AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -itrpR_mtub_opreg_300.orf -g0.656 -x5 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 = 0.656 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv0012 93 hypothetical protein Rv0012 #2 pabA 36 pabA #3 ponA 300 ponA #4 Rv0052 31 hypothetical protein Rv0052 #5 rpsF 218 rpsF #6 ssb 103 ssb #7 rpsR 41 rpsR #8 rplI 32 rplI #9 Rv0057 28 hypothetical protein Rv0057 #10 Rv0059 179 hypothetical protein Rv0059 #11 trpE 140 trpE #12 trpC 89 trpC #13 trpB 68 trpB #14 trpD 157 trpD Motif number 1 TATCGTTGCACCCCGGGCCATTCGTCGTCT 1 46 0 CCCCGGGCCA 0.904879 -48 CTACCGCCTGACCCTGCCGGCAGTCGT 2 8 0 ACCCTGCCGG 0.936709 -29 GAGTCCGCGTGCGGAGCCGATCGGTC 3 7 0 GCGGAGCCGA 0.911059 -294 CGCGGACTCCATCGAGGCGGTCAAGGCCGC 3 28 1 ATCGAGGCGG 0.889409 -273 GGCGGTCAAGGCCGCGCTCGACGGCGCGCC 3 43 1 GCCGCGCTCG 0.94822 -258 GGGCATCGGCGGCGCGCCGTCGAGCGCGGC 3 53 0 GGCGCGCCGT 0.984764 -248 TCGAGCGGGTCGCGCGGCGGGGGCATCGGC 3 73 0 CGCGCGGCGG 0.962407 -228 GGGGCGGCCAACGCGGCCGTGACCTCCTCG 3 100 0 ACGCGGCCGT 0.59822 -201 CGGTTTACCGGGCGGGGCGGCCAACGCGGC 3 113 0 GGCGGGGCGG 0.995815 -188 AGCTGATCCCCCCGCGGCGGTTTACCGGGC 3 130 0 CCCGCGGCGG 0.910449 -171 TGGCAGACGTCGCCCACCGGGGCCGCCCGG 3 163 1 CGCCCACCGG 0.888037 -138 GAACCGGGGGGCCCGGGCGGCCCCGGTGGG 3 175 0 GCCCGGGCGG 0.995443 -126 CGGTTGGGGCAGCCGGCCGGCAGGCTGTCC 3 209 0 AGCCGGCCGG 0.97912 -92 CGGCCGGCTGCCCCAACCGAGGGTGGACTT 3 220 1 CCCCAACCGA 0.677396 -81 AGTTGATCTGGCCGACCCGGGGCAAGTCCA 3 243 0 GCCGACCCGG 0.89847 -58 CGCCGCGGTGAGGTACAGCGA 3 290 0 GCCGCGGTGA 0.951265 -11 TGTCGCGAACGGCGAGGCCTATCGCGAACA 5 13 0 GGCGAGGCCT 0.92966 -206 GGTGCGACGATCCGCGGCGTGTCGTGTGCG 5 52 0 TCCGCGGCGT 0.949754 -167 GCCGCGGATCGTCGCACCGGGTTAAGCCTG 5 64 1 GTCGCACCGG 0.772163 -155 TCGGCAACTCGCCCAGGCTACACGAGAGCC 5 132 0 GCCCAGGCTA 0.769765 -87 CGAGTTGCCGACGCAGGCGACCCTCCTGCC 5 151 1 ACGCAGGCGA 0.744053 -68 CCACGGATCGACCGTGGCCGCACACGACCA 5 179 1 ACCGTGGCCG 0.921835 -40 AGCCAGTGCCTGGCAGGCCGA 6 2 0 TGGCAGGCCG 0.571727 -102 AGCCTACGTAACCGCACCGACAGCGAACAG 6 30 0 ACCGCACCGA 0.879473 -74 GTTCTTCTTCGCCGAGCCTACGTAACCGCA 6 44 0 GCCGAGCCTA 0.834941 -60 CCGCCTGGGTTCGGCGGCTGGTCGTGTTCT 6 69 0 TCGGCGGCTG 0.630023 -35 CAGCCGCCGAACCCAGGCGGACGCAGGAGG 6 79 1 ACCCAGGCGG 0.986581 -25 GGCGAGCTGAGGCCACAACA 9 1 1 GGCGAGCTGA 0.823447 -28 GGTCTCACGGAGCGTGGCCGAATCTCACGA 10 26 1 AGCGTGGCCG 0.875551 -154 GGGCCATCAGGGCGGACCGGTCCACGCATC 10 62 1 GGCGGACCGG 0.957957 -118 GGTCCACGCATCCGCGGCGGCGTTGAAGTC 10 80 1 TCCGCGGCGG 0.966524 -100 CACCCCCAGCCGCGAAGCGGCGCGCAAGGA 11 40 0 CGCGAAGCGG 0.906885 -101 GGTGCCCCCATGCGCGCCGTTTGCGCGGCG 11 66 1 TGCGCGCCGT 0.935911 -75 GCGCGCCGTTTGCGCGGCGTGCATCGTCGT 11 77 1 TGCGCGGCGT 0.951311 -64 GTCGGGCTACGCCCGGGCCGATCGGCGTAT 11 105 1 GCCCGGGCCG 0.986247 -36 CGGACCGCGCGCTGACGGTCGCTAC 12 6 1 CGCGCGCTGA 0.815167 -84 GCGCGGAAGATCCGGGGTGGATAGATCTGT 13 49 0 TCCGGGGTGG 0.931321 -20 GTCGAACTCTACCCGGGTCGGAAATTTCGG 14 37 1 ACCCGGGTCG 0.787575 -121 TCCGCGTGTCGCCCGGCCGTTTGGTTAGCG 14 76 1 GCCCGGCCGT 0.976379 -82 ACCAACCCCAACCGCGCCCTGAACACGTCG 14 114 0 ACCGCGCCCT 0.921874 -44 ********** Masking position 3 Map Score: 65.9415 Number of sites scoring better than the average of aligned sites = 74193 Number in coding regions = 69103 Number in noncoding regions = 5090 Number of orfs with sites within 600 bp upstream = 1590 Fraction of orfs with sites within 600 bp upstream = 0.255381 Motif number 2 GTCGTCTTGTCGAGGTAGTCCCGCCAGATCCCG 1 20 0 CGAGTAGCCG 0.864055 -74 CTCGACAAGACGACGAATGGCCCGGGGTGCAAC 1 39 1 CGAGAATCCC 0.91663 -55 AGGGTCAGGCGGTAGCCTGTCACG 2 23 1 GGTGCCTCAC 0.354122 -14 TTGACCGCCTCGATGGAGTCCGCGTGCGGAGCC 3 19 0 CGAGGAGCGC 0.861863 -282 ATCGGCGGCGCGCCGTCGAGCGCGGCCTTGACC 3 46 0 CGCGTCGCGC 0.990527 -255 GACGGCGCGCCGCCGATGCCCCCGCCGCGCGAC 3 62 1 CGCGATGCCC 0.994227 -239 GGGCGGCCAACGCGGCCGTGACCTCCTCGAGCG 3 96 0 CGCGCCGACC 0.933886 -205 CGGCCGCGTTGGCCGCCCCGCCCGGTAAACCGC 3 111 1 GGCGCCCCCC 0.971984 -190 ACGTCTGCCACCAAGCTGATCCCCCCGCGGCGG 3 140 0 CCAGCTGCCC 0.953971 -161 TCAGCTTGGTGGCAGACGTCGCCCACCGGGGCC 3 154 1 GGCGACGGCC 0.915591 -147 AACCGGGGGGCCCGGGCGGCCCCGGTGGGCGAC 3 171 0 CCCGGCGCCC 0.976502 -130 GCCCGGGCCCCCCGGTTCGTCCGGACAGCCTGC 3 187 1 CCCGTTCCCG 0.598847 -114 CCTCGGTTGGGGCAGCCGGCCGGCAGGCTGTCC 3 209 0 GGCGCCGCGG 0.946791 -92 CCCAACCGAGGGTGGACTTGCCCCGGGTCGGCC 3 231 1 GGTGACTCCC 0.762752 -70 ATACGGCGTTCGCTGTACCTCACCGCGGCG 3 281 1 CGCGTACCAC 0.724602 -20 CGCGGTTGGCCCCTACGAGGTGC 4 1 1 CGCGTTGCCC 0.990351 -31 CCGCTGCAGCACCTCGTAGGGGCC 4 18 0 CGCGCAGCCT 0.939611 -14 TCGCGAACGGCGAGGCCTATCGCGAACAGA 5 8 0 CGAGCCTCGC 0.940483 -211 CACGACACGCCGCGGATCGTCGCACCGGGTTAA 5 56 1 CGCGATCCGC 0.954164 -163 CCACCGCACTCCAGGCTTAACCCGGTGCGACGA 5 72 0 CCAGCTTCCC 0.80204 -147 AAAATGCCGACCAGGCACCACCGCACTCCAGGC 5 89 0 CCAGCACCCG 0.495006 -130 TCGGCATTTTCGCAGTCGAGGGCTCTCGTGTAG 5 112 1 CGCGTCGGGC 0.892466 -107 GAGTTGCCGACGCAGGCGACCCTCCTGCCACGG 5 152 1 CGCGGCGCCT 0.911897 -67 ACGGATCGACCGTGGCCGCACACGACCACAGGA 5 181 1 CGTGCCGCAC 0.923378 -38 ACTGGCTGTTCGCTGTCGGTGCGGTTACGTAGG 6 25 1 CGCGTCGGCG 0.841131 -79 GTAGGCTCGGCGAAGAAGAACACGACCAGCCGC 6 53 1 CGAGAAGCAC 0.888892 -51 GAACACGACCAGCCGCCGAACCCAGGCGGACGC 6 70 1 AGCGCCGCCC 0.941692 -34 CGCCGAATGTCCAACGGAGAGTG 8 1 1 CGCGAATCCA 0.642684 -32 CACGGAGCGTGGCCGAATCTCACGAATGATGGG 10 31 1 GGCGAATCAC 0.5674 -149 GACCGGTCCGCCCTGATGGCCCCATCATTCGTG 10 51 0 CCCGATGCCC 0.984183 -129 TCCGCGGCGGCGTTGAAGTCCCCGAGCAACACG 10 90 1 CGTGAAGCCC 0.960406 -90 CAGGGCGACAGGACGTCGAACCAGTGGGACTAA 10 154 1 GGAGTCGCCA 0.426872 -26 ACTCCTTGCGCGCCGCTTCGCGGCTGGGGGTGC 11 38 1 CGCGCTTCGG 0.851486 -103 GCTGGGGGTGCCCCCATGCGCGCCGTTTGCGCG 11 60 1 CCCCATGCGC 0.419591 -81 CGTAGCCCGACGACGATGCACGCCGCGCAAACG 11 83 0 CGAGATGCGC 0.964567 -58 TTCCCAGATACGCCGATCGGCCCGGGCGTAGCC 11 109 0 CGCGATCCCC 0.980605 -32 CGGACCGCGCGCTGACGGTCGCTACCCTTCAT 12 10 1 CGCGACGCGC 0.995901 -80 TCGTCAATTTCGACGACGTCCATGAAGGGTAGC 12 31 0 CGAGACGCAT 0.602484 -59 GCCTGCCGTTCCCTTCCCACTGT 12 77 0 GCCGCCGCCC 0.977278 -13 CCGTCGATGAGCCGCTTGCATCTT 13 2 1 CGTGATGCCG 0.88231 -67 GCGCGGAAGATCCGGGGTGGATAG 13 55 0 CGCGAAGCCG 0.981522 -14 CTGAACACGTCGACGACTTGCGCTAACCAAACG 14 93 0 CGAGACTCGC 0.929476 -65 ATCAACCAACCCCAACCGCGCCCTGAACACGTC 14 115 0 CCCACCGCCC 0.778589 -43 GCGCTGATGGTCCCATGAGGATCA 14 144 0 CGCGATGCCC 0.99578 -14 *** **** *** Masking position 5 Map Score: 83.2229 Number of sites scoring better than the average of aligned sites = 38156 Number in coding regions = 35801 Number in noncoding regions = 2355 Number of orfs with sites within 600 bp upstream = 1169 Fraction of orfs with sites within 600 bp upstream = 0.187761 Motif number 3 AGTCCCGCCAGATCCCGAGGAAAGTG 1 5 0 GACCCGGGAA 0.933648 -89 GCTACCGCCTGACCCTGCCGGCAGTCGT 2 7 0 GACCTGCGGC 0.899914 -30 CGCCGCCGATGCCCCCGCCGCGCGACCCGCTC 3 69 1 GCCCCGCGCG 0.915666 -232 CCCGCCGCGCGACCCGCTCGAGGAGGTCACGG 3 82 1 GACCGCCGAG 0.957732 -219 CGCTCGAGGAGGTCACGGCCGCGTTGGCCGCC 3 96 1 GGCACGCCGC 0.92052 -205 CCACCAAGCTGATCCCCCCGCGGCGGTTTACC 3 134 0 GACCCCCGCG 0.871512 -167 CGAACCGGGGGGCCCGGGCGGCCCCGGTGGGC 3 174 0 GGCCGGCGGC 0.975371 -127 GCCGGCAGGCTGTCCGGACGAACCGGGGGGCC 3 192 0 TGCCGGCGAA 0.837985 -109 TGATCTGGCCGACCCGGGGCAAGTCCACCCTC 3 238 0 GACCGGGCAA 0.862384 -63 CGCGGTTGGCCCCTACGAGGTGCTGCAGC 4 8 1 GGCCCTCGAG 0.934438 -24 GGCCACGGTCGATCCGTGGCAGGAGGGTCGCC 5 166 0 GACCGTGCAG 0.603512 -53 GACCGTGGCCGCACACGACCACAGGAGGTGAT 5 188 1 GCCACGCCAC 0.917506 -31 CGGCGAAGAAGAACACGACCAGCCGCCGAACC 6 60 1 GACACGCCAG 0.961302 -44 CCATCAGGGCGGACCGGTCCACGCATCCGCGG 10 65 1 GGCCGGCCAC 0.990555 -115 CGGCGTTGAAGTCCCCGAGCAACACGCGTCGT 10 97 1 GTCCCGGCAA 0.498448 -83 AGATGAGTCAGATCAGGGCGACAGGACGTCGA 10 141 1 GACAGGCGAC 0.976467 -39 CAATCGGTTGTAGCCTGACGACT 11 2 0 TACCTGCGAC 0.768802 -139 GCGCGCATGGGGGCACCCCCAGCCGCGAAGCG 11 51 0 GGCACCCCAG 0.835435 -90 GGCCCGGGCGTAGCCCGACGACGATGCACGCC 11 92 0 TACCCGCGAC 0.963344 -49 GCTAACCAAACGGCCGGGCGACACGCGGAACT 14 73 0 CGCCGGCGAC 0.920301 -85 ACCGCGCCCTGAACACGTCGACGACTTGCGCT 14 102 0 GACACGCGAC 0.982665 -56 ** **** **** Masking position 4 Map Score: 26.6336 Number of sites scoring better than the average of aligned sites = 19396 Number in coding regions = 18167 Number in noncoding regions = 1229 Number of orfs with sites within 600 bp upstream = 808 Fraction of orfs with sites within 600 bp upstream = 0.129778 Motif number 4 AACAAGGTATGCCTGCAGCTGCAACTTCT 1 75 0 TGCCTGCAGC 0.789899 -19 ACGACTGCCGGCAGGGTCAGG 2 2 1 CGACTGCCGG 0.867455 -35 GTCAGGCGGTAGCCTGTCACG 2 26 1 AGCCTGTCAC 0.548275 -11 CGATGGAGTCCGCGTGCGGAGCCGATCGGT 3 12 0 CGCGTGCGGA 0.902727 -289 GGCGCGCCGTCGAGCGCGGCCTTGACCGCC 3 43 0 CGAGCGCGGC 0.82279 -258 CGCGCTCGACGGCGCGCCGCCGATGCCCCC 3 55 1 GGCGCGCCGC 0.973767 -246 CCGTGACCTCCTCGAGCGGGTCGCGCGGCG 3 84 0 CTCGAGCGGG 0.554618 -217 CGGTGGGCGACGTCTGCCACCAAGCTGATC 3 152 0 CGTCTGCCAC 0.675581 -149 TCGTCCGGACAGCCTGCCGGCCGGCTGCCC 3 203 1 AGCCTGCCGG 0.872131 -98 CGAACGGCGAGGCCTATCGCGAACAGA 5 8 0 GGCCTATCGC 0.619152 -211 GACGATCCGCGGCGTGTCGTGTGCGCAATG 5 47 0 GGCGTGTCGT 0.875109 -172 GGTTAAGCCTGGAGTGCGGTGGTGCCTGGT 5 83 1 GGAGTGCGGT 0.564416 -136 GTCGAGGGCTCTCGTGTAGCCTGGGCGAGT 5 126 1 CTCGTGTAGC 0.76632 -93 GTGTAGCCTGGGCGAGTTGCCGACGCAGGC 5 139 1 GGCGAGTTGC 0.427757 -80 GCAGGAGGGTCGCCTGCGTCGGCAACTCGC 5 150 0 CGCCTGCGTC 0.947493 -69 GCAGGCGACCCTCCTGCCACGGATCGACCG 5 163 1 CTCCTGCCAC 0.85653 -56 CTCCTGTGGTCGTGTGCGGCCACGGTCGAT 5 185 0 CGTGTGCGGC 0.929947 -34 ACCTCATCACCTCCTGTGGTCGTGTGCGGC 5 195 0 CTCCTGTGGT 0.600971 -24 TCGGCCTGCCAGGCACTGGCTG 6 3 1 GGCCTGCCAG 0.844507 -101 AATTTCCTCCTGCGTCCGCCTGGGTT 6 88 0 CTCCTGCGTC 0.775609 -16 TCAACCACGACGCGTGTTGCTCGGGGACTT 10 105 0 CGCGTGTTGC 0.922767 -75 CTGGTTCGACGTCCTGTCGCCCTGATCTGA 10 148 0 GTCCTGTCGC 0.90715 -32 CCCGACTCCTTGCGCGCCGCTTCGCGGCTG 11 34 1 TGCGCGCCGC 0.865278 -107 CCGTTTGCGCGGCGTGCATCGTCGTCGGGC 11 82 1 GGCGTGCATC 0.727988 -59 AATTGACGAGCGCGTGTGGGTGACAGTGGG 12 55 1 CGCGTGTGGG 0.959041 -35 AAGTCAGTTCCGCGTGTCGCCCGGCCGTTT 14 68 1 CGCGTGTCGC 0.990373 -90 ********** Masking position 6 Map Score: 32.2131 Number of sites scoring better than the average of aligned sites = 26643 Number in coding regions = 24549 Number in noncoding regions = 2094 Number of orfs with sites within 600 bp upstream = 1044 Fraction of orfs with sites within 600 bp upstream = 0.167684 Motif number 5 CTATCGTTGCACCCCGGGCCATTCGTCGTC 1 47 0 ACCCCGGGCC 0.885704 -47 CACGCGGACTCCATCGAGGCGGTCAAGGCC 3 26 1 CCATCGAGGC 0.742623 -275 AAGGCCGCGCTCGACGGCGCGCCGCCGATG 3 50 1 TCGACGGCGC 0.772593 -251 GCCGCCGATGCCCCCGCCGCGCGACCCGCT 3 70 1 CCCCCGCCGC 0.807692 -231 GGCGGGGCGGCCAACGCGGCCGTGACCTCC 3 103 0 CCAACGCGGC 0.965759 -198 CCCGCCCGGTAAACCGCCGCGGGGGGATCA 3 127 1 AAACCGCCGC 0.948622 -174 CAGACGTCGCCCACCGGGGCCGCCCGGGCC 3 166 1 CCACCGGGGC 0.783496 -135 CTGTCCGGACGAACCGGGGGGCCCGGGCGG 3 185 0 GAACCGGGGG 0.489286 -116 CCGGCTGCCCCAACCGAGGGTGGACTTGCC 3 223 1 CAACCGAGGG 0.696594 -78 TGATCTGGCCGACCCGGGGCAAGTCCACCC 3 240 0 GACCCGGGGC 0.75352 -61 TCGCTGTACCTCACCGCGGCG 3 290 1 TCACCGCGGC 0.95307 -11 AGTGTCGCGAACGGCGAGGCCTATCGCGAA 5 15 0 ACGGCGAGGC 0.749914 -204 CGCACACGACACGCCGCGGATCGTCGCACC 5 52 1 ACGCCGCGGA 0.870945 -167 CTCCAGGCTTAACCCGGTGCGACGATCCGC 5 67 0 AACCCGGTGC 0.734018 -152 AGAACACGACCAGCCGCCGAACCCAGGCGG 6 69 1 CAGCCGCCGA 0.713016 -35 GGGGACTTCAACGCCGCCGCGGATGCGTGG 10 83 0 ACGCCGCCGC 0.969408 -97 TCACGCATCAACCACGACGCGTGTTGCTCG 10 112 0 ACCACGACGC 0.819993 -68 ATGGGGGCACCCCCAGCCGCGAAGCGGCGC 11 47 0 CCCCAGCCGC 0.756867 -94 GCACGCCGCGCAAACGGCGCGCATGGGGGC 11 69 0 CAAACGGCGC 0.84194 -72 GCGTAGCCCGACGACGATGCACGCCGCGCA 11 87 0 ACGACGATGC 0.478167 -54 TCGTCGGGCTACGCCCGGGCCGATCGGCGT 11 103 1 ACGCCCGGGC 0.827029 -38 AGATCTGTCATCACCGAGGCTCAAGATGCA 13 27 0 TCACCGAGGC 0.919346 -42 CAACCAACCCCAACCGCGCCCTGAACACGT 14 116 0 CAACCGCGCC 0.831982 -42 ********** Masking position 5 Map Score: 33.2271 Number of sites scoring better than the average of aligned sites = 35234 Number in coding regions = 33150 Number in noncoding regions = 2084 Number of orfs with sites within 600 bp upstream = 983 Fraction of orfs with sites within 600 bp upstream = 0.157886 Motif number 6 CATCGAGGCGGTCAAGGCCGCGCTCGACGG 3 37 1 GTCAAGGCCG 0.870516 -264 TGTGCGCAATGTCAGTGTCGCGAACGGCGA 5 28 0 GTCAGTGTCG 0.974838 -191 GTGCCTGGTCGGCATTTTCGCAGTCGAGGG 5 104 1 GGCATTTTCG 0.927688 -115 CCCATCATTCGTGAGATTCGGCCACGCTCC 10 34 0 GTGAGATTCG 0.872192 -146 ACACGCGCTCGTCAATTTCGACGACGTCCA 12 42 0 GTCAATTTCG 0.970691 -48 GCGCGGAAGATCCGGGGTGGATAG 13 55 0 GGAAGATCCG 0.886289 -14 TACCCGGGTCGGAAATTTCGGTAAGTCAGT 14 46 1 GGAAATTTCG 0.894314 -112 ATTTCGGTAAGTCAGTTCCGCGTGTCGCCC 14 60 1 GTCAGTTCCG 0.985307 -98 ********** Masking position 4 Map Score: 3.38801 Number of sites scoring better than the average of aligned sites = 825 Number in coding regions = 748 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 7 ********** No masking Map Score: 3.4912e-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 8 ********** No masking Map Score: 3.4912e-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: 3.4912e-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