AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i295_bsub_mtub_300.orf -o295_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 ypfD 232 alternate gene name: jofD; similar to ribosomal protein S1 homolog #2 cmk 78 cytidylate kinase #3 ypfB 44 alternate gene name: jofB #4 ypfA 92 alternate gene name: jofA #5 ypeB 34 alternate gene name: joeB, yzuA; similar to hypothetical proteins #6 sleB 138 spore cortex-lytic enzyme #7 ypdC 119 similar to hypothetical proteins #8 ypdA 108 similar to thioredoxin reductase #9 ypcA 155 similar to glutamate dehydrogenase #10 ypbH 158 similar to negative regulation of competence MecA homolog #11 ypbG 85 similar to hypothetical proteins #12 ypbF 62 ypbF #13 ypbD 59 ypbD #14 ypbB 265 ypbB #15 polA 103 polA #16 rpsA 162 rpsA #17 Rv1707 300 hypothetical protein Rv1707 Motif number 1 TTTGGACCAAGGAGGTTATTCAA 1 220 1 GGAGTTATTC 0.788233 -13 CAGCAACCGTGCGGCTTTTTTGTGTGCAGTT 6 19 1 GCGGTTTTTT 0.948504 -120 TTTTTTGTGTGCAGTTTTTATGTTCTGAGGG 6 34 1 GCAGTTTTAT 0.938471 -105 TTTTATCATAGGAGATTTTTTATTTTTATGC 8 22 0 GGAGTTTTTT 0.982901 -87 TGATAAAATAGGAGATTTTTTTATTCGGAAA 8 45 1 GGAGTTTTTT 0.982901 -64 GCTGATTTCAGCAGTTTTTTTTCGTTAAAAA 9 28 1 GCAGTTTTTT 0.967114 -128 CAAGCACAATGCAGTTTTTATTGCCATACGG 10 29 0 GCAGTTTTAT 0.938471 -130 AATGGGGCGTTTTCTCAAACGATA 11 4 1 GGGGGTTTTC 0.874617 -82 TAAAAAGAATGGAGAGTTTTTT 11 74 1 GGAGGTTTTT 0.952203 -12 GAACAATCTGGGAGGTTTTATTC 14 3 0 GGAGTTTTAT 0.967547 -263 CATCATTAAGGGGGATGTTATGTAGATAACC 14 158 0 GGGGTGTTAT 0.76222 -108 GCGGGAATTCGGCGATTTTTCCGCCCTGAGT 16 31 1 GGCGTTTTTC 0.882468 -132 **** ****** Masking position 9 Map Score: 16.0755 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 273 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 2 AATAAAAGGACAGGTTTGTCAAGCAATAACATTCTATCTT 1 47 0 CGTGCAGCAC 0.978056 -186 TTCTGTCAACTCCTGCGATTGGCATTTCACTT 8 87 0 CGCCCTGCGG 0.912689 -22 ACTGAGTTCACTAGTAAGACAAGCACAATGCAGTTTTTAT 10 39 0 CATGCAGCAG 0.887399 -120 AAAGATTGATCCATTTGTTCCACCAAGAACAATCTGGGAG 14 20 0 CATTCACCAC 0.775659 -246 CGGTCCAGCCTACCGAGCCCGGGCGTAAAA 15 1 1 CGCGCACCGC 0.992689 -103 TGTTGCAGTTCTGCTGGCACCTGCGCCCGCATTCCACGTC 15 49 1 CGTCCTGCGC 0.962609 -55 AACTCGGTCCCGATTGCGCCGAGCGTGAACTCAGGGCGGA 16 50 0 CATGCAGCGC 0.99146 -113 CAATCGGGACCGAGTTTGTCCAGCGTGTACCCGTCGAGTA 16 74 1 CATGCAGCGC 0.99146 -89 AGGTACCAATCTGTCCCTACGACCCAACCCTGTCCGGAGC 16 122 1 CGCTCACCCC 0.823233 -41 CAGCCAAGCTTGAACGCTGCGAGCGAGCCCATGTAGAGCG 17 47 1 TACTCAGCGC 0.69682 -254 GAGCCCATGGCAAGTTGGCCCACCGATCGGTTTGGTACCA 17 89 0 CATGCACCGG 0.954237 -212 GGGCTCACAGCGGCTATCGCGAGCGTGTAGCCGATCATCG 17 123 1 CGTCCAGCGG 0.972864 -178 GCAACCCCTGCCGCTCAGGCCACCGTCGCCTGGACGATGA 17 157 0 CGTGCACCGC 0.992077 -144 ACCAGACTTACCGGCACTCCCTGCGGCAACCATGCCGCAA 17 210 0 CGCTCTGCGC 0.958557 -91 AGGCGAGCACCTTACTAGCCGAGCGAATCCGAACCCAACC 17 270 0 CTCGCAGCGC 0.963155 -31 * * * * * **** * Masking position 10 Map Score: 18.791 Number of sites scoring better than the average of aligned sites = 576 Number in coding regions = 546 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 TATCTTCGTTGAAAAATTCAAAAAAAGTGGCATTTG 1 17 0 GAAAAAAAAA 0.968643 -216 AAAGTTTTTTGAATGATCAATAAAAAGTTTTATTAG 1 98 0 GAAGAAAAAA 0.899663 -135 GCTTTTAGCCGAATATGTATTAAAGAATCATCCAAA 1 134 0 GAAATAAAGA 0.916577 -99 CGAACTTTATGAAAAAGGGTGAAAAATTGATGAATA 2 12 0 GAAAAAAAAA 0.968643 -67 AGCACGTAATGAAAAAAAGGAAAAGACATTTAGTCC 4 24 0 GAAAAAAAGA 0.974054 -69 CAGATATGAGAAAGCATAAAAAGAGGTGTGAT 5 7 1 TGAAAAAAAA 0.818705 -28 ATGTTCTGAGGGATAACAAGGAAAGAGTGTATAAAA 6 53 1 GGAAAAAAGA 0.964995 -86 TGTCTGCACTTAAAAAAACAAAAAGAGCATACGAAT 7 31 0 TAAAAAAAGA 0.881995 -89 ATAGATGTAGGAATATAAAGGAAAGAGGTTGCCTG 7 95 1 GAAATAAAGA 0.916577 -25 TTGATGATTTGCATAAAAATAAAAAATCTCCTATGA 8 12 1 GCAAAAAAAA 0.865629 -97 TTTTTTCGTTAAAAAACATGGAAAAACATAACGTTT 9 44 1 AAAAAAAAAA 0.70879 -112 TCAATAAGACGGACAATAAAAAAAGACGTTTCTATC 11 31 0 GGAAAAAAGA 0.964995 -55 TCCGTCTTATTGATAAGTTCTAAAAAGAATGGAGAG 11 54 1 TGAAAAAAAA 0.818705 -32 TACAATATATGAACGTAAAATAAAAATAATACC 12 8 0 GAAGTAAAAA 0.72407 -55 *** ** ***** Masking position 12 Map Score: 13.5555 Number of sites scoring better than the average of aligned sites = 680 Number in coding regions = 543 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 4 TTTGAAAGCTGAACATATAACATGCCCGCT 1 167 0 GAACATATAA 0.781222 -66 CCTCGTTACAGAAAATACGATTACACTTAA 6 93 1 GAAAATACGA 0.730832 -46 AGATGAGGAGCATATGATGCATTCGTA 7 8 1 GAGCATATGA 0.986352 -112 AAAACAAAAAGAGCATACGAATGCATCATA 7 23 0 GAGCATACGA 0.961608 -97 TTCGGAAATAGAAAATATGAAGTGAAATGC 8 68 1 GAAAATATGA 0.886805 -41 TCTATGCACAGATCATATGAAGGTGTATAC 9 82 1 GATCATATGA 0.951726 -74 CTCTGAAAGGGAGCATGTGAGAAACAGAAG 9 116 1 GAGCATGTGA 0.925409 -40 TAACAATTAAGAACCTATGACTCATCATCT 10 88 1 GAACCTATGA 0.886103 -71 TCATATAACACATTATATGAGATGATGAGT 10 107 0 CATTATATGA 0.635516 -52 TTCATTGCTACAATATATGAACGTAAAATA 12 22 0 CAATATATGA 0.800319 -41 AGATTATATTCAGCATATGACTGACCATGA 13 21 1 CAGCATATGA 0.973666 -39 ATAACTGCTTCAGCATATCATGGTCAGTCA 13 38 0 CAGCATATCA 0.811953 -22 ********** Masking position 2 Map Score: 9.83539 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 439 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 TTATTGCTTGACAAACCTGTCCTTTTATTAGA 1 58 1 ACAAACTGCC 0.714426 -175 ACATCGGCAAACACTTCCATACTATTTG 3 7 1 GCAAACCTCC 0.914265 -38 AAGCCGCACAGCAACCGTGCGGCTTTTTTGTG 6 11 1 GCAACCTGGG 0.88239 -128 CAGGCAACCTCTTTCCTTTATATTC 7 105 0 GCAACCCTTC 0.84353 -15 CACGCTCGGCGCAATCGGGACCGAGTTTGTCC 16 63 1 GCAATCGGCC 0.970452 -100 TCGTCAGGTACCAATCTGTCCCTACGACCCAA 16 117 1 CCAATCGTCC 0.845225 -46 TCCCTACGACCCAACCCTGTCCGGAGCAACCC 16 135 1 CCAACCTGCC 0.982901 -28 TGCCGCTCAGGCCACCGTCGCCTGGACGATGA 17 157 0 GCCACCTCCC 0.899454 -144 GATGAATAAGGCAACCCCTGCCGCTCAGGCCA 17 175 0 GCAACCCTCC 0.984045 -126 ACTCCCTGCGGCAACCATGCCGCAAGAGGATG 17 203 0 GCAACCTGCG 0.969443 -98 AGTCTGGTCGGCAACCTGGCCCGCTGCGGGTT 17 242 1 GCAACCGGCC 0.994763 -59 GAATCCGAACCCAACCCGCAGCGGGCCAGGTT 17 254 0 CCAACCGCGC 0.86186 -47 ****** ** ** Masking position 4 Map Score: 8.83391 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 200 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TTGAATAACCTCCTTGGTCCAAACC 1 218 0 TAACCTCCTT 0.966462 -15 TGTATAAAAATAACCTCGTTACAGAAAATA 6 80 1 TAACCTCGTT 0.847097 -59 CTTTTCAAGCCTCCTACTGCAAATTT 6 123 0 AAGCCTCCTA 0.963681 -16 TAAAAATAAAAAATCTCCTATGATAAAATA 8 25 1 AAATCTCCTA 0.959234 -84 CCGAATAAAAAAATCTCCTATTTTATCATA 8 43 0 AAATCTCCTA 0.959234 -66 TTGAGTTAACCTCCTAGAATCTTCTG 9 140 0 TAACCTCCTA 0.985128 -16 GAATAAAACCTCCCAGATTGTTCTT 14 6 1 AAACCTCCCA 0.963691 -260 ********** Masking position 2 Map Score: 5.93778 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 38 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 7 TCAGAACATAAAAACTGCACACAAAAAAGCC 6 31 0 AAAACTGCAA 0.972587 -108 AATGCAACGGAAAACTGCTGATTTCAGCAGT 9 12 1 AAAACTGCTA 0.964598 -144 TTAACGAAAAAAAACTGCTGAAATCAGCAGT 9 25 0 AAAACTGCTA 0.964598 -131 TATGGCAATAAAAACTGCATTGTGCTTGTCT 10 32 1 AAAACTGCAT 0.933496 -127 ATATAACTGCTTCAGCATATCAT 13 47 0 ATAACTGCTC 0.913548 -13 GCCCGGGCGTAAAACTGAAACGTGTTGCAGT 15 27 1 AAAACTGAAC 0.878589 -77 AGGTGCCAGCAGAACTGCAACACGTTTCAGT 15 40 0 AGAACTGCAC 0.953269 -64 ********* * Masking position 4 Map Score: 4.47903 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 153 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 TTAAAACGGTTTGAAAGCTGAACATATAAC 1 176 0 TTGAAAGCTG 0.957463 -57 AAAAAAACTGCTGAAATCAGCAGTTTTCCG 9 19 0 CTGAAATCAG 0.890201 -137 TGTCTTACTAGTGAACTCAGTGTAAACTGA 10 58 1 GTGAACTCAG 0.961678 -101 CATTTTTCTGTTGAAATGTGGCAGCAACAT 14 104 0 TTGAAATGTG 0.865427 -162 CGATTTCTGTTTGAAATCTGTTAAAATAAA 14 200 1 TTGAAATCTG 0.970935 -66 TGCGCCGAGCGTGAACTCAGGGCGGAAAAA 16 46 0 GTGAACTCAG 0.961678 -117 CCAGCCAAGCTTGAACGCTGCGAGCGAGCC 17 46 1 TTGAACGCTG 0.964516 -255 ********** Masking position 5 Map Score: 4.16874 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 131 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 GCCCGCTTTTAGCCGAATATGTATTAAAGA 1 144 0 AGCCGAATAT 0.678185 -89 ACGGTTTGAAAGCTGAACATATAACATGCC 1 171 0 AGCTGAACAT 0.657422 -62 AAGCCGCACAGCAACCGTGCG 6 2 1 AGCCGCACAG 0.976661 -137 CACACAAAAAAGCCGCACGGTTGCTGTGCG 6 15 0 AGCCGCACGG 0.985289 -124 GTGCCGAGCGTGCATCTGGGG 16 2 1 TGCCGAGCGT 0.961149 -161 GTCCCGATTGCGCCGAGCGTGAACTCAGGG 16 54 0 CGCCGAGCGT 0.917658 -109 TTTGGTACCAAACCGATCGGTGGGCCAACT 17 87 1 AACCGATCGG 0.784557 -214 GCGAGCGTGTAGCCGATCATCGTCCAGGCG 17 141 1 AGCCGATCAT 0.943413 -160 AGGCAACCCCTGCCGCTCAGGCCACCGTCG 17 169 0 TGCCGCTCAG 0.938952 -132 GCGGCATGGTTGCCGCAGGGAGTGCCGGTA 17 212 1 TGCCGCAGGG 0.821799 -89 CGGGCCAGGTTGCCGACCAGACTTACCGGC 17 235 0 TGCCGACCAG 0.916435 -66 GCACCTTACTAGCCGAGCGAATCCGAACCC 17 274 0 AGCCGAGCGA 0.911906 -27 ********** Masking position 3 Map Score: 8.18327 Number of sites scoring better than the average of aligned sites = 1249 Number in coding regions = 1206 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 GTCCAGCCTACCGAGCCCGGGCGTAAAACT 15 13 1 CCGAGCCCGG 0.635085 -91 GACGTGGAATGCGGGCGCAGGTGCCAGCAG 15 59 0 GCGGGCGCAG 0.976422 -45 TCGCCGAATTCCCGCCCCAGATGCACGCTC 16 16 0 CCCGCCCCAG 0.703947 -147 GACGTTTGGTGCCATCGCGGATAGCAGCCA 17 19 1 GCCATCGCGG 0.789463 -282 GCGGATAGCAGCCAGCCAAGCTTGAACGCT 17 35 1 GCCAGCCAAG 0.94473 -266 AACGCTGCGAGCGAGCCCATGTAGAGCGTT 17 59 1 GCGAGCCCAT 0.980263 -242 GATAGCCGCTGTGAGCCCATGGCAAGTTGG 17 111 0 GTGAGCCCAT 0.814083 -190 AGCGGCTATCGCGAGCGTGTAGCCGATCAT 17 131 1 GCGAGCGTGT 0.826752 -170 CCAACCCGCAGCGGGCCAGGTTGCCGACCA 17 246 0 GCGGGCCAGG 0.937841 -55 ACCTTACTAGCCGAGCGAATCCGAACCCAA 17 272 0 CCGAGCGAAT 0.831582 -29 ********** Masking position 6 Map Score: 4.26084 Number of sites scoring better than the average of aligned sites = 723 Number in coding regions = 657 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 GTTTTAATTAAGCTGTGTAGGTTTGGACCA 1 199 1 AGCTGTGTAG 0.764301 -34 CAATCCTTAGAGGAGAAAAGAGCAAGGAGA 2 53 1 AGGAGAAAAG 0.857608 -26 AAACAGGAGGAAAGGACTAAATGT 4 5 1 AGGAGGAAAG 0.959887 -88 TTGAATGCGAAAGAGTGAAGTCA 4 80 1 AAGAGTGAAG 0.778264 -13 GATCATATGAAGGTGTATACTATTCTCTGA 9 92 1 AGGTGTATAC 0.813786 -64 AAGTAGAGGCAGGAGGGAACGTT 10 146 1 AGGAGGGAAC 0.930693 -13 AAAATGGACAAGGTGTGAAGCGT 12 50 1 AGGTGTGAAG 0.969165 -13 GGAAGAATGTAGGTGGATAGG 14 255 1 AGGTGGATAG 0.937172 -11 ********** Masking position 9 Map Score: 1.71663 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 212 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 12 ACGAAGATAGAATGTTATTGCTTGACAAACCTG 1 44 1 AATGTTTGCT 0.843938 -189 CAGGCAACCTCTTTCCTTTATATTCCT 7 103 0 CAACTTTTCT 0.678349 -17 TGCTGAATATAATCTTTTTGCTGTT 13 3 0 AATCTTTGCG 0.985256 -57 TACTTATTGTAATGATGTTGCTGCCACATTTCA 14 90 1 AATGTTTGCG 0.95942 -176 AAGCATTCTCAATCATTTTTCTGTTGAAATGTG 14 114 0 AATCTTTTCG 0.963128 -152 CGTAAAACTGAAACGTGTTGCAGTTCTGCTGGC 15 34 1 AAACTTTGCG 0.976557 -70 CGATGGCACCAAACGTCGTTCTGCT 17 3 0 AAACTGTTCG 0.812201 -298 TTGCCTTATTCATCCTCTTGCGGCATGGTTGCC 17 193 1 CATCTTTGCG 0.974254 -108 **** * **** * Masking position 2 Map Score: 1.67336 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 254 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 ********** No masking Map Score: -4.51662e-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 AGGAGAAAAGAGCAAGGAGAGGAATT 2 63 1 AGCAAAGAGG 0.966123 -16 CTTAAAAATTTGCAGTAGGAGGCTTGAAAAG 6 118 1 TGCAGGGAGG 0.989609 -21 TTTTTTTAAGTGCAGACAGATGTAAAATTTTA 7 49 1 TGCAGAGATG 0.97591 -71 ATGATTTGTGTGCAAGTAGAGGCAGGAGGGAA 10 133 1 TGCAAAGAGG 0.989455 -26 GCGGCAACCATGCCGCAAGAGGATGAATAAGG 17 196 0 TGCCGAGAGG 0.989609 -105 ***** ***** Masking position 10 Map Score: 0.454041 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 44 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 ********** No masking Map Score: -4.51662e-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