AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 rplY 216 rplY #2 lpqT 35 lpqT #3 prsA 91 prsA #4 glmU 254 glmU #5 Rv1112 131 hypothetical protein Rv1112 #6 mrsA 124 mrsA #7 rplM 233 rplM #8 Rv3447c 113 hypothetical protein Rv3447c #9 ftsH 66 ftsH #10 Rv3627c 137 hypothetical protein Rv3627c Motif number 1 TGTGCCCCAACCGTGCGGACAA 1 3 0 CCGTGCGGAC 0.929501 -214 GCACAGCTATCCGAGCAGCTCACAAGGATC 1 28 1 CCGAGCAGCT 0.820734 -189 GCCGTGACGCCCGGCTAGGCTAACCCATGG 1 78 0 CCGGCTAGGC 0.941691 -139 CTGTAGACCGCCGACCACCCTCGCCGTGAC 1 100 0 CCGACCACCC 0.976697 -117 CGGTGTTCTGCCGGCCTGCTGTAGACCGCC 1 118 0 CCGGCCTGCT 0.924193 -99 GGCCGACAAGCTGTCGCGACCCTGGCCGTG 1 159 1 CTGTCGCGAC 0.718857 -58 GCGACCCTGGCCGTGCCCCCAAACGAGGTA 1 174 1 CCGTGCCCCC 0.989881 -43 AACGAGGTAACCGAGCCACCCAGGAGCGAC 1 195 1 CCGAGCCACC 0.839442 -22 GCCCGCCGGATGCCCTCAAGGATGA 2 21 0 CCGGATGCCC 0.610329 -15 AGTCGCATCCCGGCTACCCGGCGACAAAT 3 10 1 CCGGCTACCC 0.964597 -82 GGCGACAAATCCGGGCGGTGCGCTACGTAC 3 30 1 CCGGGCGGTG 0.632698 -62 CCTGGCGCGCGTCACCCGCGT 4 2 1 CTGGCGCGCG 0.822845 -253 GCCGGAAAACCCGACGCGGGTGACGCGCGC 4 15 0 CCGACGCGGG 0.911025 -240 GTCGGGTTTTCCGGCGCCTTATCCGGCCCT 4 30 1 CCGGCGCCTT 0.784079 -225 GGCCCTTTATCCGGTCCGGCCACATCAACA 4 54 1 CCGGTCCGGC 0.957335 -201 CGTCTACCCACCGGCCCCACGCAAACCGAT 4 89 0 CCGGCCCCAC 0.983551 -166 AACGCTGTCGCCGTCTACCCACCGGCCCCA 4 100 0 CCGTCTACCC 0.94425 -155 GATGTGCAATCCGTCGTGGTGTAATCGGCA 4 169 1 CCGTCGTGGT 0.800693 -86 CCTTGAAGCTCCGTCGCCAGGACTCGAACC 4 228 0 CCGTCGCCAG 0.664569 -27 GCCTGTACCGCCGACCTCGCCCGCTGCGCT 5 45 1 CCGACCTCGC 0.913497 -87 CACACGTCGACCGTACCGGCAATGGCGCCG 5 77 1 CCGTACCGGC 0.88128 -55 TAAGGCGAGGCGGTGCCGCCTTCGGCGCCA 5 99 0 CGGTGCCGCC 0.810294 -33 CACCGACACGCCGACGAGCGCACACAAACA 6 37 0 CCGACGAGCG 0.944245 -88 GTTGCGCGCTCCGGGGCCCGGAA 7 4 0 CCGGGGCCCG 0.609777 -230 CGGCTCTCCCCCGTCGGGACCACACAGGGG 7 37 0 CCGTCGGGAC 0.959135 -197 CGGGGGAGAGCCGTCGGGACCACACAGTCA 7 54 1 CCGTCGGGAC 0.959135 -180 GAGCAGCTTACCGACGAGCATCCACGCAGG 7 90 0 CCGACGAGCA 0.748977 -144 CGCACGCCAACCGAGCAGCTTACCGACGAG 7 102 0 CCGAGCAGCT 0.820734 -132 CGACATTGACCCGAGGTCCCGGCGTACCGC 7 129 0 CCGAGGTCCC 0.937407 -105 GACCAACCCGCCGTTCACGCCTGACCGGCG 7 168 1 CCGTTCACGC 0.81896 -66 TCACGCCTGACCGGCGCCCGGGGCACCCCG 7 182 1 CCGGCGCCCG 0.607716 -52 CGGGTGGATCCCGGGGTGCCCCGGGCGCCG 7 193 0 CCGGGGTGCC 0.980361 -41 CGATCGAGAACCGGCTACCGTTCCGGTGAT 8 30 0 CCGGCTACCG 0.845661 -84 GCGCTGCATACCGTCGCCCAGC 8 102 1 CCGTCGCCCA 0.918927 -12 CGATCATCGGCCGTGCCGGCCAGGTCCTTC 9 47 0 CCGTGCCGGC 0.985503 -20 TTGGACCTGCCCGTTGTCCCATGCACTCTG 10 29 0 CCGTTGTCCC 0.841321 -109 TCCAATGCGTCCGTGGACACCCTAGTCGAG 10 54 1 CCGTGGACAC 0.928651 -84 TGCCACGGTACCGGCTCGACTAGGGTGTCC 10 68 0 CCGGCTCGAC 0.959593 -70 CGAGCCGGTACCGTGGCAGCGTCGCCCGGC 10 80 1 CCGTGGCAGC 0.829919 -58 TTCTGCCGAACCGGCCGGGCGACGCTGCCA 10 93 0 CCGGCCGGGC 0.984643 -45 TCCTGCCTTTCCGGTCCCATTCTGCCGAAC 10 112 0 CCGGTCCCAT 0.623493 -26 ********** Masking position 3 Map Score: 71.1512 Number of sites scoring better than the average of aligned sites = 48866 Number in coding regions = 45571 Number in noncoding regions = 3295 Number of orfs with sites within 600 bp upstream = 1346 Fraction of orfs with sites within 600 bp upstream = 0.21619 Motif number 2 GTTAGCCTAGCCGGGCGTCACGGCGAGGGT 1 84 1 CCGGGCGTCA 0.926286 -133 CGGTCTACAGCAGGCCGGCAGAACACCGTT 1 120 1 CAGGCCGGCA 0.931714 -97 GTTATCGACGGAGGCCGACAAGCTGTCGCG 1 147 1 GAGGCCGACA 0.953661 -70 CGTTTGGGGGCACGGCCAGGGTCGCGACAG 1 169 0 CACGGCCAGG 0.845171 -48 ATGGCAGCCGTCATCCTTGAGGG 2 4 1 GCAGCCGTCA 0.841456 -32 GCCCGCCGGATGCCCTCAAG 2 26 0 GCCCGCCGGA 0.715549 -10 ATCCCGGCTACCCGGCGACAAATCCGGGCG 3 17 1 CCCGGCGACA 0.965082 -75 TACGTAGCGCACCGCCCGGATTTGTCGCCG 3 29 0 ACCGCCCGGA 0.662057 -63 TTCGATCCCAAACGGCGAGGGCAGCGCG 3 74 1 AACGGCGAGG 0.819738 -18 CCTGGCGCGCGTCACCCGCGTCGG 4 5 1 GCGCGCGTCA 0.857172 -250 AGGCGCCGGAAAACCCGACGCGGGTGACGC 4 19 0 AAACCCGACG 0.445584 -236 GGACCGGATAAAGGGCCGGATAAGGCGCCG 4 41 0 AAGGGCCGGA 0.46917 -214 CTTTATCCGGTCCGGCCACATCAACAAGGG 4 58 1 TCCGGCCACA 0.819135 -197 GTCTACCCACCGGCCCCACGCAAACCGATA 4 88 0 CGGCCCCACG 0.524022 -167 CCGGTGGGTAGACGGCGACAGCGTTGACTG 4 105 1 GACGGCGACA 0.961094 -150 AGACGGTGTCAACGCCGTCAGCACAGTCAA 4 128 0 AACGCCGTCA 0.628094 -127 AGGTTCGAGTCCTGGCGACGGAGCTTCAAG 4 227 1 CCTGGCGACG 0.662146 -28 CCGCTCGATTCACCCCCACATCCCAGGT 5 9 0 CACCCCCACA 0.741798 -123 TGTCAGCGCAGCGGGCGAGGTCGGCGGTAC 5 49 0 GCGGGCGAGG 0.972596 -83 CAATGGCGCCGAAGGCGGCACCGCCTCGCC 5 96 1 GAAGGCGGCA 0.861294 -36 GAGCCAAGTTTAAGGCGAGGCGGTGCCGCC 5 109 0 TAAGGCGAGG 0.714397 -23 CATCACTTTCGGGCGACAAGCGTGCATG 6 9 1 TCGGGCGACA 0.940542 -116 GGTTCACCGACACGCCGACGAGCGCACACA 6 41 0 CACGCCGACG 0.9553 -84 GGATATGTGCGCAGCCGTCAACTGTGAAAG 6 96 1 GCAGCCGTCA 0.841456 -29 TGCGCGCTCCGGGGCCCGGAA 7 2 0 GGGGCCCGGA 0.620569 -232 GGGCCCCGGAGCGCGCAACAGACCCCTGTG 7 15 1 GCGCGCAACA 0.337416 -219 CCGACGGCTCTCCCCCGTCGGGACCACACA 7 41 0 TCCCCCGTCG 0.692953 -193 ACGGGGGAGAGCCGTCGGGACCACACAGTC 7 53 1 GCCGTCGGGA 0.540121 -181 TGGCGTGCGGTACGCCGGGACCTCGGGTCA 7 123 1 TACGCCGGGA 0.831241 -111 GAACCGACATTGACCCGAGGTCCCGGCGTA 7 133 0 TGACCCGAGG 0.314782 -101 TCAATGTCGGTTCGCCGAGACCAACCCGCC 7 150 1 TTCGCCGAGA 0.510378 -84 CGGGCGCCGGTCAGGCGTGAACGGCGGGTT 7 172 0 TCAGGCGTGA 0.53569 -62 CGCCTGACCGGCGCCCGGGGCACCCCGGGA 7 185 1 GCGCCCGGGG 0.91242 -49 GCGCCCGGGGCACCCCGGGATCCACCCGAG 7 195 1 CACCCCGGGA 0.846396 -39 ACCCCGGGATCCACCCGAGAGAAAAGAAGG 7 206 1 CCACCCGAGA 0.847551 -28 CGACGGTATGCAGCGCGAGAATCCGCCGCA 8 88 0 CAGCGCGAGA 0.877027 -26 GCTGGGCGACGGTATGCAGCG 8 103 0 CTGGGCGACG 0.748333 -11 CATCGGCCGTGCCGGCCAGGTCCTTCCCGA 9 43 0 GCCGGCCAGG 0.920417 -24 CTGATCTGAAGGAGCCGACGC 10 2 0 GGAGCCGACG 0.783478 -136 GCCGAACCGGCCGGGCGACGCTGCCACGGT 10 89 0 CCGGGCGACG 0.975093 -49 ********** Masking position 6 Map Score: 52.1339 Number of sites scoring better than the average of aligned sites = 82802 Number in coding regions = 77778 Number in noncoding regions = 5024 Number of orfs with sites within 600 bp upstream = 1539 Fraction of orfs with sites within 600 bp upstream = 0.247189 Motif number 3 GCTCGGATAGCTGTGCCCCAACCGTGCGGACA 1 12 0 CTGTGCCAAC 0.728612 -205 ACCACCCTCGCCGTGACGCCCGGCTAGGCTAA 1 85 0 CCGTGGCCCG 0.803102 -132 TGCCGGCCTGCTGTAGACCGCCGACCACCCTC 1 108 0 CTGTACCGCC 0.897909 -109 CCGTCGATAACGGTGTTCTGCCGGCCTGCTGT 1 126 0 CGGTGCTGCC 0.991932 -91 CAAATCCGGGCGGTGCGCTACGTACCATGGGT 3 35 1 CGGTGCTACG 0.924912 -57 CGCGCTGCCCTCGCCGTTTGGGAT 3 78 0 CGCTGCTCGC 0.713872 -14 AACCCGACGCGGGTGACGCGCGCCAGG 4 6 0 GGGTGGCGCG 0.752011 -249 GCCCTTTATCCGGTCCGGCCACATCAACAAGG 4 55 1 CGGTCGCCAC 0.651295 -200 TGCGTGGGGCCGGTGGGTAGACGGCGACAGCG 4 96 1 CGGTGTAGAC 0.660552 -159 GTGAATCGAGCGGTGACTTGCCTGTACCGCCG 5 26 1 CGGTGTTGCC 0.937346 -106 CGACCTCGCCCGCTGCGCTGACACACGTCGAC 5 56 1 CGCTGCTGAC 0.856922 -76 GTCGGCGTGTCGGTGAACCAACAGGCATATTC 6 52 1 CGGTGCCAAC 0.942593 -73 CAACAGACCCCTGTGTGGTCCCGACGGGGGAG 7 30 1 CTGTGGTCCC 0.863162 -204 GTCAAAATGACTGTGTGGTCCCGACGGCTCTC 7 59 0 CTGTGGTCCC 0.863162 -175 GGATGCTCGTCGGTAAGCTGCTCGGTTGGCGT 7 97 1 CGGTACTGCT 0.63148 -137 GGTTGGCGTGCGGTACGCCGGGACCTCGGGTC 7 120 1 CGGTACCGGG 0.875667 -114 GGGTTGGTCTCGGCGAACCGACATTGACCCGA 7 145 0 CGGCGCCGAC 0.904209 -89 GACCGGCGCCCGGGGCACCCCGGGATCCACCC 7 190 1 CGGGGCCCCG 0.493374 -44 GCTACCGTTCCGGTGATCCGAGAATAAAGGGG 8 15 0 CGGTGCCGAG 0.955255 -99 GCTGGGCGACGGTATGCAGCGCGAGAATCCG 8 93 0 CGGTACAGCG 0.73887 -21 TCCAATGCGTCCGTGGACACCCTAGTCGAGCC 10 54 1 CCGTGCACCC 0.685409 -84 CTAGTCGAGCCGGTACCGTGGCAGCGTCGCCC 10 75 1 CGGTAGTGGC 0.77565 -63 ***** ***** Masking position 1 Map Score: 25.41 Number of sites scoring better than the average of aligned sites = 20386 Number in coding regions = 19026 Number in noncoding regions = 1360 Number of orfs with sites within 600 bp upstream = 843 Fraction of orfs with sites within 600 bp upstream = 0.1354 Motif number 4 ATTCGATCCTTGTGAGCTGCTCGGATAGCT 1 32 0 TGTGAGCTGC 0.968373 -185 CGTCGATAACGGTGTTCTGCCGGCCTGCTG 1 127 0 GGTGTTCTGC 0.846212 -90 AAATCCGGGCGGTGCGCTACGTACCATGGG 3 36 1 GGTGCGCTAC 0.963719 -56 CGCCATTGCCGGTACGGTCGACGTGTGTCA 5 74 0 GGTACGGTCG 0.813457 -58 TGCATGTTTGTGTGCGCTCGTCGGCGTGTC 6 33 1 TGTGCGCTCG 0.961915 -92 AGAGTGGATATGTGCGCAGCCGTCAACTGT 6 91 1 TGTGCGCAGC 0.956692 -34 AGGGGTCTGTTGCGCGCTCCGGGGCCCGGA 7 12 0 TGCGCGCTCC 0.955696 -222 AACAGACCCCTGTGTGGTCCCGACGGGGGA 7 31 1 TGTGTGGTCC 0.966933 -203 TCAAAATGACTGTGTGGTCCCGACGGCTCT 7 60 0 TGTGTGGTCC 0.966933 -174 GATGCTCGTCGGTAAGCTGCTCGGTTGGCG 7 98 1 GGTAAGCTGC 0.90074 -136 GCTCGGTTGGCGTGCGGTACGCCGGGACCT 7 116 1 CGTGCGGTAC 0.851848 -118 GCTGGGCGACGGTATGCAGCGCGAGAATCC 8 94 0 GGTATGCAGC 0.791238 -20 ********** Masking position 2 Map Score: 12.0788 Number of sites scoring better than the average of aligned sites = 4979 Number in coding regions = 4691 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028 Motif number 5 CTCACAAGGATCGAATTTCCCCAATGCAGT 1 46 1 TCGAATTTCC 0.895814 -171 TGGGATCGAATTGGATTACCCATGGTACGT 3 54 0 TTGGATTACC 0.918005 -38 CAACCCTCCTTGAAGCTCCGTCGCCAGGA 4 236 0 TTGAAGCTCC 0.765938 -19 AAGTCACCGCTCGATTCACCCCCACATCCC 5 15 0 TCGATTCACC 0.976214 -117 AATATGCCTGTTGGTTCACCGACACGCCGA 6 53 0 TTGGTTCACC 0.976214 -72 CGGGTCAATGTCGGTTCGCCGAGACCAACC 7 146 1 TCGGTTCGCC 0.979295 -88 CCCTTTATTCTCGGATCACCGGAACGGTAG 8 16 1 TCGGATCACC 0.990565 -98 CGCCCGGTATTCGGTTGTCCACAAGCGACT 8 58 1 TCGGTTGTCC 0.948687 -56 ********** Masking position 1 Map Score: 7.32822 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 569 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 6 GTAGCCATGGGTTAGCCTAGCCGGGCGTCA 1 74 1 GTTAGCCTAG 0.842715 -143 ATGGCAGCCGTCATCCTTGAGGGCATCCG 2 10 1 GTCATCCTTG 0.895162 -26 CCTGGCGCGCGTCACCCGCGTCGGGTTTTC 4 11 1 GTCACCCGCG 0.888697 -244 CACGCAAACCGATACCCTTGTTGATGTGGC 4 72 0 GATACCCTTG 0.748141 -183 GGTAGACGGCGACAGCGTTGACTGTGCTGA 4 111 1 GACAGCGTTG 0.925699 -144 TGTCAACGCCGTCAGCACAGTCAACGCTGT 4 122 0 GTCAGCACAG 0.852482 -133 GATTCACCCCCACATCCCAGGT 5 3 0 CACATCCCAG 0.506282 -129 GTACAGGCAAGTCACCGCTCGATTCACCCC 5 23 0 GTCACCGCTC 0.722464 -109 GTCGACGTGTGTCAGCGCAGCGGGCGAGGT 5 58 0 GTCAGCGCAG 0.967904 -74 CGGCGCCCGGGGCACCCCGGGATCCACCCG 7 193 1 GGCACCCCGG 0.91464 -41 TGCGTCCGTGGACACCCTAGTCGAGCCGGT 10 59 1 GACACCCTAG 0.963423 -79 CCGGTACCGTGGCAGCGTCGCCCGGCCGGT 10 84 1 GGCAGCGTCG 0.895431 -54 ********** Masking position 4 Map Score: 4.74916 Number of sites scoring better than the average of aligned sites = 7659 Number in coding regions = 7169 Number in noncoding regions = 490 Number of orfs with sites within 600 bp upstream = 404 Fraction of orfs with sites within 600 bp upstream = 0.0648892 Motif number 7 GCACACAAACATGCACGCTTGTCGCCCGAA 6 18 0 ATGCACGCTT 0.974789 -107 CTGCGCACATATCCACTCTTGGCAGCGAAT 6 80 0 ATCCACTCTT 0.953181 -45 ACCGACGAGCATCCACGCAGGTCAAAATGA 7 81 0 ATCCACGCAG 0.986183 -153 GTCCTTCCCGATACACGCAGCTGGAAAGTC 9 24 0 ATACACGCAG 0.963426 -43 CCGTTGTCCCATGCACTCTGATCTGAAGGA 10 19 0 ATGCACTCTG 0.978659 -119 ********** Masking position 5 Map Score: 2.83888 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 147 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 ********** No masking Map Score: -1.94446e-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: -1.94446e-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: -1.94446e-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