AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i295_bsub_mtub_100.orf -o295_bsub_mtub_100.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 rpsA 162 rpsA #8 Rv1707 300 hypothetical protein Rv1707 Motif number 1 GTTATTGCTTGACAAACCTGTCCTTTTATTAGA 1 57 1 GACAAACGCC 0.899088 -176 ACATCGGCAAACACTTCCATACTATTTG 3 6 1 GGCAAACTCC 0.913466 -39 GTGCCGAGCGTGCATCTGGGGCGGG 7 3 1 GCCGAGCGAT 0.89718 -160 TCCCGATTGCGCCGAGCGTGAACTCAGGGCGGA 7 50 0 GCCGAGCGAC 0.992508 -113 CGCAATCGGGACCGAGTTTGTCCAGCGTGTACC 7 72 1 ACCGAGTGCC 0.823841 -91 GTCCCTACGACCCAACCCTGTCCGGAGCAACCC 7 134 1 CCCAACCGCC 0.980112 -29 ATAGCAGCCAGCCAAGCTTGAACGCTGCGAGCG 8 39 1 GCCAAGCGAC 0.989456 -262 GCTTGAACGCTGCGAGCGAGCCCATGTAGAGCG 8 54 1 TGCGAGCGCC 0.981576 -247 GTGAGCCCATGGCAAGTTGGCCCACCGATCGGT 8 98 0 GGCAAGTGCC 0.983893 -203 CAGCGGCTATCGCGAGCGTGTAGCCGATCATCG 8 130 1 CGCGAGCGAG 0.860394 -171 TCATCGTCCAGGCGACGGTGGCCTGAGCGGCAG 8 157 1 GGCGACGGCC 0.842417 -144 GGATGAATAAGGCAACCCCTGCCGCTCAGGCCA 8 175 0 GGCAACCTCC 0.880243 -126 CACTCCCTGCGGCAACCATGCCGCAAGAGGATG 8 203 0 GGCAACCGCG 0.983562 -98 AAGTCTGGTCGGCAACCTGGCCCGCTGCGGGTT 8 241 1 GGCAACCGCC 0.996999 -60 CACCTTACTAGCCGAGCGAATCCGAACCCAACC 8 270 0 GCCGAGCACC 0.973658 -31 ******* * ** Masking position 5 Map Score: 24.415 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 698 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 AAGCCGCACAGCAACCGTGCGGCTTT 6 2 1 AGCCGCCGAC 0.995084 -137 ATCGCCGAATTCCCGCCCCAGATGCACGCTCGGCA 7 12 0 TCCCGCCAAC 0.858307 -151 TCGGCGATTTTTCCGCCCTGAGTTCACGCTCGGCG 7 39 1 TTCCGCCGGC 0.990419 -124 TCCAGCGTGTACCCGTCGAGTAGCCTCGTCAGGTA 7 92 1 ACCCGTGGAC 0.858074 -71 GCTGGCTGCTATCCGCGATGGCACCAAACGTCGTT 8 16 0 ATCCGCAGCC 0.891868 -285 TTTGGTACCAAACCGATCGGTGGGCCAACTTGCCA 8 87 1 AACCGACGGC 0.952506 -214 CGCTCGCGATAGCCGCTGTGAGCCCATGGCAAGTT 8 113 0 AGCCGCGGGC 0.997149 -188 GCGAGCGTGTAGCCGATCATCGTCCAGGCGACGGT 8 141 1 AGCCGACTGC 0.924333 -160 AGGCAACCCCTGCCGCTCAGGCCACCGTCGCCTGG 8 164 0 TGCCGCCGCC 0.995753 -137 GCGGCATGGTTGCCGCAGGGAGTGCCGGTAAGTCT 8 212 1 TGCCGCGGGC 0.995784 -89 CGGGCCAGGTTGCCGACCAGACTTACCGGCACTCC 8 230 0 TGCCGACGCA 0.889783 -71 TCCGAACCCAACCCGCAGCGGGCCAGGTTGCCGAC 8 248 0 ACCCGCGGGA 0.961185 -53 ****** * * * * Masking position 4 Map Score: 15.3207 Number of sites scoring better than the average of aligned sites = 757 Number in coding regions = 671 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 AATCATCCAAAAAAGTTTTTTGAATGATCAATAA 1 111 0 AAAAGTTTAA 0.826482 -122 GTTTGGACCAAGGAGGTTATTCAA 1 219 1 AGGAGGTTAA 0.977309 -14 AACTTTATGAAAAAGGGTGAAAAATTGATGAATA 2 12 0 AAAAGGTAAA 0.975691 -67 AAAGCATAAAAAGAGGTGTGATAA 5 21 1 AAGAGGGAAA 0.978388 -14 ATAACAAGGAAAGAGTGTATAAAAATAACCTCGT 6 65 1 AAGAGTTAAA 0.975691 -74 AATTTGCAGTAGGAGGCTTGAAAAG 6 124 1 AGGAGGTAAA 0.990001 -15 ACCATGCCGCAAGAGGATGAATAAGGCAACCCCT 8 188 0 AAGAGGTAAA 0.993249 -113 ****** * * ** Masking position 4 Map Score: 4.41409 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 146 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 CTGAACATATAACATGCCCGCTTTTAGCCGA 1 158 0 AAATGCCCGC 0.956087 -75 TTTCGCATTCAATATACTCACGTTTTTATTA 4 61 0 AAATACTCAC 0.812067 -32 CAGAACATAAAAACTGCACACAAAAAAGCCG 6 30 0 AACTGCACAC 0.894853 -109 ATTCCCGCCCCAGATGCACGCTCGGCAC 7 8 0 CAATGCACGC 0.983298 -155 GGCTACTCGACGGGTACACGCTGGACAAACT 7 86 0 CGGTACACGC 0.880767 -77 AAACGCTCTACATGGGCTCGCTCGCAGCGTT 8 59 0 CAGGGCTCGC 0.988969 -242 GCCAACTTGCCATGGGCTCACAGCGGCTATC 8 110 1 CAGGGCTCAC 0.972258 -191 CTCGGCTAGTAAGGTGCTCGCCTG 8 287 1 AAGTGCTCGC 0.990081 -14 ** ******** Masking position 7 Map Score: 4.46547 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 343 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 CGTAGGGACAGATTGGTACCTGACGAGGCT 7 113 0 GATTGGTACC 0.970763 -50 ATTGTTGGGTTGCTCCGGACAGG 7 150 0 GTTGGGTTGC 0.97101 -13 GCAGAACGACGTTTGGTGCCATCGCGGATA 8 12 1 GTTTGGTGCC 0.989227 -289 CATGTAGAGCGTTTGGTACCAAACCGATCG 8 76 1 GTTTGGTACC 0.990927 -225 CCCGCTGCGGGTTGGGTTCGGATTCGCTCG 8 261 1 GTTGGGTTCG 0.97101 -40 ********** Masking position 7 Map Score: 3.89257 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 6 GTTGAAAAATTCAAAAAAAGTGGCATTTGC 1 16 0 TCAAAAAAAG 0.924314 -217 AGTATTAACTTCTAATAAAAGGACAGGTTT 1 70 0 TCTAATAAAA 0.834531 -163 TTTTGAATGATCAATAAAAAGTTTTATTAG 1 98 0 TCAATAAAAA 0.884499 -135 TAAAGAATCATCCAAAAAAGTTTTTTGAAT 1 120 0 TCCAAAAAAG 0.84619 -113 TAGCCGAATATGTATTAAAGAATCATCCAA 1 135 0 TGTATTAAAG 0.90289 -98 CCTACACAGCTTAATTAAAACGGTTTGAAA 1 190 0 TTAATTAAAA 0.677406 -43 AAGCACGTAATGAAAAAAAGGAAAAGACAT 4 31 0 TGAAAAAAAG 0.902892 -62 TACTCACGTTTTTATTAAAGCACGTAATGA 4 48 0 TTTATTAAAG 0.804878 -45 AAGGAAAGAGTGTATAAAAATAACCTCGTT 6 70 1 TGTATAAAAA 0.853515 -69 ********** Masking position 4 Map Score: 2.14617 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 693 Number in noncoding regions = 222 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 7 AACTTCTAATAAAAGGACAGGTTTGTCAAG 1 64 0 AAAAGGACAG 0.961366 -169 GGAGAAAAGAGCAAGGAGAGGAATT 2 64 1 GCAAGGAGAG 0.982295 -15 AAACAGGAGGAAAGGACTAAATGTCTTTT 4 10 1 GAAAGGACTA 0.859138 -83 CGTAATGAAAAAAAGGAAAAGACATTTAGT 4 26 0 AAAAGGAAAA 0.750798 -67 CTGAGGGATAACAAGGAAAGAGTGTATAAA 6 58 1 ACAAGGAAAG 0.945552 -81 GGGTTGGGTCGTAGGGACAGATTGGTACCT 7 122 0 GTAGGGACAG 0.931914 -41 CATGGTTGCCGCAGGGAGTGCCGGTAAGTC 8 216 1 GCAGGGAGTG 0.941999 -85 ********** Masking position 7 Map Score: 1.67596 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 488 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 8 AATTAAAACGGTTTGAAAGCTGAACATATAAC 1 176 0 GTTGAAACTG 0.925622 -57 AGCTGTGTAGGTTTGGACCAAGGAGGTTATTC 1 209 1 GTTGGACAAG 0.955968 -24 ATTGCGCCGAGCGTGAACTCAGGGCGGAAAAA 7 46 0 GCTGAACCAG 0.9903 -117 AGCCAGCCAAGCTTGAACGCTGCGAGCGAGCC 8 44 1 GCTGAACCTG 0.993212 -257 GGCCACCGTCGCCTGGACGATGATCGGCTACA 8 148 0 GCTGGACATG 0.985937 -153 ** ***** *** Masking position 7 Map Score: 0.698251 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 78 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: -3.45081e-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 10 ********** No masking Map Score: -3.45081e-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 11 ********** No masking Map Score: -3.45081e-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