AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i020_TCA_mtub_reg_100.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 sucA 192 sucA #2 sucB 263 sucB #3 aceE 51 aceE #4 pdhA 258 pdhA #5 sdhA 128 sdhA Motif number 1 CAGAGAGACCGGGCAACGCGCG 1 3 0 GGGCAACGCG 0.981297 -190 GCCAGCGATTCGCCAGAGAGACCGGGCAAC 1 16 0 CGCCAGAGAG 0.78244 -177 AGCCTTTATGGGGCAGACCGTTCACCGACT 1 54 1 GGGCAGACCG 0.869365 -139 CAAGCGCATTGCGCGGCGCCTGCTGGCAGT 1 81 0 GCGCGGCGCC 0.979857 -112 AACTTATGTTGGCCACGGCCGCTGTTCGCC 1 138 0 GGCCACGGCC 0.6882 -55 TTCACCATTCGGGCAAAACGAATGGCTGGT 1 166 1 GGGCAAAACG 0.819595 -27 ACGAATGGCTGGTCGAAGAG 1 183 1 GGTCGAAGAG 0.567141 -10 CGCACCTCCGCCCACCGGGACTTGCTGTT 2 10 1 GCCCACCGGG 0.981778 -254 GCTACGGTTTGGGCGACTGGTTGCAACAGC 2 34 0 GGGCGACTGG 0.923876 -230 TAGCAAGGACGGCCGACTGCACCGATGTCC 2 60 1 GGCCGACTGC 0.845295 -204 GCACCGATGTCCCCGCCGAGGTGTCGGCAA 2 78 1 CCCCGCCGAG 0.960189 -186 TGTCGGCAACGGCCGCCGGGGCCACCAACT 2 99 1 GGCCGCCGGG 0.901905 -165 CACACATCCAGGGCGCGGCGAGTTGGTGGC 2 119 0 GGGCGCGGCG 0.531137 -145 CTGTCACTGCGCCCGGAGCGACACACATCC 2 140 0 GCCCGGAGCG 0.982098 -124 TCACACGGTCGCGCACCGGGTGCGGAACCC 2 191 0 GCGCACCGGG 0.982636 -73 CCGTGTGATAGGCCAGAGGTGGACCTGCGC 2 213 1 GGCCAGAGGT 0.836965 -51 GATCGTCGGTCGGCGCAGGTCCACCTCTGG 2 225 0 CGGCGCAGGT 0.957217 -39 TTCGGGTGATCCGCGAGGGT 3 42 1 CCGCGAGGGT 0.745511 -10 GGGCGCAGATCCCCCGCGAC 4 1 1 GGGCGCAGAT 0.877813 -258 CGCAGATCCCCCGCGACACGGTTGCGATGC 4 14 1 CCGCGACACG 0.914707 -245 GCCAGTGTTGCGGCGAGCGGAAGCTTTGGT 4 94 1 CGGCGAGCGG 0.768729 -165 CGAAGTTGATCGCCGGCCGCACCAAAGCTT 4 114 0 CGCCGGCCGC 0.895206 -145 ATCAACTTCGGCTCGCAGCGGTTTCCCAGG 4 134 1 GCTCGCAGCG 0.900277 -125 GCTGTGAGCGCCGCACCACCAGCGCCGACG 4 172 1 CCGCACCACC 0.791558 -87 GCACCACCAGCGCCGACGCTAAGGATGGAA 4 184 1 CGCCGACGCT 0.959036 -75 AAGGCCCGGAAGGAGCACATGAT 5 4 1 GCCCGGAAGG 0.877737 -125 CACATGATCACGCCACCTCTCCCCCGCAAG 5 26 1 CGCCACCTCT 0.64942 -103 GCCACCTCTCCCCCGCAAGCGGGCGGTACC 5 37 1 CCCCGCAAGC 0.803742 -92 GCGACGAGGGGGCCGCAGCGATGAGGTGGG 5 67 0 GGCCGCAGCG 0.856033 -62 GCACCCCCAGCCGCGAAGCGACGAGGGGGC 5 84 0 CCGCGAAGCG 0.972204 -45 GATGCAGTGGGGGCACCCCCAGCCGCGAAG 5 96 0 GGGCACCCCC 0.921124 -33 CGCCGCCGCCGACGATGCAG 5 119 0 CGCCGCCGCC 0.716304 -10 ********** Masking position 4 Map Score: 56.2482 Number of sites scoring better than the average of aligned sites = 106622 Number in coding regions = 99817 Number in noncoding regions = 6805 Number of orfs with sites within 600 bp upstream = 1626 Fraction of orfs with sites within 600 bp upstream = 0.261163 Motif number 2 CGCGCGTTGCCCGGTCTCTCTGGC 1 2 1 GCGCTGCCGG 0.9666 -191 GGTCTCTCTGGCGAATCGCTGGCAAAGCGTTAG 1 23 1 GCGATGTGGC 0.962675 -170 CAAGCGCATTGCGCGGCGCCTGCTGGCAGTCGG 1 78 0 GCGCGGCTGC 0.982128 -115 AAGTCCCGGTGGGCGGAGGTGCG 2 1 0 GGGCGGTGCG 0.865515 -263 GCGGGGACATCGGTGCAGTCGGCCGTCCTTGCT 2 61 0 CGGTCGCGGC 0.762132 -203 GATGTCCCCGCCGAGGTGTCGGCAACGGCCGCC 2 83 1 CCGAGGCGGC 0.994302 -181 CCAGGGCGCGGCGAGTTGGTGGCCCCGGCGGCC 2 109 0 GCGATGTGGC 0.962675 -155 GTCGCTCCGGGCGCAGTGACAGGATAGGTTTCG 2 148 1 GCGCGGCAGG 0.953719 -116 ACACGGTCGCGCACCGGGTGCGGAACCCAGGTG 2 186 0 GCACGGGCGG 0.814412 -78 CACCCGAACTCGGTCGGGTTCGCTTGCGCTGTT 3 17 0 CGGTGGTCGC 0.938169 -35 CGCATCGCAACCGTGTCGCGGGGGATCTGCGCC 4 12 0 CCGTTGGGGG 0.904081 -247 CGACACGGTTGCGATGCGTTCGCGATCGGTCCG 4 27 1 GCGAGGTCGC 0.947018 -232 GCCCCCAAATGTGAAGAGTCCGGACCGATCGCG 4 47 0 GTGAGGCCGG 0.963901 -212 GGAAGCGCCAGTGTTGCGGCGAGCGGAAGCTTT 4 88 1 GTGTGGCGAG 0.554731 -171 GCCTGGGAAACCGCTGCGAGCCGAAGTTGATCG 4 132 0 CCGCGGGCCG 0.876708 -127 CAGGCGGGATGTGCTGTGAGCGCCGCACCACCA 4 160 1 GTGCGGGCGC 0.974746 -99 TGCGTTCCATCCTTAGCGTCGGCGCTGGTGGTG 4 185 0 CCTTGGCGGC 0.828933 -74 ACGCGTAACCGCGTTGTGATCGCGAGCTGAGGA 4 230 1 GCGTGGTCGC 0.983949 -29 TGATCGCGAGCTGAGGAGACGGT 4 246 1 CTGAGGCGGT 0.695936 -13 CCCGCTTGCGGGGGAGAGGTGGCGTGATCATGT 5 27 0 GGGGGGTGGC 0.925582 -102 GGGGGCCGCAGCGATGAGGTGGGGGTACCGCCC 5 57 0 GCGAGGTGGG 0.989276 -72 CAGCCGCGAAGCGACGAGGGGGCCGCAGCGATG 5 74 0 GCGAGGGGGC 0.993671 -55 CGTCGCTTCGCGGCTGGGGGTGCCCCCACTGCA 5 91 1 CGGCGGGTGC 0.883358 -38 GGTGCCCCCACTGCATCGTCGGCGGCGGCG 5 109 1 CTGCTGCGGC 0.928867 -20 **** * * **** Masking position 8 Map Score: 42.7774 Number of sites scoring better than the average of aligned sites = 37034 Number in coding regions = 34708 Number in noncoding regions = 2326 Number of orfs with sites within 600 bp upstream = 1080 Fraction of orfs with sites within 600 bp upstream = 0.173466 Motif number 3 GATTCGCCAGAGAGACCGGGCAACGCGCG 1 10 0 AGAGACCGGG 0.619185 -183 CAGACCGTTCACCGACTGCCAGCAGGCGCC 1 67 1 ACCGACTGCC 0.605448 -126 TAGTTGAAGTCCTGCAAGCGCATTGCGCGG 1 95 0 CCTGCAAGCG 0.63435 -98 CGAGGCGAACAGCGGCCGTGGCCAACATAA 1 135 1 AGCGGCCGTG 0.81627 -58 ATTCGTTTTGCCCGAATGGTGAACTTATGT 1 159 0 CCCGAATGGT 0.426091 -34 CGCACCTCCGCCCACCGGGA 2 1 1 CGCACCTCCG 0.728527 -263 ACCAACTCGCCGCGCCCTGGATGTGTGTCG 2 122 1 CGCGCCCTGG 0.861247 -142 GGTTTCGACATCCACCTGGGTTCCGCACCC 2 174 1 TCCACCTGGG 0.661253 -90 ACCTGGGTTCCGCACCCGGTGCGCGACCGT 2 187 1 CGCACCCGGT 0.779487 -77 GCACCCGGTGCGCGACCGTGTGATAGGCCA 2 198 1 CGCGACCGTG 0.928454 -66 AACTCAAACAGCGCAAGCGAACCCGACCG 3 10 1 AGCGCAAGCG 0.873263 -42 CGCAAGCGAACCCGACCGAGTTCGGGTGAT 3 22 1 CCCGACCGAG 0.90433 -30 GCGAACGCATCGCAACCGTGTCGCGGGGGA 4 20 0 CGCAACCGTG 0.936052 -239 AAGAGTCCGGACCGATCGCGAACGCATCGC 4 37 0 ACCGATCGCG 0.594998 -222 CCATTATGCCCCCAAATGTGAAGAGTCCGG 4 57 0 CCCAAATGTG 0.669416 -202 TAATGGAGGAAGCGCCAGTGTTGCGGCGAG 4 81 1 AGCGCCAGTG 0.919313 -178 CACAGCACATCCCGCCTGGGAAACCGCTGC 4 148 0 CCCGCCTGGG 0.833807 -111 TGAGCGCCGCACCACCAGCGCCGACGCTAA 4 176 1 ACCACCAGCG 0.931506 -83 TCTTCTGACGCGTAACCGCGTTGTGATCGC 4 223 1 CGTAACCGCG 0.822853 -36 CCACCTCTCCCCCGCAAGCGGGCGGTACCC 5 38 1 CCCGCAAGCG 0.956421 -91 TGGGGGCACCCCCAGCCGCGAAGCGACGAG 5 89 0 CCCAGCCGCG 0.504764 -40 ********** Masking position 8 Map Score: 23.5103 Number of sites scoring better than the average of aligned sites = 38919 Number in coding regions = 36057 Number in noncoding regions = 2862 Number of orfs with sites within 600 bp upstream = 1255 Fraction of orfs with sites within 600 bp upstream = 0.201574 Motif number 4 AGCGCATTGCGCGGCGCCTGCTGGCAGTCGG 1 78 0 GCGGGCCTGC 0.654487 -115 CGCACCTCCGCCCACCGGGACT 2 2 1 GCACTCCGCC 0.966411 -262 GGTTGCAACAGCAAGTCCCGGTGGGCGGAGG 2 15 0 GCAATCCCGG 0.804775 -249 CGCACCGGGTGCGGAACCCAGGTGGATGTCG 2 179 0 GCGGACCCAG 0.901495 -85 GTCGGTCGGCGCAGGTCCACCTCTGGCCTAT 2 220 0 GCAGTCCACC 0.896342 -44 ACCCTCGCGGATCACCCGAACTCGGTC 3 35 0 GCGGTCACCC 0.971574 -17 GGGCGCAGATCCCCCGCGACACGGT 4 5 1 GCAGTCCCCC 0.943881 -254 CGCAACACTGGCGCTTCCTCCATTATGCCCC 4 75 0 GCGCTCCTCC 0.981686 -184 GGCGCTCACAGCACATCCCGCCTGGGAAACC 4 153 0 GCACTCCCGC 0.982074 -106 TGTGAGCGCCGCACCACCAGCGCCGACGCTA 4 174 1 GCACACCAGC 0.921298 -85 CCGCAAGCGGGCGGTACCCCCACCTCATCGC 5 49 1 GCGGACCCCC 0.72779 -80 CCTCATCGCTGCGGCCCCCTCGTCGCTTCGC 5 71 1 GCGGCCCCTC 0.932533 -58 CGATGCAGTGGGGGCACCCCCAGCCGCGAAG 5 96 0 GGGGACCCCC 0.652219 -33 **** ****** Masking position 7 Map Score: 25.0425 Number of sites scoring better than the average of aligned sites = 4113 Number in coding regions = 3814 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 259 Fraction of orfs with sites within 600 bp upstream = 0.0415997 Motif number 5 TCTCTCTGGCGAATCGCTGGCAAAGCGTTA 1 25 1 GAATCGCTGG 0.654396 -168 GCCGCTGTTCGCCTCGATTCTTCTGCTAGT 1 121 0 GCCTCGATTC 0.658729 -72 CTCGGCGGGGACATCGGTGCAGTCGGCCGT 2 68 0 ACATCGGTGC 0.880848 -196 CGTTGCCGACACCTCGGCGGGGACATCGGT 2 80 0 ACCTCGGCGG 0.899234 -184 GGCCACCAACTCGCCGCGCCCTGGATGTGT 2 118 1 TCGCCGCGCC 0.796782 -146 CCCTGGATGTGTGTCGCTCCGGGCGCAGTG 2 136 1 GTGTCGCTCC 0.893942 -128 TTCGACATCCACCTGGGTTCCGCACCCGGT 2 177 1 ACCTGGGTTC 0.3351 -87 CCTCGATCGATCGTCGGTCGGCGCAGGTCC 2 233 0 TCGTCGGTCG 0.972583 -31 TTCTGTTGACTCCTCGATCGATCGTCGGTC 2 244 0 TCCTCGATCG 0.815737 -20 GGATCACCCGAACTCGGTCGGGTTCGCTTG 3 24 0 AACTCGGTCG 0.640764 -28 CATCGCAACCGTGTCGCGGGGGATCTGCGC 4 13 0 GTGTCGCGGG 0.726346 -246 TGTGCTGTGAGCGCCGCACCACCAGCGCCG 4 169 1 GCGCCGCACC 0.697 -90 TCCATCCTTAGCGTCGGCGCTGGTGGTGCG 4 183 0 GCGTCGGCGC 0.586437 -76 TACCCCCACCTCATCGCTGCGGCCCCCTCG 5 63 1 TCATCGCTGC 0.927112 -66 TGCGGCCCCCTCGTCGCTTCGCGGCTGGGG 5 80 1 TCGTCGCTTC 0.936859 -49 CCCCACTGCATCGTCGGCGGCGGCG 5 114 1 TCGTCGGCGG 0.952875 -15 ********** Masking position 6 Map Score: 9.57633 Number of sites scoring better than the average of aligned sites = 29201 Number in coding regions = 27221 Number in noncoding regions = 1980 Number of orfs with sites within 600 bp upstream = 1010 Fraction of orfs with sites within 600 bp upstream = 0.162223 Motif number 6 ********** No masking Map Score: -1.80235e-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 7 ********** No masking Map Score: -1.80235e-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: -1.80235e-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