AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -imodE_mtub_opreg_100.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 Rv0870c 164 hypothetical protein Rv0870c #2 Rv0981 300 hypothetical protein Rv0981 #3 Rv0983 43 hypothetical protein Rv0983 #4 modA 161 modA #5 subI 124 subI #6 moaA 148 moaA #7 moaB 50 moaB #8 moaC3 184 moaC3 Motif number 1 CAACAGAAGACGCGTCCCGCCTGCGCGGGACGCGA 1 49 1 CGCCGCTGCG 0.873048 -116 CCCGCCTGCGCGGGACGCGATGACGATCTGAAGAT 1 64 1 CGGCGTGACG 0.796665 -101 GAAGATCCTACTCGGATCGTCGGCCGCCGAGCACC 1 93 1 CTCCGCGGCC 0.967763 -72 TCGTCGGCCGCCGAGCACCCCTGCTTACCCCTCAC 1 109 1 CCGCCCTGCT 0.936792 -56 TTACCCCTCACGCGGTAGGCTTGCGCTACCGCTGG 1 133 1 CGCGGTTGCG 0.592125 -32 ACCGTTTATTCGGACGATCCCTGCCGTTCCACGCC 2 16 1 CGGTCCTGCC 0.897945 -285 AATGTTGGTGCGGTTTGTGCCTGCGCCCAGGCGTG 2 45 0 CGGTGCTGCG 0.974841 -256 CTCGTCCGCGCGGGTTTCGCCTGCTGACACACGAT 2 120 0 CGGCGCTGCT 0.974859 -181 TGGCTGATGTGGCTAAACCTCGTCGAACAAACCCG 2 226 1 GGCCCCGTCG 0.926188 -75 TCGAACAAACCCGCATACCACGGCGCGCCTCTCAG 2 248 1 CCGCCCGGCG 0.992845 -53 TCTCAGGCCAGTCTCAGGCGCTGCGACGACACTG 2 277 1 GTCGCCTGCG 0.887144 -24 TGAACCCAGACCCTGGACCGTTGCCTGGAATCGCA 4 31 1 CCCCCTTGCC 0.867835 -131 TGCCTGGAATCGCATCGTGATGGCGTAAGCTCCGG 4 52 1 CGCTGTGGCG 0.846589 -110 GGGGAAACTCCGCACCGCCACGACGCGCAGACGAT 4 113 1 CGCCCCGACG 0.769925 -49 CTAATGGTTACCAAGATCGTCTGCGCGTCGTGGCG 4 128 0 CCACGCTGCG 0.96949 -34 TTGTCGCTGACTCCCCACCCGTGCGCGGTCTGATG 5 13 1 CTCCCGTGCG 0.973521 -112 GTTCAGCGATCGCCTTTCCGCCGCTACGGGAACGT 5 70 1 CGCCCCCGCT 0.925002 -55 TGGCGACCTTCCGGTGCGGGACTTTGGA 5 107 0 CGACCGTGCG 0.874903 -18 CATAAACGCAGGCTCATGCGCTGCGCCACGATGCG 6 19 1 GGCGCCTGCG 0.935806 -130 CAATCGTTACCGAAATGCATCGGCGCATCGTGGCG 6 42 0 CGACACGGCG 0.579518 -107 TCTTGAGGCGCTCTAACCGACTGCGTCCAAAGTGG 6 101 1 CTCCGCTGCG 0.991389 -48 TGGAGTCTCCGGACATGCCGGGGCGGTTCAGTGTC 8 32 1 GGACCGGGCG 0.715405 -153 CACTGTTTGACTCGCGTCGACTTCGACCTCGCCGA 8 112 1 CTCCGCTTCG 0.923864 -73 GTGCACTGCGCTGAAAGCCTCGGCGAGGTCGAAGT 8 131 0 CTGCCCGGCG 0.990653 -54 *** ** ***** Masking position 14 Map Score: 43.6615 Number of sites scoring better than the average of aligned sites = 28019 Number in coding regions = 26008 Number in noncoding regions = 2011 Number of orfs with sites within 600 bp upstream = 983 Fraction of orfs with sites within 600 bp upstream = 0.157886 Motif number 2 CGTCAGACAAGCAGGTGAGACCA 1 2 0 GCGGTGGACC 0.913857 -163 TCCCGCGCAGGCGGGACGCGTCTTCTGTTGCC 1 47 0 GCGGACCGTC 0.896047 -118 TCCCGCCTGCGCGGGACGCGATGACGATCTGA 1 63 1 GCGGACCGAT 0.938146 -102 TTGCGCTACCGCTGGAGGCGAT 1 153 1 GCGGAGCGAT 0.959358 -12 TTCCACCAATGTTGGTGCGGTTTGTGCCTGCG 2 55 0 GTGGTGGGTT 0.857605 -246 TCTCGTCCGCGCGGGTTTCGCCTGCTGACACA 2 124 0 GCGGTTCGCC 0.865749 -177 GGCCAATGTGGCTGATGTGGCTAAACCTCGTC 2 218 1 GCGATGGGCT 0.907338 -83 CCTGAGACTGGCCTGAGAGGCGCGCCGTGGTA 2 263 0 GCTGAGGGCG 0.967064 -38 GTGGACTGGCATGGGTGTGGCTTTCAACAGTA 3 20 0 ATGGTGGGCT 0.721113 -24 TGGGTTCAGCGTTGAACACGAGGAGGTC 4 7 0 GTGAACCGAG 0.653779 -155 TGCGCGTCGTGGCGGTGCGGAGTTTCCCCGAA 4 110 0 GGGGTGGGAG 0.936649 -52 CAGACCGCGCACGGGTGGGGAGTCAGCGACAA 5 13 0 ACGGTGGGAG 0.854669 -112 GCTGAACATTGCAGGACTCACGAACTCCACAT 5 45 0 GCGGACCACG 0.931722 -80 TTCCCGTAGCGGCGGAAAGGCGATCGCTGAAC 5 70 0 GGGGAAGGCG 0.716474 -55 ATGAGCCTGCGTTTATGGCGCGTTG 6 4 0 GTTATGCGCG 0.627626 -145 AACCGCCCCGGCATGTCCGGAGACTCCAGTTC 8 28 0 GCTGTCGGAG 0.887907 -157 ATAACAAGCGGTCGGTGCGGTTGACTTGTTGG 8 68 1 GTGGTGGGTT 0.857604 -117 CGGTTGACTTGTTGGACGCGCCAGATGCACTG 8 85 1 GTGGACCGCC 0.950076 -100 CAGATGCACTGTTTGACTCGCGTCGACTTCGA 8 106 1 GTTGACCGCG 0.883093 -79 AATGCAGCCAGCAGGTGGCACG 8 173 1 GCGGTGCACG 0.962687 -12 ** **** **** Masking position 1 Map Score: 20.7661 Number of sites scoring better than the average of aligned sites = 31167 Number in coding regions = 29189 Number in noncoding regions = 1978 Number of orfs with sites within 600 bp upstream = 1077 Fraction of orfs with sites within 600 bp upstream = 0.172984 Motif number 3 GCAACAGAAGACGCGTCCCGCCTGCGCGGG 1 48 1 ACGCGTCCCG 0.978641 -117 CAGATCGTCATCGCGTCCCGCGCAGGCGGG 1 64 0 TCGCGTCCCG 0.978641 -101 ACCCCTGCTTACCCCTCACGCGGTAGGCTT 1 125 1 ACCCCTCACG 0.835998 -40 ATCGCCTCCAGCGGTAGCGCA 1 154 0 TCGCCTCCAG 0.97416 -11 GTGTCAGCAGGCGAAACCCGCGCGGACGAG 2 125 1 GCGAAACCCG 0.821956 -176 ATACCACGGCGCGCCTCTCAGGCCAGTCTC 2 262 1 GCGCCTCTCA 0.93171 -39 CGCCTCTCAGGCCAGTCTCAGGCGCTGCGA 2 273 1 GCCAGTCTCA 0.748381 -28 ACTGTTGAAAGCCACACCCATGCCAGTCCA 3 21 1 GCCACACCCA 0.885515 -23 CCACACCCATGCCAGTCCACGC 3 32 1 GCCAGTCCAC 0.907726 -12 CCATCACGATGCGATTCCAGGCAACGGTCC 4 45 0 GCGATTCCAG 0.920285 -117 TGTCGCTGACTCCCCACCCGTGCGCGGTCT 5 14 1 TCCCCACCCG 0.874878 -111 GTCGGTTAGAGCGCCTCAAGAGAGTTTCGT 6 92 0 GCGCCTCAAG 0.971696 -57 CGATTGATCAACGACTCCACAGTTGAGGAA 7 25 1 ACGACTCCAC 0.848185 -26 GGCATGTCCGGAGACTCCAGTTCTTGGAAA 8 21 0 GAGACTCCAG 0.861582 -164 AGTGCATCTGGCGCGTCCAACAAGTCAACC 8 86 0 GCGCGTCCAA 0.980652 -99 CGAAGTCGACGCGAGTCAAACAGTGCATCT 8 107 0 GCGAGTCAAA 0.851066 -78 ********** Masking position 7 Map Score: 17.8048 Number of sites scoring better than the average of aligned sites = 10568 Number in coding regions = 9727 Number in noncoding regions = 841 Number of orfs with sites within 600 bp upstream = 653 Fraction of orfs with sites within 600 bp upstream = 0.104883 Motif number 4 CACCAATGTTGGTGCGGTTTGTGCCTGCGCCC 2 52 0 GGTGCGGTTT 0.975602 -249 CAGAACCCCAGGTGCAGTGTGCACCACGTTCC 2 83 0 GGTGCAGGTC 0.995111 -218 TTGTGCAGTTACTGTTGAAAGCC 3 2 1 TGTGCAGTAT 0.815999 -42 GACTGGCATGGGTGTGGCTTTCAACAGTAACT 3 17 0 GGTGTGGTTC 0.845129 -27 CCAGGGTCTGGGTTCAGCGTTGAACACGAGGA 4 15 0 GGTTCAGGTG 0.927668 -147 TCCAGGCAACGGTCCAGGGTCTGGGTTCAGCG 4 28 0 GGTCCAGGTT 0.982174 -134 GCGTCGTGGCGGTGCGGAGTTTCCCCGAATAG 4 107 0 GGTGCGGGTT 0.991998 -55 AGTCCTGCAATGTTCAGCGATCGCCTTTCCGC 5 59 1 TGTTCAGGAC 0.895515 -66 ACGGGAACGTTGTCCAAAGTCCCGCACCGGAA 5 95 1 TGTCCAAGTC 0.708258 -30 CGCCCCGGCATGTCCGGAGACTCCAGTTCTTG 8 25 0 TGTCCGGGAT 0.891399 -160 ATGCCGGGGCGGTTCAGTGTCCATAACAAGCG 8 46 1 GGTTCAGGTC 0.985231 -139 ACAAGCGGTCGGTGCGGTTGACTTGTTGGACG 8 71 1 GGTGCGGTGC 0.946722 -114 ******* ** * Masking position 3 Map Score: 12.5302 Number of sites scoring better than the average of aligned sites = 3087 Number in coding regions = 2855 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 5 ACGCGTCCCGCCTGCGCGGGACGCGATGAC 1 58 1 CCTGCGCGGG 0.811285 -107 ATCTGAAGATCCTACTCGGATCGTCGGCCG 1 89 1 CCTACTCGGA 0.804147 -76 GGGGTTCTGCCCTCATCGTGTGTCAGCAGG 2 106 1 CCTCATCGTG 0.990007 -195 CACAAATCGCCCTACTCTTGACCACCAAAC 2 173 1 CCTACTCTTG 0.867662 -128 GACCTCCTCGTGTTCAACGCTG 4 3 1 CCTCCTCGTG 0.994894 -159 TTGCCTGGAATCGCATCGTGATGGCGTAAG 4 51 1 TCGCATCGTG 0.901627 -111 CTGGACAGTAGCTATTCGGGGAAACTCCGC 4 96 1 GCTATTCGGG 0.845141 -66 AAGATCGTCTGCGCGTCGTGGCGGTGCGGA 4 121 0 GCGCGTCGTG 0.955648 -41 TCGCTGACTCCCCACCCGTGCGCGGTCTGA 5 16 1 CCCACCCGTG 0.82165 -109 AAATGCATCGGCGCATCGTGGCGCAGCGCA 6 35 0 GCGCATCGTG 0.979521 -114 TGGCTGCATTGCTCATCGTGCACTGCGCTG 8 153 0 GCTCATCGTG 0.985332 -32 ********** Masking position 7 Map Score: 10.1752 Number of sites scoring better than the average of aligned sites = 2320 Number in coding regions = 2109 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 6 GTTGCCAATCCGAGCGATCCGTCAGACAAG 1 23 0 CGAGCGATCC 0.963831 -142 CGATGACGATCTGAAGATCCTACTCGGATC 1 81 1 CTGAAGATCC 0.848157 -84 TGCTCGGCGGCCGACGATCCGAGTAGGATC 1 96 0 CCGACGATCC 0.982476 -69 ACCGTTTATTCGGACGATCCCTGCCGTTCC 2 16 1 CGGACGATCC 0.992203 -285 TAAACCTCGTCGAACAAACCCGCATACCAC 2 239 1 CGAACAAACC 0.757106 -62 GCGATTCCAGGCAACGGTCCAGGGTCTGGG 4 35 0 GCAACGGTCC 0.820053 -127 CCACGACGCGCAGACGATCTTGGTAACCAT 4 130 1 CAGACGATCT 0.82465 -32 AGTCCCGCACCGGAAGGTCGCCA 5 112 1 CGGAAGGTCG 0.928316 -13 CAAGGGTTAACTAACAATCGTTACCGAAAT 6 61 0 CTAACAATCG 0.819144 -88 GCCGAACGAACAGTCGATTGATCAAC 7 7 1 CGAACAGTCG 0.937673 -44 GTGTCCATAACAAGCGGTCGGTGCGGTTGA 8 62 1 CAAGCGGTCG 0.866408 -123 ********** Masking position 9 Map Score: 7.6944 Number of sites scoring better than the average of aligned sites = 4111 Number in coding regions = 3805 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 7 GACGCGTCCCGCCTGCGCGGGACGCGATGA 1 57 1 GCCTGCGCGG 0.980887 -108 GTGCCTGCGCCCAGGCGTGGAACGGCAGGG 2 34 0 CCAGGCGTGG 0.942049 -267 CAGGCCAGTCTCAGGCGCTGCGACGACACT 2 280 1 TCAGGCGCTG 0.987045 -21 GACTCCCCACCCGTGCGCGGTCTGATGTGG 5 21 1 CCGTGCGCGG 0.891348 -104 TGGCGACCTTCCGGTGCGGGACTTTGGAC 5 106 0 TCCGGTGCGG 0.975778 -19 AGCCTGCGTTTATGGCGCGTTG 6 3 0 TATGGCGCGT 0.856267 -146 AAACGCAGGCTCATGCGCTGCGCCACGATG 6 22 1 TCATGCGCTG 0.967576 -127 AAACAGTGCATCTGGCGCGTCCAACAAGTC 8 90 0 TCTGGCGCGT 0.981592 -95 ********** Masking position 5 Map Score: 8.00286 Number of sites scoring better than the average of aligned sites = 3988 Number in coding regions = 3686 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 280 Fraction of orfs with sites within 600 bp upstream = 0.0449727 Motif number 8 GACGGATCGCTCGGATTGGCAACAGAAGAC 1 30 1 TCGGATTGGC 0.787026 -135 GGTAAGCAGGGGTGCTCGGCGGCCGACGAT 1 108 0 GGTGCTCGGC 0.765552 -57 GCGCCCAGGCGTGGAACGGCAGGGATCGTC 2 28 0 GTGGAACGGC 0.92614 -273 GTTTGTGCCTGCGCCCAGGCGTGGAACGGC 2 38 0 GCGCCCAGGC 0.872594 -263 GGCGATTTGTGCTGCTTGGCGGAAGAGTTC 2 154 0 GCTGCTTGGC 0.971062 -147 CTGAGACTGGCCTGAGAGGCGCGCCGTGGT 2 264 0 CCTGAGAGGC 0.786949 -37 TGCAGTTACTGTTGAAAGCCACACCCATGC 3 14 1 GTTGAAAGCC 0.714496 -30 GCGTGGACTGGCATGGGTGTGG 3 32 0 GTGGACTGGC 0.926152 -12 GATCGTCTGCGCGTCGTGGCGGTGCGGAGT 4 119 0 GCGTCGTGGC 0.821634 -43 TCCCGTAGCGGCGGAAAGGCGATCGCTGAA 5 71 0 GCGGAAAGGC 0.986829 -54 CGTGCACTGCGCTGAAAGCCTCGGCGAGGT 8 137 0 GCTGAAAGCC 0.909927 -48 CCACCTGCTGGCTGCATTGCTCATCGTGCA 8 161 0 GCTGCATTGC 0.796209 -24 ********** Masking position 10 Map Score: 5.47319 Number of sites scoring better than the average of aligned sites = 11452 Number in coding regions = 10574 Number in noncoding regions = 878 Number of orfs with sites within 600 bp upstream = 638 Fraction of orfs with sites within 600 bp upstream = 0.102473 Motif number 9 TGGTCTCACCTGCTTGTCTGA 1 2 1 GGTCTCACCT 0.893228 -163 CTGGGCGCAGGCACAAACCGCACCAACATT 2 50 1 GCACAAACCG 0.977736 -251 CTGGGGTTCTGCCCTCATCGTGTGTCAGCA 2 104 1 GCCCTCATCG 0.933106 -197 CCGCCAAGCAGCACAAATCGCCCTACTCTT 2 162 1 GCACAAATCG 0.922957 -139 TGGCTGATGTGGCTAAACCTCGTCGAACAA 2 226 1 GGCTAAACCT 0.82551 -75 TGGCCAAACCTAATGGTTACC 4 151 0 GGCCAAACCT 0.973315 -11 CTCTTGAGGCGCTCTAACCGACTGCGTCCA 6 100 1 GCTCTAACCG 0.971203 -49 ********** Masking position 7 Map Score: 2.87684 Number of sites scoring better than the average of aligned sites = 2424 Number in coding regions = 2229 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 10 GGGGTAAGCAGGGGTGCTCGGCGGCCGACGA 1 109 0 GGGGTCTCGG 0.844 -56 CAATGTTGGTGCGGTTTGTGCCTGCGCCCAG 2 50 0 GCGGTTGTGC 0.856512 -251 ACCAACATTGGTGGAACGTGGTGCACACTGC 2 71 1 GTGGACGTGG 0.979097 -230 AGAACCCCAGGTGCAGTGTGCACCACGTTCC 2 83 0 GTGCATGTGC 0.96041 -218 AGGGCGATTTGTGCTGCTTGGCGGAAGAGTT 2 155 0 GTGCTCTTGG 0.94541 -146 GAGGCGCGCCGTGGTATGCGGGTTTGTTCGA 2 248 0 GTGGTTGCGG 0.970422 -53 GCGGTCTGATGTGGAGTTCGTGAGTCCTGCA 5 37 1 GTGGATTCGT 0.791475 -88 AAATGCATCGGCGCATCGTGGCGCAGCGCAT 6 34 0 GCGCACGTGG 0.959786 -115 CGATGCGCCGATGCATTTCGGTAACGATTGT 6 47 1 ATGCATTCGG 0.733324 -102 GAGTCAAACAGTGCATCTGGCGCGTCCAACA 8 94 0 GTGCACTGGC 0.879074 -91 ATTGCTCATCGTGCACTGCGCTGAAAGCCTC 8 145 0 GTGCATGCGC 0.785296 -40 ***** ***** Masking position 3 Map Score: 8.58193 Number of sites scoring better than the average of aligned sites = 4881 Number in coding regions = 4499 Number in noncoding regions = 382 Number of orfs with sites within 600 bp upstream = 310 Fraction of orfs with sites within 600 bp upstream = 0.0497912 Motif number 11 ********** No masking Map Score: 1.06825e-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 12 ********** No masking Map Score: 1.06825e-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 13 ********** No masking Map Score: 1.06825e-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