AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -imalT_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 Rv1234 149 hypothetical protein Rv1234 #2 Rv1781c 263 hypothetical protein Rv1781c #3 Rv2041c 37 hypothetical protein Rv2041c #4 pncA 40 pncA #5 Rv2044c 85 hypothetical protein Rv2044c #6 lipT 48 lipT #7 ugpA 86 ugpA #8 infB 85 infB #9 Rv2840c 126 hypothetical protein Rv2840c #10 Rv2842c 194 hypothetical protein Rv2842c Motif number 1 CGAACGGCGAGCATCGTTGCCGGGATAGGTTGAT 1 15 0 GCTCGGCGGG 0.818511 -135 ATCCACTCAACCCGCGAGCGACCGAGGCCCACCG 1 47 0 CCGCGCGCCG 0.963985 -103 CGTTTCATGTCCAGTCAGGTCCAGCTACTCCCGG 1 87 0 CCGTCGTCAG 0.506698 -63 TGGACATTGACCTGGGTATTTGCCACTGCGCGGA 2 43 1 CCGGGTTGCC 0.862863 -221 CACGACGAATCCTTGGGGGATCCGCGCAGTGGCA 2 63 0 CCTGGGACCG 0.946674 -201 GCTACCATGCCCAGTGAAGACACGACGAATCCTT 2 83 0 CCGTGGAACG 0.959005 -181 TCTTCACTGGGCATGGTAGCGGCGAATGACCGAG 2 97 1 GCTGGGCGCG 0.987041 -167 AACGAGGTAGACTGCGGAGCGGACAGTTCCACAG 2 136 0 ACGCGGCGAC 0.76147 -128 GGCTCAGATTCCTGCGCTCGCCCGCACACGGGTG 2 220 1 CCGCGCGCCG 0.963277 -44 CGCCCATCTTGCGTCCGGCACCCGTGTGCGGGCG 2 238 0 GCTCCCACCG 0.581455 -26 GATTTTGGGTCCTGTGGTACAACGACCG 3 5 0 CCGTGACACG 0.91057 -33 GCAAACTGCCCGGGCAGTCGCCCGAACGTATG 4 9 1 CCGGGGTGCC 0.981905 -32 TTTCCAGGTCGCGGCGCTCCGGCCACTGACAGAA 5 16 0 GCGCGCCGCC 0.990659 -70 TACCACCGTTGATACAACGACGGTTTCGT 5 67 0 CCTTGACACG 0.723628 -19 CGACAGGCTAGCCGCCCCGCCCCCATTCCTGCAC 6 13 1 GCGCCGCCCC 0.974346 -36 CTGGCCGACATTGCCGTGACGGCGGTGATTG 7 8 1 ACTTGGTACG 0.457737 -79 GGTTCATCGACCGTGGCGGCAAACTCGCCGACAG 7 41 1 CCTGGGCAAC 0.632635 -46 CGGCGCAGTGTAGCTCCGTATTCTGTCG 7 69 0 GCGTGGCCCG 0.99532 -18 GCACACCGTGAAGTCCCGATGACAATGC 8 5 1 ACGTGGTCCG 0.891287 -81 CATAGCTAAACCCGAGGCGCGGCCCACGACTGTC 8 41 1 CCGAGGCGCC 0.962968 -45 AGCCCGATTGCCCGGCTATCTGCCGTGGGATAAC 9 19 0 CCGGCTCGCC 0.854318 -108 TCGGGCTTGCCCGGTGACGCTACACTTAGCCGTG 9 46 1 CCGTGGCACA 0.845528 -81 GCTACACTTAGCCGTGATCCAGCGCGAGCCTTCG 9 64 1 GCGTGCCGCG 0.989771 -63 GATTATCCGGGCGTCGATGCGCCGAGGCCGAAGG 9 92 0 GCTCGGCCCG 0.988795 -35 CGGTCCGCGGGGATTATCCGGGCGTCGATG 9 107 0 GCGGGTACCG 0.833736 -20 GTCTCGCCTGCCTTCGTAGCGGCGTCTTTCTGAT 10 25 0 CCTCGGCGCG 0.99378 -170 CACGAATGACGCCGTGATCACGCCGTTCAACGTC 10 56 0 GCGTGCAGCC 0.91886 -139 CACGCAGCAGCCGGCGTAGCTACCAACGATACGC 10 97 0 CCGCGGCACC 0.991939 -98 TACGCCGGCTGCTGCGTGCCGGCGGGACACTGGG 10 113 1 GCGCGCCGCG 0.994531 -82 GGAGGCGCCGCCAGGGCGGCTCCCAGTGTCCCGC 10 134 0 CCGGGGCCCC 0.995577 -61 CTTGAGTTGTCCGGTCATCTAGCGGAGGCGCCGC 10 157 0 CCGTCCTGCG 0.879201 -38 ** *** ** *** Masking position 2 Map Score: 51.5133 Number of sites scoring better than the average of aligned sites = 52670 Number in coding regions = 49153 Number in noncoding regions = 3517 Number of orfs with sites within 600 bp upstream = 1301 Fraction of orfs with sites within 600 bp upstream = 0.208962 Motif number 2 ATCAACCTATCCCGGCAACGATGCTCGCCG 1 15 1 CCCGGCAACG 0.959079 -135 CAACGATGCTCGCCGTTCGGTGGGCCTCGG 1 30 1 CGCCGTTCGG 0.812189 -120 GGTGGGCCTCGGTCGCTCGCGGGTTGAGTG 1 48 1 GGTCGCTCGC 0.848765 -102 TCCAGCTACTCCCGGCACACTATCCACTCA 1 72 0 CCCGGCACAC 0.965723 -78 TCTCATTCTCCTCCGCCCCCCTTTTTCAGC 1 126 0 CTCCGCCCCC 0.981017 -24 TTTGCCACTGCGCGGATCCCCCAAGGATTC 2 61 1 CGCGGATCCC 0.942228 -203 CTCGGTCATTCGCCGCTACCATGCCCAGTG 2 101 0 CGCCGCTACC 0.992545 -163 CTGTGGAACTGTCCGCTCCGCAGTCTACCT 2 136 1 GTCCGCTCCG 0.950137 -128 GCACAGCACGGTTGGCTACCGAACACCACT 2 182 0 GTTGGCTACC 0.507369 -82 TCCTGCGCTCGCCCGCACACGGGTGCCGGA 2 229 1 GCCCGCACAC 0.945939 -35 CCATCTTGCGTCCGGCACCCGTGTGCGGGC 2 239 0 TCCGGCACCC 0.895462 -25 GTGGCCGGAGCGCCGCGACCTGGAAAGGCA 5 24 1 CGCCGCGACC 0.943756 -62 AGGCTAGCCGCCCCGCCCCCATTCCTGCAC 6 17 1 CCCCGCCCCC 0.99383 -32 AACCAATCACCGCCGTCACGGCAATGTCGG 7 15 0 CGCCGTCACG 0.800281 -72 CATCGACCGTGGCGGCAAACTCGCCGACAG 7 45 1 GGCGGCAAAC 0.913649 -42 AAACCCGAGGCGCGGCCCACGACTGTCGCC 8 48 1 CGCGGCCCAC 0.982608 -38 AGCCCGATTGCCCGGCTATCTGCCGTGGGA 9 23 0 CCCGGCTATC 0.833982 -104 CTCGGCGCATCGACGCCCGGATAATCCCCG 9 100 1 CGACGCCCGG 0.666438 -27 ATCAGAAAGACGCCGCTACGAAGGCAGGCG 10 25 1 CGCCGCTACG 0.984552 -170 CCAGTGTCCCGCCGGCACGCAGCAGCCGGC 10 116 0 GCCGGCACGC 0.965145 -79 GCGCCGCCAGGGCGGCTCCCAGTGTCCCGC 10 134 0 GGCGGCTCCC 0.99544 -61 CCGCCCTGGCGGCGCCTCCGCTAGATGACC 10 149 1 GGCGCCTCCG 0.86548 -46 ********** Masking position 5 Map Score: 36.2576 Number of sites scoring better than the average of aligned sites = 32114 Number in coding regions = 29926 Number in noncoding regions = 2188 Number of orfs with sites within 600 bp upstream = 1114 Fraction of orfs with sites within 600 bp upstream = 0.178927 Motif number 3 ACCCGCGAGCGACCGAGGCCCACCGAACGGCGAGC 1 37 0 GCCGAGGCCG 0.99126 -113 CGGTTCTCATTCTCCTCCGCCCCCCTTTTT 1 130 0 CCATTCTCCC 0.767351 -20 AAATACCCAGGTCAATGTCCAGGTGTTCTGAGCAG 2 29 0 GCAATGTCCG 0.939641 -235 GGGGGATCCGCGCAGTGGCAAATACCCAGGTCAAT 2 48 0 CCAGTGGCAC 0.953212 -216 AGCGGCGAATGACCGAGTCCGCCTGTGGAACTGTC 2 114 1 GCCGAGTCCG 0.982239 -150 TGACGGAAGGCTCAGATTCCTGCGCTCGCCCGCAC 2 212 1 CCAGATTCCC 0.72891 -52 GCACACGGGTGCCGGACGCAAGATGGGCGAC 2 243 1 GCGGACGCAG 0.748418 -21 AAACTGCCCGGGCAGTCGCCCGAACGTATGGTGGA 4 13 1 GCAGTCGCCC 0.989677 -28 ACCTTTTCTGTCAGTGGCCGGAGCGCCGCGACCT 5 10 1 GCAGTGGCCC 0.994714 -76 CCGCCGTCACGGCAATGTCGGCCAG 7 1 0 GCAATGTCGG 0.755953 -86 TTGGTTCATCGACCGTGGCGGCAAACTCGCCGACA 7 39 1 GCCGTGGCGA 0.760142 -48 TTAGCTATGACGCATTGTCATCGGGACTTCACGGT 8 15 0 CCATTGTCAG 0.626905 -71 CGCGGCCCACGACTGTCGCCTCATGGACAGGAGAT 8 58 1 GCTGTCGCCG 0.947614 -28 GGCGTCGATGCGCCGAGGCCGAAGGCTCGCGCTGG 9 82 0 CCCGAGGCCG 0.985695 -45 CCTGCCATCAGAAAGACGCCGCTACGAAGGCAGGC 10 19 1 GAAGACGCCC 0.756224 -176 CAGGGCGGCTCCCAGTGTCCCGCCGGCACGCAGCA 10 122 0 CCAGTGTCCG 0.987907 -73 * ******** * Masking position 9 Map Score: 14.8012 Number of sites scoring better than the average of aligned sites = 12783 Number in coding regions = 11915 Number in noncoding regions = 868 Number of orfs with sites within 600 bp upstream = 612 Fraction of orfs with sites within 600 bp upstream = 0.0982975 Motif number 4 GGTGATCAACCTATCCCGGCA 1 1 1 GGTGATCACC 0.979128 -149 CAGACCGGAAGGTGATCTAGC 2 1 0 GGTGATCAGC 0.993592 -263 CGTGCTCCCGATTTTGGGTCC 3 27 0 CGTGCTCCGA 0.850964 -11 TCCAGGTCGCGGCGCTCCGGCCACTGACAGA 5 17 0 GGCGCTCGGC 0.903443 -69 GCGGTGATTGGTTCATCGACCGTGGCGGCAA 7 32 1 GTTCATCACC 0.68002 -55 CGCCGTGCGTTATCCCACGGCAGATAGC 9 8 1 CGTTATCCAC 0.68765 -119 CTAAGTGTAGCGTCACCGGGCAAGCCCGATT 9 44 0 CGTCACCGGC 0.91813 -83 TACACTTAGCCGTGATCCAGCGCGAGCCTTC 9 66 1 CGTGATCAGC 0.993592 -61 CGAATGACGCCGTGATCACGCCGTTCAACGT 10 57 0 CGTGATCCGC 0.993464 -138 TGAGTTGTCCGGTCATCTAGCGGAGGCGCCG 10 158 0 GGTCATCAGC 0.98764 -37 ******* *** Masking position 7 Map Score: 8.86143 Number of sites scoring better than the average of aligned sites = 3208 Number in coding regions = 3020 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 5 CCAGGTGTTCTGAGCAGACCGGAAGGTGAT 2 16 0 TGAGCAGACC 0.72075 -248 TTGGGGGATCCGCGCAGTGGCAAATACCCA 2 55 0 CGCGCAGTGG 0.979708 -209 AACTGTCCGCTCCGCAGTCTACCTCGTTGA 2 142 1 TCCGCAGTCT 0.450174 -122 GGTAGCCAACCGTGCTGTGCTGACGGAAGG 2 192 1 CGTGCTGTGC 0.843241 -72 CGCAGGAATCTGAGCCTTCCGTCAGCACAG 2 206 0 TGAGCCTTCC 0.793578 -58 GCAAACTGCCCGGGCAGTCGCCCGAACGTA 4 11 1 CGGGCAGTCG 0.983742 -30 GCGGCATGCGCAGTGCAGGAATGGGG 6 33 0 TGCGCAGTGC 0.940669 -16 CCGACATTGCCGTGACGGCGGTGATTGGTT 7 15 1 CGTGACGGCG 0.80869 -72 GCACACCGTGAAGTCCCGATGACAAT 8 7 1 CGTGAAGTCC 0.831374 -79 GCGACAGTCGTGGGCCGCGCCTCGGGTTTA 8 47 0 TGGGCCGCGC 0.791139 -39 TGCCCGGCTATCTGCCGTGGGATAACGCAC 9 15 0 TCTGCCGTGG 0.905706 -112 GGCAGATAGCCGGGCAATCGGGCTTGCCCG 9 29 1 CGGGCAATCG 0.799425 -98 TGATCCAGCGCGAGCCTTCGGCCTCGGCGC 9 78 1 CGAGCCTTCG 0.921303 -49 CGGGCGTCGATGCGCCGAGGCCGAAGGCTC 9 89 0 TGCGCCGAGG 0.897837 -38 CAACGTCTCGCCTGCCTTCGTAGCGGCGTC 10 33 0 CCTGCCTTCG 0.843694 -162 CCGGCTGCTGCGTGCCGGCGGGACACTGGG 10 117 1 CGTGCCGGCG 0.97694 -78 ********** Masking position 4 Map Score: 12.9007 Number of sites scoring better than the average of aligned sites = 25983 Number in coding regions = 24127 Number in noncoding regions = 1856 Number of orfs with sites within 600 bp upstream = 1054 Fraction of orfs with sites within 600 bp upstream = 0.16929 Motif number 6 GGCAACGATGCTCGCCGTTCGGTGGGCCTC 1 28 1 CTCGCCGTTC 0.930731 -122 CAGCGCCATCGTTTCATGTCCAGTCAGGTC 1 100 0 GTTTCATGTC 0.90695 -50 GCTAGATCACCTTCCGGTCTGCTCAGAAC 2 10 1 CCTTCCGGTC 0.912051 -254 ACACCACTACGTTGCAGGTCAACGAGGTAG 2 160 0 GTTGCAGGTC 0.917129 -104 ACCTTTTCTGTCAGTGGCCGGA 5 3 1 CTTTTCTGTC 0.923507 -83 CATCTCTCGGGTTGCCTTTCCAGGTCGCGG 5 36 0 GTTGCCTTTC 0.939553 -50 GGCGGGGCGGCTAGCCTGTCGGG 6 4 0 CTAGCCTGTC 0.979778 -45 GTGTAGCTCCGTATTCTGTCGGCGAGTTTG 7 60 0 GTATTCTGTC 0.809166 -27 TACATCTCCTGTCCATGAGGCGA 8 73 0 ATCTCCTGTC 0.913719 -13 CGTTCAACGTCTCGCCTGCCTTCGTAGCGG 10 37 0 CTCGCCTGCC 0.957923 -158 ********** Masking position 10 Map Score: 6.21503 Number of sites scoring better than the average of aligned sites = 2796 Number in coding regions = 2545 Number in noncoding regions = 251 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 7 AGTGTGCCGGGAGTAGCTGGACCTGACTGGAC 1 81 1 GGTAGCTGAC 0.779626 -69 GAGTCCGCCTGTGGAACTGTCCGCTCCGCAGT 2 128 1 GGGAACTTCC 0.81901 -136 CCATACGTTCGGGCGACTGCCCGGGCAGTTTG 4 12 0 GGCGACTCCC 0.506753 -29 CTGTCAGTGGCCGGAGCGCCGCGACCTGGAAA 5 18 1 CGGAGCGCGC 0.64167 -68 AATGGGGGCGGGGCGGCTAGCCTGTCGGG 6 8 0 GGCGGCTGCC 0.535938 -41 GTATTCTGTCGGCGAGTTTGCCGCCACGGTCG 7 48 0 GCGAGTTGCC 0.550027 -39 CCGACAGAATACGGAGCTACACTGCGCCG 7 68 1 AGGAGCTCAC 0.744444 -19 AGCTAAACCCGAGGCGCGGCCCACGACTGTCG 8 44 1 GGGCGCGCCC 0.729435 -42 TCACGGCTAAGTGTAGCGTCACCGGGCAAGCC 9 49 0 GGTAGCGCAC 0.649845 -78 GCAGCAGCCGGCGTAGCTACCAACGATACGCC 10 96 0 GGTAGCTCCA 0.621303 -99 GGCGGGACACTGGGAGCCGCCCTGGCGGCGCC 10 133 1 TGGAGCCCCC 0.519717 -62 TCATCTAGCGGAGGCGCCGCCAGGGCGGCTCC 10 145 0 GGGCGCCCCA 0.861657 -50 AACTCAAGATGAGGAGCTCGCC 10 183 1 GGGAGCTGCC 0.682508 -12 * ****** *** Masking position 7 Map Score: 7.47863 Number of sites scoring better than the average of aligned sites = 7761 Number in coding regions = 7117 Number in noncoding regions = 644 Number of orfs with sites within 600 bp upstream = 480 Fraction of orfs with sites within 600 bp upstream = 0.077096 Motif number 8 CGACCGAGGCCCACCGAACGGCGAGCATCG 1 33 0 CCACCGAACG 0.873107 -117 ACTCAACCCGCGAGCGACCGAGGCCCACCG 1 47 0 CGAGCGACCG 0.955641 -103 GAACACCTGGACATTGACCTGGGTATTTGC 2 36 1 ACATTGACCT 0.462624 -228 ATGGTAGCGGCGAATGACCGAGTCCGCCTG 2 109 1 CGAATGACCG 0.986617 -155 GTCCTGTGGTACAACGACCG 3 1 0 ACAACGACCG 0.97225 -37 TACGTTCGGGCGACTGCCCGGGCAGTTTGC 4 11 0 CGACTGCCCG 0.943215 -30 GGCGCTCCGGCCACTGACAGAAAAGGT 5 8 0 CCACTGACAG 0.890519 -78 CACCGTTGATACAACGACGGTTTCGTACAT 5 63 0 ACAACGACGG 0.924053 -23 CGCCGTCACGGCAATGTCGGCCAG 7 5 0 GCAATGTCGG 0.405028 -82 GGTCGATGAACCAATCACCGCCGTCACGGC 7 23 0 CCAATCACCG 0.921857 -64 GGTGATTGGTTCATCGACCGTGGCGGCAAA 7 34 1 TCATCGACCG 0.862702 -53 CGAGGCGCGGCCCACGACTGTCGCCTCATG 8 53 1 CCCACGACTG 0.669445 -33 CGGGCAAGCCCGATTGCCCGGCTATCTGCC 9 29 0 CGATTGCCCG 0.913419 -98 CCAGGAATCACGAATGACGCCGTGATCACG 10 68 0 CGAATGACGC 0.714473 -127 ********** Masking position 3 Map Score: 8.13501 Number of sites scoring better than the average of aligned sites = 7178 Number in coding regions = 6624 Number in noncoding regions = 554 Number of orfs with sites within 600 bp upstream = 444 Fraction of orfs with sites within 600 bp upstream = 0.0713138 Motif number 9 ********** No masking Map Score: 1.66429e-14 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: 1.66429e-14 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: 1.66429e-14 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