AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_mtub_reg_300.orf -o00740_mtub_300.ace -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ribC 84 ribC #2 Rv1413 213 hypothetical protein Rv1413 #3 ribA2 104 ribA2 #4 Rv1936 224 hypothetical protein Rv1936 #5 Rv2206 128 hypothetical protein Rv2206 #6 cobT 78 cobT #7 ribF 210 ribF Motif number 1 GCACCCCACTCGCCGACCGGCCAACTCACA 1 33 0 CGCCGACCGG 0.98495 -52 TGGGGTGCGGGTCCGCGGGATTGCTGCCTA 1 55 1 GTCCGCGGGA 0.829079 -30 CTCCCTCCCTCGGCGAGCGATG 2 3 0 CGGCGAGCGA 0.929307 -211 CGCTCGCCGAGGGAGGGAGCCCCATGTCTT 2 14 1 GGGAGGGAGC 0.834126 -200 ATCCCTTTCGCGGCGACGGCGGAACTCATT 2 114 0 CGGCGACGGC 0.964219 -100 TGGGGACGCAGGGCGATCCCTTTCGCGGCG 2 129 0 GGGCGATCCC 0.794913 -85 TATGGGCGATCTCAGGCAGCTTGTGCGTCT 2 164 0 CTCAGGCAGC 0.734701 -50 CCATATGCAACTCCGCGCGGGCGCGCGGCC 2 189 1 CTCCGCGCGG 0.934191 -25 CGTCAGGCCGCGCGCCCGCGCGGAG 2 199 0 GGCCGCGCGC 0.857246 -15 CCGTGACCAAGTGCGACAGGA 3 2 0 GTGCGACAGG 0.843435 -103 TGTCAGGCCTGGCCGCACGCGAAGCCCACG 3 71 0 GGCCGCACGC 0.969398 -34 TATACGCAAAGGGCGCCACCGCAGCGCGCC 4 170 1 GGGCGCCACC 0.965636 -55 GTCGGATGCCCGGCGCGCTGCGGTGGCGCC 4 181 0 CGGCGCGCTG 0.655045 -44 CGCGCCGGGCATCCGACCGGTACAACCAGG 4 194 1 ATCCGACCGG 0.87415 -31 GCACCAATGACTGCGGCCCAGGCACGGGCC 5 13 1 CTGCGGCCCA 0.809241 -116 AAGCGACTTGCGCCGGGCCCGTGCCTGGGC 5 28 0 CGCCGGGCCC 0.935858 -101 CTAAGTTTGGGGCCGGCAAGCGACTTGCGC 5 45 0 GGCCGGCAAG 0.927176 -84 CCCCAAACTTAGCCGCGAGGAACGGAGAGC 5 63 1 AGCCGCGAGG 0.952721 -66 CCGCGAGGAACGGAGAGCCGAAAAGGCCGC 5 75 1 CGGAGAGCCG 0.469217 -54 GAGCCGAAAAGGCCGCAAACCGGGCCCGGA 5 89 1 GGCCGCAAAC 0.727894 -40 GCGTTCCGTCATCCGGGCCCGGTTTGCGGC 5 100 0 ATCCGGGCCC 0.918024 -29 GATGACGGAACGCCGGGAACGC 5 117 1 CGCCGGGAAC 0.958214 -12 GATCGGTTCGGTCCGCCCGCTGAGCACTAG 6 45 0 GTCCGCCCGC 0.990386 -34 GAACCGATCAAGCCGGCGAAAGG 6 66 1 AGCCGGCGAA 0.534173 -13 ATCGTTCGGTATGCGCGCGCCAATTCTCTG 7 63 1 ATGCGCGCGC 0.951919 -148 GCGGCACCGTGGCCGGTCCCAGAGAATTGG 7 82 0 GGCCGGTCCC 0.934341 -129 CGTCCGGGAACGCCGGCGGCACCGTGGCCG 7 97 0 CGCCGGCGGC 0.989972 -114 CCCGGACGTGCTGCGCCAGGTGTCCGGCGG 7 119 1 CTGCGCCAGG 0.933101 -92 GCCAGGTGTCCGGCGGCCGCGTGCATGGTG 7 133 1 CGGCGGCCGC 0.995332 -78 CCAGCGGCCGATCCGGGAACACCATGCACG 7 152 0 ATCCGGGAAC 0.710119 -59 TTCCCGGATCGGCCGCTGGCCAGAGCCCAC 7 163 1 GGCCGCTGGC 0.916575 -48 GTGGTCGGCCAGGCGCCAGATTCACCGGTG 7 190 0 AGGCGCCAGA 0.843067 -21 TCTGGCGCCTGGCCGACCACC 7 200 1 GGCCGACCAC 0.964724 -11 ********** Masking position 5 Map Score: 56.1007 Number of sites scoring better than the average of aligned sites = 93417 Number in coding regions = 87625 Number in noncoding regions = 5792 Number of orfs with sites within 600 bp upstream = 1581 Fraction of orfs with sites within 600 bp upstream = 0.253935 Motif number 2 GGGTGTCTGTGAGTTGGCCGGTCGGCGAGTGG 1 26 1 GAGTGCCGGT 0.905538 -59 CGGTCGGCGAGTGGGGTGCGGGTCCGCGGGAT 1 44 1 GTGGGGCGGG 0.964253 -41 CCAGGTTAGGCAGCAATCCCGCGGACCCGCAC 1 59 0 CAGCACCCGC 0.726626 -26 CGGGCGTATCGATCTCGTCCGGAATGCAAGAC 2 39 0 GATCCTCCGG 0.937502 -175 CGCGGTCGATCAGCACGTCGGGCGTATCGATC 2 57 0 CAGCCTCGGG 0.984713 -157 TCGGGCGAATGAGTTCCGCCGTCGCCGCGAAA 2 107 1 GAGTCGCCGT 0.93291 -107 CGTCAGGCCGCGCGCCCGCGCGGAGTTGC 2 195 0 CCGCCCCCGC 0.755671 -19 ATGAACCATTGAGCCAGGCGGTATTGCCGTGA 3 26 0 GAGCAGCGGT 0.803349 -79 AATGGAACACGTGGGCTTCGCGTGCGGCCAGG 3 62 1 GTGGCTCGCG 0.598602 -43 TAACCTCGCACAGGTCAGCCGTTCACGTCCAG 4 23 0 CAGGCGCCGT 0.968618 -202 TGACCTGTGCGAGGTTACCCGTCCCTTAGCCA 4 38 1 GAGGTCCCGT 0.651522 -187 GGCGCCACCGCAGCGCGCCGGGCATCCGACCG 4 181 1 CAGCCCCGGG 0.99135 -44 GCGCGCCGGGCATCCGACCGGTACAACCAGGA 4 193 1 CATCGCCGGT 0.851336 -32 GCACCAATGACTGCGGCCCAGGCACGGGCCCG 5 13 1 CTGCGCCAGG 0.820659 -116 GCCGGCAAGCGACTTGCGCCGGGCCCGTGCCT 5 32 0 GACTGGCCGG 0.658685 -97 TCGCGGCTAAGTTTGGGGCCGGCAAGCGACTT 5 49 0 GTTTGGCCGG 0.714564 -80 GGCGTTCCGTCATCCGGGCCCGGTTTGCGGCC 5 99 0 CATCGGCCCG 0.6425 -30 GCGTTCCCGGCGTTCCGTCATCCGGGCC 5 111 0 CCGGGTCCGT 0.726384 -18 CACCGGGTGAGATGACTTCCGGCGTCCG 6 7 0 GATGCTCCGG 0.906557 -72 GAGCACTAGGGTGTACACCGGGTGAGATGACT 6 22 0 GTGTCCCGGG 0.930656 -57 GTACACCCTAGTGCTCAGCGGGCGGACCGAAC 6 38 1 GTGCCGCGGG 0.980097 -41 TCGCCGGCTTGATCGGTTCGGTCCGCCCGCTG 6 53 0 GATCGTCGGT 0.774405 -26 GACCATTGATCAGGTGATCAGGGAGTGGGTCT 7 12 0 CAGGGTCAGG 0.806532 -199 GGACCGGCCACGGTGCCGCCGGCGTTCCCGGA 7 93 1 CGGTCGCCGG 0.876845 -118 ACACCTGGCGCAGCACGTCCGGGAACGCCGGC 7 110 0 CAGCCTCCGG 0.987242 -101 CGTGCTGCGCCAGGTGTCCGGCGGCCGCGTGC 7 125 1 CAGGGCCGGC 0.922446 -86 CTCTGGCCAGCGGCCGATCCGGGAACACCATG 7 156 0 CGGCGTCCGG 0.930414 -55 CCGCTGGCCAGAGCCCACCGGTGAATCTGGCG 7 175 1 GAGCCCCGGT 0.976158 -36 GGTGGTCGGCCAGGCGCCAGATT 7 198 0 GTGGCGCCAG 0.547071 -13 **** * ***** Masking position 9 Map Score: 38.6951 Number of sites scoring better than the average of aligned sites = 47776 Number in coding regions = 44769 Number in noncoding regions = 3007 Number of orfs with sites within 600 bp upstream = 1275 Fraction of orfs with sites within 600 bp upstream = 0.204786 Motif number 3 TCAGCACGTCGGGCGTATCGATCTCGTCCG 2 50 0 GGGCGTATCG 0.703272 -164 TACGCCCGACGTGCTGATCGACCGCGACAT 2 63 1 GTGCTGATCG 0.917157 -151 ACGCAGGGCGATCCCTTTCGCGGCGACGGC 2 124 0 ATCCCTTTCG 0.432104 -90 GATCTCAGGCAGCTTGTGCGTCTTCACGTG 2 157 0 AGCTTGTGCG 0.642273 -57 TGGAACACGTGGGCTTCGCGTGCGGCCAGG 3 64 1 GGGCTTCGCG 0.941878 -41 CTAGCTGTCAGGCCTGGCCGCACGCGAAGC 3 76 0 GGCCTGGCCG 0.79458 -29 GTGAACGGCTGACCTGTGCGAGGTTACCCG 4 29 1 GACCTGTGCG 0.924688 -196 TAGCCAACATGTCCATAGCCAATACGCACA 4 64 1 GTCCATAGCC 0.849398 -161 ATGGGAATTTGTCTATATCGATCACTCTCA 4 94 0 GTCTATATCG 0.443981 -131 CTGCGGTGGCGCCCTTTGCGTATATCACAG 4 164 0 GCCCTTTGCG 0.91881 -61 ACTTGCGCCGGGCCCGTGCCTGGGCCGCAG 5 23 0 GGCCCGTGCC 0.882101 -106 CCCGGCGCAAGTCGCTTGCCGGCCCCAAAC 5 41 1 GTCGCTTGCC 0.451819 -88 CCCGGTTTGCGGCCTTTTCGGCTCTCCGTT 5 83 0 GGCCTTTTCG 0.967277 -46 GTACACCCTAGTGCTCAGCGGGCGGACCGA 6 38 1 GTGCTCAGCG 0.809103 -41 CCTTTCGCCGGCTTGATCGGTTCGGTCCG 6 60 0 GGCTTGATCG 0.87966 -19 GTTCCCGGACGTGCTGCGCCAGGTGTCCGG 7 116 1 GTGCTGCGCC 0.858555 -95 ATCGGCCGCTGGCCAGAGCCCACCGGTGAA 7 170 1 GGCCAGAGCC 0.676449 -41 ********** Masking position 9 Map Score: 6.59756 Number of sites scoring better than the average of aligned sites = 26049 Number in coding regions = 24406 Number in noncoding regions = 1643 Number of orfs with sites within 600 bp upstream = 956 Fraction of orfs with sites within 600 bp upstream = 0.15355 Motif number 4 CAGACACCCTCTACGATGCAGGGT 1 5 0 CTACGATGCA 0.914606 -80 GGCCTGACAGCTAGGTAGCAAAG 3 92 1 CTAGGTAGCA 0.96125 -13 TACACAAGTGCTTCTTTGCATGGGAATTTG 4 113 0 CTTCTTTGCA 0.879988 -112 TACCAAGATACTTCGTTGTACACAAGTGCT 4 131 0 CTTCGTTGTA 0.979085 -94 AACGAAGTATCTTGGTAGTACTGTGATATA 4 144 1 CTTGGTAGTA 0.963962 -81 GTCAACCCTTCCTGGTTGTACCGGTCGGAT 4 204 0 CCTGGTTGTA 0.949797 -21 CCGCTGAGCACTAGGGTGTACACCGGGTGA 6 29 0 CTAGGGTGTA 0.945253 -50 ********** Masking position 10 Map Score: 3.81761 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 118 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 CGCACCAGGTTAGGCAGCAAT 1 74 0 GCACCAGGTT 0.942681 -11 GAGGGAGGGAGCCCCATGTCTTGCATTCCG 2 22 1 GCCCCATGTC 0.944137 -192 AGATCGATACGCCCGACGTGCTGATCGACC 2 56 1 GCCCGACGTG 0.87915 -158 GAACTCATTCGCCCGATGTTGCGGTCAAGG 2 93 0 GCCCGATGTT 0.910565 -121 GAAAGGGATCGCCCTGCGTCCCCACGTGAA 2 135 1 GCCCTGCGTC 0.911336 -79 TCCTGTCGCACTTGGTCACGGCAATAC 3 8 1 GCACTTGGTC 0.825446 -97 GATGCCCGGCGCGCTGCGGTGGCGCCCTTT 4 177 0 GCGCTGCGGT 0.82486 -48 CAAGCGACTTGCGCCGGGCCCGTGCCTGGG 5 29 0 GCGCCGGGCC 0.891616 -100 CGCCCGCTGAGCACTAGGGTGTACACCGGG 6 32 0 GCACTAGGGT 0.835491 -47 AACGCCGGCGGCACCGTGGCCGGTCCCAGA 7 89 0 GCACCGTGGC 0.898055 -122 GACACCTGGCGCAGCACGTCCGGGAACGCC 7 113 0 GCAGCACGTC 0.838969 -98 GACGTGCTGCGCCAGGTGTCCGGCGGCCGC 7 123 1 GCCAGGTGTC 0.74434 -88 ********** Masking position 2 Map Score: 8.11372 Number of sites scoring better than the average of aligned sites = 10993 Number in coding regions = 10193 Number in noncoding regions = 800 Number of orfs with sites within 600 bp upstream = 607 Fraction of orfs with sites within 600 bp upstream = 0.0974944 Motif number 6 GGCCGGTCGGCGAGTGGGGTGCGGGTCCGC 1 41 1 CGAGTGGGGT 0.910486 -44 GGTCGATCAGCACGTCGGGCGTATCGATCT 2 56 0 CACGTCGGGC 0.946019 -158 TGTGCGTCTTCACGTGGGGACGCAGGGCGA 2 143 0 CACGTGGGGA 0.960045 -71 CGCGGAGTTGCATATGGGCGATCTCAGGCA 2 176 0 CATATGGGCG 0.871961 -38 TATGCAACTCCGCGCGGGCGCGCGGCCTGA 2 192 1 CGCGCGGGCG 0.830215 -22 CTGAATGGAACACGTGGGCTTCGCGTGCGG 3 59 1 CACGTGGGCT 0.992641 -46 ACGTGGGCTTCGCGTGCGGCCAGGCCTGAC 3 70 1 CGCGTGCGGC 0.92829 -35 TGGCTATGGACATGTTGGCTAAGGGACGGG 4 55 0 CATGTTGGCT 0.868098 -170 CTCTCATGTGCGTATTGGCTATGGACATGT 4 70 0 CGTATTGGCT 0.460966 -155 CCTGGCGCAGCACGTCCGGGAACGCCGGCG 7 109 0 CACGTCCGGG 0.87798 -102 GAACACCATGCACGCGGCCGCCGGACACCT 7 136 0 CACGCGGCCG 0.864058 -75 GCCAGATTCACCGGTGGGCTCTGGCCAGCG 7 176 0 CCGGTGGGCT 0.855725 -35 ********** Masking position 1 Map Score: 8.72416 Number of sites scoring better than the average of aligned sites = 6547 Number in coding regions = 5984 Number in noncoding regions = 563 Number of orfs with sites within 600 bp upstream = 458 Fraction of orfs with sites within 600 bp upstream = 0.0735625 Motif number 7 CCAACTCACAGACACCCTCTACGATGCAGGGT 1 9 0 GCACCCTACA 0.757262 -76 GGAGCCCCATGTCTTGCATTCCGGACGAGATCGA 2 29 1 GCTGCTTCCG 0.925531 -185 GATCGACCGCGACATCCTTGACCGCAACATCGGG 2 78 1 GCACCTGACG 0.993551 -136 ACTTGGTCACGGCAATACCGCCTGGCTCAATGGT 3 20 1 GCATACGCCG 0.865918 -85 TTCGCGTGCGGCCAGGCCTGACAGCTAGGTAGCA 3 78 1 GCAGCTGACG 0.985581 -27 CCTCGCACAGGTCAGCCGTTCACGTCCAGTAAGG 4 18 0 GCACCTTCAG 0.945567 -207 CGTCAACCCTTCCTGGTTGTACCGG 4 210 0 GCACCTTCCG 0.995485 -15 CGGCACCAATGACTGCGGCCCAGGC 5 2 1 GCACATGACG 0.977512 -127 CCGGCGTTCCGTCATCCGGGCCCGGTTTGCGGCC 5 99 0 GCACCGGCCG 0.995145 -30 TACACCGGGTGAGATGACTTCCGGCGTCCG 6 7 0 GGAGATTCCG 0.763205 -72 GAACGCCGGCGGCACCGTGGCCGGTCCCAGAGAA 7 86 0 GCACGGGCCG 0.971366 -125 * ** ** **** * Masking position 1 Map Score: 13.205 Number of sites scoring better than the average of aligned sites = 5484 Number in coding regions = 5138 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 303 Fraction of orfs with sites within 600 bp upstream = 0.0486669 Motif number 8 ********** No masking Map Score: -1.27654e-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 9 ********** No masking Map Score: -1.27654e-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: -1.27654e-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