTGAACACA 7 57 1 AGGGAGGGAA 0.989862 -15 TCTTTCTGTAAAGAAGGTGAATCCG 9 38 1 AAGAAGGGAA 0.940376 -15 AATGTAAAACAAGAAAGAGAAAAGTTCCCTA 10 43 0 AAGAAAGGAA 0.848148 -91 AACAAGCTAGAGGAAGTAGAACTGT 11 5 0 AGGAAGTGAA 0.940376 -58 GGTTGTATCTTAGGAGGTGAAACAC 12 5 0 TAGGAGGGAA 0.826073 -199 TAGCATGCTCAGTAAGTTGAGTGCATCAGGC 14 105 1 AGTAAGTGAG 0.850756 -122 CAACAAAAGAGGAAGGCGAGAGGGGGTGAC 15 10 1 AGGAAGGGAG 0.982249 -26 CAGCGTAAGAAGTGAGGTGAGCAGTCG 17 155 1 AGTGAGGGAG 0.972443 -17 ******* *** Masking position 5 Map Score: 15.7597 Number of sites scoring better than the average of aligned sites = 695 Number in coding regions = 462 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 3 TTTTCAAAATGCTCATCCGTGATATGCGGCA 2 196 0 GCTCACCGTG 0.844302 -25 TGACTTTTTTTCTTGCCCGGGATAAAAGGAA 5 113 1 TCTTGCCGGG 0.915681 -87 CCAACGGACTGGCTGTCAGGCTATCCCACGC 13 24 1 GGCTGCAGGC 0.587346 -277 TGTCAGGCTATCCCACGCGGCTGCGAGGTGC 13 37 1 TCCCAGCGGC 0.936265 -264 TCCGATTGGTTGCCAAGCGGCACCTCGCAGC 13 56 0 TGCCAGCGGC 0.936268 -245 ACAATCGATCGGTCAACGGTGCTTTGTTGTC 13 88 1 GGTCACGGTG 0.67002 -213 TTTGTTGTCGTGCCGACCGTCGCGGGTGGCC 13 110 1 TGCCGCCGTC 0.875305 -191 GCGTCTGGCTGGCCAGGCGCGTCAGCCTGTG 13 164 0 GGCCAGCGCG 0.829933 -137 GGTCCGTCCTGGCCGCGAGGGTGTCGTAGCC 13 207 1 GGCCGGAGGG 0.9297 -94 TGCTCTCCGGGCTTGACCGGGGCCTCTCCCA 14 15 1 GCTTGCCGGG 0.955955 -212 TGTTCCCGCGTGTCGGCAGGGCACACGCTCG 14 55 0 TGTCGCAGGG 0.888629 -172 TGCTAACGCTGGTCGTGCGGGTCTTGTTCCC 14 79 0 GGTCGGCGGG 0.986067 -148 GTCGAGGCAAGCTTGAGCGGGGTGCACTCAT 14 163 1 GCTTGGCGGG 0.945836 -64 TTATGCCGCTTCTCAAGCGGCTATCCACAAA 16 30 0 TCTCAGCGGC 0.934052 -45 TCCAGCATGATCTCGTCGGGCTTCAGCCACT 17 30 0 TCTCGCGGGC 0.935934 -142 GTCTGCCGATGGTCAGGGGGCGTGTGCCCCG 17 70 0 GGTCAGGGGC 0.913854 -102 CATTTTACGTTCTCGGCGGCCACTGACCGTC 17 112 0 TCTCGCGGCC 0.72704 -60 TTCTTACGCTGCCTGACCGGCTTCATTTTAC 17 135 0 GCCTGCCGGC 0.803986 -37 ***** ***** Masking position 9 Map Score: 18.443 Number of sites scoring better than the average of aligned sites = 1666 Number in coding regions = 1543 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 AGATACCTGAAGTGTTTTTCTT 1 3 0 AGTGTTTTTC 0.782366 -298 TATTATAGTGAGCTTCTTTCTCATTATTTC 1 82 0 AGCTTCTTTC 0.952715 -219 TAAGGAATCCTGCGCTTTCCCGAGAAATAC 1 185 0 TGCGCTTTCC 0.713215 -116 TCGAAACAATTGCTTTTTTCGGGAACAATA 1 213 0 TGCTTTTTTC 0.851116 -88 ACACATGATAGGCGTTTGTCACAATCGGCA 1 242 1 GGCGTTTGTC 0.886795 -59 TTCAAATGGATGTTCCTTTCTTTTGCATAT 2 119 0 TGTTCCTTTC 0.727972 -102 AGTGAAGGGAAGCTCCTTTCCAGAATCAAA 3 37 1 AGCTCCTTTC 0.956249 -151 TTATGAAATGTGTTCTTTTCGGTCAGCTCC 5 38 0 TGTTCTTTTC 0.594148 -162 ATCGAAGGGCAGCACCTGTCCTTCTCCTTA 7 30 1 AGCACCTGTC 0.850138 -42 CTTGTACTGCGGCTTCTTTCTGTAAAGAAG 9 24 1 GGCTTCTTTC 0.926575 -29 GAATCCCTCCAGCGCTTGTCTAGTAATTAC 11 42 0 AGCGCTTGTC 0.931356 -21 ATAAATGTAAAGTATTTTTCATTGAAGGTT 12 116 1 AGTATTTTTC 0.451224 -88 GCACTTCGCGAGCGTCTGGCTGGCCAGGCG 13 176 0 AGCGTCTGGC 0.782895 -125 GAATATGTAGAGCTTCTTTCCTGCACTATG 14 194 0 AGCTTCTTTC 0.952715 -33 TCATCTAGCAGGCGTCTGCCGATGGTCAGG 17 84 0 GGCGTCTGCC 0.806058 -88 ********** Masking position 7 Map Score: 10.3793 Number of sites scoring better than the average of aligned sites = 1607 Number in coding regions = 1394 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 5 GTCGGATGTCAGCTGCCGCATATCACGGAT 2 183 1 AGCTGCCGCA 0.948294 -38 TCATTAAAATAGAAGCGGTCTACCATCGTT 3 72 0 AGAAGCGGTC 0.879632 -116 AAGCCGCCGCAGTCTTGTACT 9 2 1 AGCCGCCGCA 0.959791 -51 TACAGAAAGAAGCCGCAGTACAAGACTGCG 9 18 0 AGCCGCAGTA 0.835439 -35 AGATGGGGCACACCCAACGG 13 1 1 AGATGGGGCA 0.852536 -300 AGGGTGTCGTAGCCGCGGTCGTAGTGTGAG 13 224 1 AGCCGCGGTC 0.971452 -77 TAGCCGCTTGAGAAGCGGCATAAAGACGCG 16 38 1 AGAAGCGGCA 0.955033 -37 AGCGGCATAAAGACGCGGCATAGGAGAATC 16 51 1 AGACGCGGCA 0.97989 -24 TGGACACGTTAGTCGGGGCACACGCCCCCT 17 57 1 AGTCGGGGCA 0.919054 -115 ACCGTCATCTAGCAGGCGTCTGCCGATGGT 17 88 0 AGCAGGCGTC 0.791035 -84 GATGACGGTCAGTGGCCGCCGAGAACGTAA 17 109 1 AGTGGCCGCC 0.808637 -63 ********** Masking position 1 Map Score: 10.4927 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 827 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 AGGATTCCTTATTGTTCCCGAAAAAAGCAA 1 204 1 ATTGTTCCCG 0.984552 -97 GAAAAAAGCAATTGTTTCGACACATGATAG 1 223 1 ATTGTTTCGA 0.820597 -78 GCGGTCTACCATCGTTTCCGATTTGATTCT 3 58 0 ATCGTTTCCG 0.955727 -130 AAGTACCTATATTGTTGCCATTTGCTGAAT 12 164 0 ATTGTTGCCA 0.92127 -40 TGACCGATCGATTGTTTCCGATTGGTTGCC 13 73 0 ATTGTTTCCG 0.983344 -228 TCGTGCGGGTCTTGTTCCCGCGTGTCGGCA 14 68 0 CTTGTTCCCG 0.958853 -159 ********** Masking position 5 Map Score: 2.3314 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 99 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 AAAATGGCTTTCTCCTGAATCGTTTCTTGT 2 152 0 TCTCCTGAAT 0.968224 -69 TTTAAAAATTTCTCCTGGATTTGATGTTAA 4 15 1 TCTCCTGGAT 0.984359 -96 AAGTCAGGCATCTCTTGGCTTTGACTTTTT 5 92 1 TCTCTTGGCT 0.907901 -108 CTCGCTTCACTCTCCCGAATTTCTCACATA 5 180 0 TCTCCCGAAT 0.961921 -20 GCACTGCTCTCCGGGCTTGACCGGGGC 14 8 1 TCTCCGGGCT 0.971618 -219 GACCGGGGCCTCTCCCAGCTACGCCCCGAG 14 29 1 TCTCCCAGCT 0.890979 -198 GGTGAATCCTCCTGAATATGTAGAGCT 14 210 0 CCTCCTGAAT 0.903623 -17 ********** Masking position 3 Map Score: 4.71732 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 106 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 CGATTGCTTTGAAAAGGCGGAAATACGAGC 2 41 0 GAAAAGGCGG 0.911867 -180 ACTAAGTTAAGAAAAGGAGGAAATTGAG 4 93 1 GAAAAGGAGG 0.889338 -18 TTACATAGCAGGAGGTTATTCAA 6 6 1 TAGCAGGAGG 0.963956 -18 TCCTTACACTTTGAGGGAGGTGAACACA 7 54 1 TTGAGGGAGG 0.802796 -18 TACTAGACAAGCGCTGGAGGGATTCA 11 47 1 GCGCTGGAGG 0.965025 -16 GGTACTTAATGTGAAGGAGGCCCCTGT 12 187 1 GTGAAGGAGG 0.956282 -17 TCACATCTCTGCGCTGGCGGATCAGGTGTC 13 259 0 GCGCTGGCGG 0.972121 -42 CAAGCTTGCCTCGACGGCGGTGTGCTGTCA 14 148 0 TCGACGGCGG 0.921445 -79 GACCGTCATCTAGCAGGCGTCTGCCGATGG 17 89 0 TAGCAGGCGT 0.771442 -83 ********** Masking position 6 Map Score: 2.51301 Number of sites scoring better than the average of aligned sites = 909 Number in coding regions = 807 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 9 GTACAAAAATCAGCCCGTTGTATGAAAAAG 1 53 1 CAGCCCGTTG 0.988207 -248 GCCTGACAGCCAGTCCGTTGGGTGTGCCCC 13 15 0 CAGTCCGTTG 0.990535 -286 TGTTGTCGTGCCGACCGTCGCGGGTGGCCG 13 112 1 CCGACCGTCG 0.981819 -189 CGTCGCCTTCCGTCCGTTGATCTCACATC 13 282 0 CCGTCCGTTG 0.993876 -19 ********** Masking position 8 Map Score: 2.26465 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 9 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 TTTGTTTTTAATCATTTTGTCAGAGTATTATAGT 1 103 0 ATCTTTTGTA 0.952437 -198 CCGCTTGAATATCATATAGAGAGAACAGAGAGGT 1 273 1 ATCTATAGAA 0.782066 -28 TTTCAAAGCAATCGATTTGTGGTATACACATGCA 2 57 1 ATCATTTGTA 0.879962 -164 AGAAAGGAACATCCATTTGAACGAACAAGAAACG 2 128 1 ATCATTTGAA 0.921631 -93 GAATCCTTACATCGTATTGACACATAATATAACA 4 45 1 ATCTATTGAA 0.952437 -66 ATTAGATTGTATCATTTTGAATTATGATTTTTCA 5 145 0 ATCTTTTGAA 0.96981 -55 TTGTGGTTTGATACTTTTGTTATAGAATTAGCAC 8 62 1 ATATTTTGTA 0.69099 -58 AATCTTTACAATCCTATTGATATAATCTAAGCTA 10 75 1 ATCTATTGAA 0.952437 -59 *** ****** * Masking position 1 Map Score: 1.57254 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 138 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 TGTCACAATCGGCATCCGCTTGAATATCAT 1 258 1 GGCATCCGCT 0.943629 -43 TTATAGAATTAGCACTCGCTTATTGAGAGT 8 81 1 AGCACTCGCT 0.772819 -39 AGATGGGGCACACCCAACGGACTGGC 13 7 1 GGCACACCCA 0.912374 -294 TGTCAACGCGGCCACCCGCGACGGTCGGCA 13 120 0 GCCACCCGCG 0.943952 -181 CGATATTGCGGTCACAGGCTGACGCGCCTG 13 152 1 GTCACAGGCT 0.847445 -149 CGCCTGGCCAGCCAGACGCTCGCGAAGTGC 13 176 1 GCCAGACGCT 0.952847 -125 GTGTCGGCAGGGCACACGCTCGGGGCGTAG 14 47 0 GGCACACGCT 0.994665 -180 GTCGCGTCACCCCCTCTCGCCTTCC 15 21 0 GTCACCCCCT 0.904416 -15 CGTTAGTCGGGGCACACGCCCCCTGACCAT 17 63 1 GGCACACGCC 0.990314 -109 CCTGACCATCGGCAGACGCCTGCTAGATGA 17 84 1 GGCAGACGCC 0.964188 -88 ********** Masking position 4 Map Score: 9.47384 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 240 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 ********** No masking Map Score: -8.6443e-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 13 ********** No masking Map Score: -8.6443e-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 14 ********** No masking Map Score: -8.6443e-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