AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00150_mtub_reg_100.orf -o00150_mtub_100.ace -a/home/amcguire/genomes/ORF_mtub.txt -z/home/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 Rv0187 300 hypothetical protein Rv0187 #2 Rv0552 77 hypothetical protein Rv0552 #3 menD 42 menD #4 Rv0557 61 hypothetical protein Rv0557 #5 Rv1009 207 hypothetical protein Rv1009 #6 cobG 224 cobG #7 cobL 67 cobL #8 Rv2073c 29 hypothetical protein Rv2073c #9 Rv2689c 173 hypothetical protein Rv2689c Motif number 1 CAATTCGTCGCCGCAGGTGCAGCG 1 5 1 TCGTCGCCGC 0.866644 -296 GCGGTAGGCGTCACCGGCGCCAGCACAGTG 1 32 1 TCACCGGCGC 0.958842 -269 ACAGCCACAGCCCTCGTGGCTGCAGGTCAG 1 86 1 CCCTCGTGGC 0.913707 -215 GCGCGACCACCGACCGTCGCGCGCCAGCAG 1 275 0 CGACCGTCGC 0.9795 -26 ACCGTATGGCCGGGCCGCGC 3 1 0 CGGGCCGCGC 0.957505 -42 ACCATTTCGACAGCCGGCGCTGACAGT 4 45 1 CAGCCGGCGC 0.943056 -17 TGTTATGGGCCGCTCGGCGCGC 5 3 0 CGCTCGGCGC 0.992282 -205 GCGGCCCATAACACCCGCGCGCCGGAGTTG 5 20 1 ACACCCGCGC 0.948201 -188 GCCGCGGCACACCGCGACGCTATCGGCAGC 6 48 0 ACCGCGACGC 0.779476 -177 GTGTGCCGCGGCGTCCGCGCGGTCGCTCGT 6 66 1 GCGTCCGCGC 0.815324 -159 CTCGTGGAGCGACTCGGCGCCCTCAAACCC 6 102 1 GACTCGGCGC 0.938955 -123 TCGATTGCGCGCATCGTGGCGGGTTTGAGG 6 122 0 GCATCGTGGC 0.902686 -103 CCGAGGATCAGGGTCAGGGCGTTTTCGATT 6 146 0 GGGTCAGGGC 0.810778 -79 ATGGGTCGCCGCCTCGCCGCGCTCAGGTCC 6 186 0 GCCTCGCCGC 0.572228 -39 GCTGCGCTCTGCATCGTCGCGGA 7 4 0 GCATCGTCGC 0.981311 -64 GCGGGCGGTACCCCCACCGCATCGCTGCGC 7 27 0 CCCCCACCGC 0.948355 -41 CTTGCGGGGGAGAGCGGCGCCG 7 56 1 AGAGCGGCGC 0.967019 -12 CTCTGCATCGTCGCCGGCGCGGGTCAATCG 9 22 0 TCGCCGGCGC 0.544962 -152 GCGCCGCTCCTCCCCATCGCTTTGCTCTGC 9 46 0 TCCCCATCGC 0.957184 -128 GCGATGGGGAGGAGCGGCGCCAGTGACCCG 9 56 1 GGAGCGGCGC 0.984227 -118 CTCTGCATCGTCGCCGGCGCGGGTCACTGG 9 75 0 TCGCCGGCGC 0.544962 -99 GCGCCGCTCCTCCCCATCGCTTTGCTCTGC 9 99 0 TCCCCATCGC 0.957184 -75 GCGATGGGGAGGAGCGGCGCCAGTGACCCG 9 109 1 GGAGCGGCGC 0.984227 -65 CTCTGCATCGTCGCCGGCGCGGGTCACTGG 9 128 0 TCGCCGGCGC 0.544962 -46 GCGCCGCTCCTCCCCATCGCTTTGCTCTGC 9 152 0 TCCCCATCGC 0.957184 -22 GCGATGGGGAGGAGCGGCGCCA 9 162 1 GGAGCGGCGC 0.984227 -12 ********** Masking position 5 Map Score: 66.2999 Number of sites scoring better than the average of aligned sites = 25321 Number in coding regions = 23620 Number in noncoding regions = 1701 Number of orfs with sites within 600 bp upstream = 897 Fraction of orfs with sites within 600 bp upstream = 0.144073 Motif number 2 CAATTCGTCGCCGCAGGTGCAGCGGTAGG 1 10 1 GCCGCAGGTG 0.825594 -291 AGGCGTCACCGGCGCCAGCACAGTGGCATG 1 37 1 GGCGCCAGCA 0.990311 -264 TCGATGCGAACCCGACAGCCACAGCCCTCG 1 72 1 CCCGACAGCC 0.945002 -229 CAGGCAACCGCCCACCGGCCTGGGGGTTTA 1 248 0 CCCACCGGCC 0.858548 -53 CCGACCGTCGCGCGCCAGCAGGCAACCGCC 1 266 0 CGCGCCAGCA 0.99456 -35 GGTCGGTGGTCGCGCTAGCGT 1 290 1 CGCGCTAGCG 0.853643 -11 TTGGATCTGCCGTGCCCTCGTAATCTCGAA 2 37 1 CGTGCCCTCG 0.919726 -41 GCCCATAACACCCGCGCGCCGGAGTTGCTC 5 23 1 CCCGCGCGCC 0.639408 -185 GCGCTATATCCCCGACCTCGGCAACACTCA 5 148 0 CCCGACCTCG 0.956819 -60 GGCCACCTGTCGCGCCCTCAGAAGGTGTAG 6 19 1 CGCGCCCTCA 0.986228 -206 AGGTGTAGCTGCCGATAGCGTCGCGGTGTG 6 41 1 GCCGATAGCG 0.862481 -184 CCGCGGCGTCCGCGCGGTCGCTCGTGCCCG 6 71 1 CGCGCGGTCG 0.9691 -154 GGAGCGACTCGGCGCCCTCAAACCCGCCAC 6 107 1 GGCGCCCTCA 0.975101 -118 CGCCACGATGCGCGCAATCGAAAACGCCCT 6 131 1 CGCGCAATCG 0.97708 -94 TCGCCGCCTCGCCGCGCTCAGGTCCCGTCG 6 181 0 GCCGCGCTCA 0.868659 -44 GCCGCTCTCCCCCGCAAGCGGGCGGTACCC 7 44 0 CCCGCAAGCG 0.988742 -24 CGGCGCCGCTCTCCCCCGCAAGCG 7 54 0 GCCGCTCTCC 0.875591 -14 TCACGCTAGCGCAGGCAATAA 8 2 1 CACGCTAGCG 0.892987 -28 TCGATTGACCCGCGCCGGCGACGATGCAGA 9 21 1 CGCGCCGGCG 0.980998 -153 GGGGAGGAGCGGCGCCAGTGACCCGCGCCG 9 61 1 GGCGCCAGTG 0.977981 -113 GCCAGTGACCCGCGCCGGCGACGATGCAGA 9 74 1 CGCGCCGGCG 0.980998 -100 GGGGAGGAGCGGCGCCAGTGACCCGCGCCG 9 114 1 GGCGCCAGTG 0.977981 -60 GCCAGTGACCCGCGCCGGCGACGATGCAGA 9 127 1 CGCGCCGGCG 0.980998 -47 ********** Masking position 4 Map Score: 58.0932 Number of sites scoring better than the average of aligned sites = 23870 Number in coding regions = 22354 Number in noncoding regions = 1516 Number of orfs with sites within 600 bp upstream = 814 Fraction of orfs with sites within 600 bp upstream = 0.130742 Motif number 3 CAATTCGTCGCCGCAGGTGCAGCG 1 3 1 ATCGTCCCGC 0.840235 -298 GTGCAGCGGTAGGCGTCACCGGCGCCAGCACA 1 27 1 AGCGTCCCGG 0.970642 -274 GCACAGTGGCATGGGACTTCGATGCGAACCCG 1 54 1 AGGGACTCGA 0.665289 -247 AACTACGAGGCTGGGACCTTGCTGACCTGCAG 1 105 0 CGGGACTTGC 0.805246 -196 GGGATTCCTCGGGGATCCCCGACACGGATGAG 1 153 0 GGGATCCCGA 0.964472 -148 AGTAGCTGTTCTGGATTACCGACAGCTGACCA 1 188 0 CGGATTCCGA 0.69209 -113 GGCCAATGTTGAGCAACTCCGGCGCGCGGGTG 5 31 0 GGCAACCCGG 0.945403 -177 CGGTGTGCCGCGGCGTCCGCGCGGTCGCTCGT 6 64 1 CGCGTCGCGC 0.966604 -161 CCGACTCGTGGAGCGACTCGGCGCCCTCAAAC 6 98 1 GGCGACCGGC 0.888062 -127 TTTCGATTGCGCGCATCGTGGCGGGTTTGAGG 6 122 0 GGCATCTGGC 0.930755 -103 ATCAGGGTCAGGGCGTTTTCGATTGCGCGCAT 6 138 0 GGCGTTTCGA 0.746244 -87 ACGCCCTGACCCTGATCCTCGGCCTCCCGACG 6 154 1 CTGATCTCGG 0.689707 -71 GTACGGGAGAATGGGTCGCCGCCTCGCCGCGC 6 194 0 AGGGTCCCGC 0.977906 -31 TCGCTGCGCTCTGCATCGTCGCGGA 7 4 0 CGCATCTCGC 0.990532 -64 GGTACCCCCACCGCATCGCTGCGCTCTGCATC 7 19 0 CGCATCCTGC 0.967038 -49 CGGGGCATCTTCGATTGACCCGCG 9 3 1 GGCATCTCGA 0.964432 -171 TCGCTTTGCTCTGCATCGTCGCCGGCGCGGGT 9 28 0 CGCATCTCGC 0.990532 -146 CGTCGCCGGCGCGGGTCACTGGCGCCGCTCCT 9 65 0 GGGGTCCTGG 0.917135 -109 TCGCTTTGCTCTGCATCGTCGCCGGCGCGGGT 9 81 0 CGCATCTCGC 0.990532 -93 CGTCGCCGGCGCGGGTCACTGGCGCCGCTCCT 9 118 0 GGGGTCCTGG 0.917135 -56 TCGCTTTGCTCTGCATCGTCGCCGGCGCGGGT 9 134 0 CGCATCTCGC 0.990532 -40 * ***** **** Masking position 11 Map Score: 41.067 Number of sites scoring better than the average of aligned sites = 17885 Number in coding regions = 16737 Number in noncoding regions = 1148 Number of orfs with sites within 600 bp upstream = 750 Fraction of orfs with sites within 600 bp upstream = 0.120463 Motif number 4 GCGCCGGTGACGCCTACCGCTGCACCTGCGGCGACGAA 1 14 0 CGCCTGCCTG 0.920467 -287 GCATCGAAGTCCCATGCCACTGTGCTGGCGCCGGTGAC 1 41 0 CCCCTGCTGG 0.937228 -260 GTTCGTCATTCGTATCACCCTCATCCGTGTCGGGGATC 1 134 1 CGTCTCCCGT 0.885265 -167 TGTCGGGGATCCCCGAGGAATCCCAGGTGGTCAGCTGT 1 161 1 CCCATCAGGT 0.430139 -140 CTGGTAAACCCCCAGGCCGGTGGGCGGTTGCCTGCTGG 1 244 1 CCCGTGCGGT 0.912561 -57 ACGCTAGCGCGACCACCGACCGTCGCGCGCCAG 1 278 0 AGCACCCCGT 0.576342 -23 GCGCGGCCCGGCCATACGGTCCGGCTGTGACACT 3 7 1 CCCACGCCGG 0.935328 -36 AGAGTTCGCACGCCGTATGCCGCTACGCAACCATTTCG 4 16 1 CGCCCGACGC 0.983831 -46 CGCCGAGCGGCCCATAACACCCGCGCGCCGGAGTTGCT 5 14 1 CCCCCCGCGC 0.932733 -194 CCCTCCGAAACCTAGAGGCCCCACCCGTTCGATCACAA 5 77 0 CCTCCCCCGT 0.95354 -131 AGAGTCAACGCGCTATATCCCCGACCTCGGCAACACTC 5 149 0 CGCCCCCCTC 0.913417 -59 CCCACTCCGGCCACCTGTCGCGCCCTCA 6 1 1 CCCGCCCTGT 0.82289 -224 GCGCGGACGCCGCGGCACACCGCGACGCTATCGGCAGC 6 48 0 CGCCCGACGC 0.983831 -177 TCCGCGCGGTCGCTCGTGCCCGACTCGTGGAGCGACTC 6 79 1 CGCCCGTCGT 0.993195 -146 CGACTCGGCGCCCTCAAACCCGCCACGATGCGCGCAAT 6 111 1 CCCCCGACGA 0.921008 -114 CGCCTCGCCGCGCTCAGGTCCCGTCGGGAGGCCGAGGA 6 169 0 CGCCCCCGGG 0.974019 -56 GAGGCGGCGACCCATTCTCCCGTACGGTGGACGG 6 201 1 CCCCCGCGGT 0.992073 -24 CCCACCGCATCGCTGCGCTCTGCATCGTCGCGGA 7 7 0 CGCCTGTCGT 0.982088 -61 GCGCCGCTCTCCCCCGCAAGCGGGCGGTACCCCCACCG 7 38 0 CCCGCGCGGT 0.969418 -30 TCCTCCCCATCGCTTTGCTCTGCATCGTCGCCGGCGCG 9 31 0 CGCCTGTCGT 0.982088 -143 GAGGAGCGGCGCCAGTGACCCGCGCCGGCGACGATGCA 9 64 1 GCCCCGCCGG 0.974106 -110 TCCTCCCCATCGCTTTGCTCTGCATCGTCGCCGGCGCG 9 84 0 CGCCTGTCGT 0.982088 -90 GAGGAGCGGCGCCAGTGACCCGCGCCGGCGACGATGCA 9 117 1 GCCCCGCCGG 0.974106 -57 TCCTCCCCATCGCTTTGCTCTGCATCGTCGCCGGCGCG 9 137 0 CGCCTGTCGT 0.982088 -37 *** *** **** Masking position 3 Map Score: 45.601 Number of sites scoring better than the average of aligned sites = 19829 Number in coding regions = 18363 Number in noncoding regions = 1466 Number of orfs with sites within 600 bp upstream = 875 Fraction of orfs with sites within 600 bp upstream = 0.14054 Motif number 5 TTTAAGTAGCTGTTCTGGATTACCGACAGC 1 194 0 TGTTCTGGAT 0.940967 -107 GCGCCGGAGTTGCTCAACATTGGCCGGTTC 5 38 1 TGCTCAACAT 0.944906 -170 CGCATCGCTGCGCTCTGCATCGTCGCGGA 7 10 0 CGCTCTGCAT 0.993951 -58 CCCATCGCTTTGCTCTGCATCGTCGCCGGC 9 34 0 TGCTCTGCAT 0.99778 -140 CCCATCGCTTTGCTCTGCATCGTCGCCGGC 9 87 0 TGCTCTGCAT 0.99778 -87 CCCATCGCTTTGCTCTGCATCGTCGCCGGC 9 140 0 TGCTCTGCAT 0.99778 -34 ********** Masking position 4 Map Score: 13.432 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 22 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 ACTGTGCTGGCGCCGGTGACGCCTACCGCT 1 31 0 CGCCGGTGAC 0.982623 -270 CCAGCACAGTGGCATGGGACTTCGATGCGA 1 51 1 GGCATGGGAC 0.68002 -250 GCAGCCACGAGGGCTGTGGCTGTCGGGTTC 1 79 0 GGGCTGTGGC 0.94991 -222 CGAACTACGAGGCTGGGACCTTGCTGACCT 1 109 0 GGCTGGGACC 0.794923 -192 ACCGCCCACCGGCCTGGGGGTTTACCAGAT 1 242 0 GGCCTGGGGG 0.841723 -59 CCAGGCCGGTGGGCGGTTGCCTGCTGGCGC 1 255 1 GGGCGGTTGC 0.890979 -46 GGGCGGTTGCCTGCTGGCGCGCGACGGTCG 1 265 1 CTGCTGGCGC 0.681523 -36 GCGCGACGGTCGGTGGTCGCGCTAGCGT 1 283 1 CGGTGGTCGC 0.930284 -18 AGGATCACTACGCTTGGAGCCC 2 66 1 CGCTTGGAGC 0.70722 -12 CGGACCGTATGGCCGGGCCGCGC 3 4 0 GGCCGGGCCG 0.85364 -39 CCATACGGTCCGGCTGTGACACTCTGTACT 3 22 1 CGGCTGTGAC 0.934157 -21 CTGTCAGCGCCGGCTGTCGAAATGGTTGCG 4 41 0 CGGCTGTCGA 0.440621 -21 TGTTATGGGCCGCTCGGCGCGC 5 3 0 CGCTCGGCGC 0.664931 -205 GCTCAACATTGGCCGGTTCGTTACCGTCTT 5 49 1 GGCCGGTTCG 0.505503 -159 GTGATCGAACGGGTGGGGCCTCTAGGTTTC 5 79 1 GGGTGGGGCC 0.932431 -129 CTCTAGGTTTCGGAGGGCCCATTTTGCTTT 5 98 1 CGGAGGGCCC 0.901861 -110 GCTACACCTTCTGAGGGCGCGACAGGTGGC 6 20 0 CTGAGGGCGC 0.461366 -205 CGCGGCGTCCGCGCGGTCGCTCGTGCCCGA 6 72 1 GCGCGGTCGC 0.716959 -153 CTCGGCCTCCCGACGGGACCTGAGCGCGGC 6 171 1 CGACGGGACC 0.650085 -54 CCCCGCAAGCGGGCGGTACCCCCACCGCAT 7 35 0 GGGCGGTACC 0.914911 -33 GATTGACCCGCGCCGGCGACGATGCAGAGC 9 23 1 CGCCGGCGAC 0.963107 -151 GGAGGAGCGGCGCCAGTGACCCGCGCCGGC 9 63 1 CGCCAGTGAC 0.840921 -111 CAGTGACCCGCGCCGGCGACGATGCAGAGC 9 76 1 CGCCGGCGAC 0.963107 -98 GGAGGAGCGGCGCCAGTGACCCGCGCCGGC 9 116 1 CGCCAGTGAC 0.840921 -58 CAGTGACCCGCGCCGGCGACGATGCAGAGC 9 129 1 CGCCGGCGAC 0.963107 -45 ********** Masking position 6 Map Score: 33.2006 Number of sites scoring better than the average of aligned sites = 52553 Number in coding regions = 49571 Number in noncoding regions = 2982 Number of orfs with sites within 600 bp upstream = 1270 Fraction of orfs with sites within 600 bp upstream = 0.203983 Motif number 7 CAATTCGTCGCCGCAGGTGCAGCGGT 1 7 1 GTCGCCGCAG 0.90656 -294 GGTGACGCCTACCGCTGCACCTGCGGCGAC 1 17 0 ACCGCTGCAC 0.968624 -284 CACAGCCCTCGTGGCTGCAGGTCAGCAAGG 1 91 1 GTGGCTGCAG 0.86393 -210 CACGCCGTATGCCGCTACGCAACCATTTCG 4 24 1 GCCGCTACGC 0.965935 -38 GGTGTTATGGGCCGCTCGGCGCGC 5 5 0 GCCGCTCGGC 0.741615 -203 CCGAAACCTAGAGGCCCCACCCGTTCGATC 5 81 0 GAGGCCCCAC 0.763157 -127 GACGCTATCGGCAGCTACACCTTCTGAGGG 6 33 0 GCAGCTACAC 0.805671 -192 CCGCGCGGACGCCGCGGCACACCGCGACGC 6 58 0 GCCGCGGCAC 0.976387 -167 AGGGCGCCGAGTCGCTCCACGAGTCGGGCA 6 95 0 GTCGCTCCAC 0.96797 -130 TCAAACCCGCCACGATGCGCGCAATCGAAA 6 124 1 CACGATGCGC 0.675283 -101 TCCGCGACGATGCAGAGCGCAGCGA 7 6 1 GACGATGCAG 0.955968 -62 CCCCCACCGCATCGCTGCGCTCTGCATCGT 7 17 0 ATCGCTGCGC 0.84286 -51 CGGCGCCGCTCTCCCCCGCAAGCG 7 54 0 GCCGCTCTCC 0.770168 -14 CGGGTCAATCGAAGATGCCCCG 9 3 0 GAAGATGCCC 0.579118 -171 CCGCGCCGGCGACGATGCAGAGCAAAGCGA 9 30 1 GACGATGCAG 0.955968 -144 GGTCACTGGCGCCGCTCCTCCCCATCGCTT 9 54 0 GCCGCTCCTC 0.967785 -120 CCGCGCCGGCGACGATGCAGAGCAAAGCGA 9 83 1 GACGATGCAG 0.955968 -91 GGTCACTGGCGCCGCTCCTCCCCATCGCTT 9 107 0 GCCGCTCCTC 0.967785 -67 CCGCGCCGGCGACGATGCAGAGCAAAGCGA 9 136 1 GACGATGCAG 0.955968 -38 TGGCGCCGCTCCTCCCCATCGCTT 9 160 0 GCCGCTCCTC 0.967785 -14 ********** Masking position 4 Map Score: 34.0713 Number of sites scoring better than the average of aligned sites = 12904 Number in coding regions = 12006 Number in noncoding regions = 898 Number of orfs with sites within 600 bp upstream = 612 Fraction of orfs with sites within 600 bp upstream = 0.0982975 Motif number 8 ATGACGAACTACGAGGCTGGGACCTTGCTG 1 113 0 ACGAGGCTGG 0.84347 -188 GAGGAATCCCAGGTGGTCAGCTGTCGGTAA 1 175 1 AGGTGGTCAG 0.925926 -126 ACCCCCAGGCCGGTGGGCGGTTGCCTGCTG 1 251 1 CGGTGGGCGG 0.992691 -50 GCGCGACGGTCGGTGGTCGCGCTAGCGT 1 283 1 CGGTGGTCGC 0.981812 -18 AGTTGCTCAACATTGGCCGGTTCGTTACCG 5 45 1 CATTGGCCGG 0.787095 -163 TTCGCTGTGTAGGTGGTTGAGTGTTGCCGA 5 131 1 AGGTGGTTGA 0.871684 -77 TTGAGTGTTGCCGAGGTCGGGGATATAGCG 5 147 1 CCGAGGTCGG 0.963442 -61 CGGTGATTGGGTCTGATGAA 5 198 0 CGGTGATTGG 0.878868 -10 AGGGCGCGACAGGTGGCCGGAGTGGG 6 7 0 AGGTGGCCGG 0.995128 -218 AGGTCCCGTCGGGAGGCCGAGGATCAGGGT 6 162 0 GGGAGGCCGA 0.863675 -63 TTCTCCCGTACGGTGGACGG 6 215 1 CGGTGGACGG 0.989071 -10 ********** Masking position 5 Map Score: 13.5746 Number of sites scoring better than the average of aligned sites = 7684 Number in coding regions = 7220 Number in noncoding regions = 464 Number of orfs with sites within 600 bp upstream = 388 Fraction of orfs with sites within 600 bp upstream = 0.0623193 Motif number 9 ********** No masking Map Score: -2.35657e-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: -2.35657e-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: -2.35657e-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