AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i146_NADH-formate_Dehydrogenase_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 Rv0079 300 hypothetical protein Rv0079 #2 Rv0081 94 hypothetical protein Rv0081 #3 nuoA 300 nuoA #4 nuoH 115 nuoH Motif number 1 TTGGGCCGTTCACGACCCAGCCT 1 3 1 GGGCGTTCAC 0.781221 -298 AGCAGATGCAGCGCATGAGGCTGGGTCGTGA 1 20 0 GCGCTGAGGC 0.957346 -281 CCACACGTGCGCCCAGTAGGCTTTGAGTGTG 1 109 0 GCCCGTAGGC 0.96745 -192 CCTACTGGGCGCACGTGTGGCAACGAGTCGA 1 120 1 GCACTGTGGC 0.865193 -181 ACACGAAATGCCGCCGTTGGGCCGCGGACTA 1 154 1 CCGCGTTGGG 0.95932 -147 CGGAAAATTCGGCTAGTCCGCGGCCCAACGG 1 167 0 GGCTGTCCGC 0.941545 -134 CCGAATTTTCCGGGTGGTGACACAGCCCACA 1 186 1 CGGGGGTGAC 0.801098 -115 GTGACACAGCCCACATTTGGCATGGGACTTT 1 202 1 CCACTTTGGC 0.797011 -99 GGGACTTTCGGCCCTGTCCGCGTCCGTGTCG 1 225 1 GCCCGTCCGC 0.990858 -76 CCTGTCCGCGTCCGTGTCGGCCAGACAAGCT 1 237 1 TCCGGTCGGC 0.790552 -64 CAAGCTTTGGGCATTGGCCACAATCGGGCCA 1 262 1 GCATGGCCAC 0.604736 -39 CCGATTGGCCGCGGGCGGCCCGCACGCAT 2 9 1 CCGCGGCGGC 0.99691 -86 TCATACAATTCGCCGGGACGCGCAATCCCCA 3 67 1 CGCCGGACGC 0.979154 -234 GCTGGGTCCGGCGTCGGTCGCTGCGAAGCAA 3 101 0 GCGTGGTCGC 0.950524 -200 GAAGCAGAACCCGTGGCTGGGTCCGGCGTCG 3 116 0 CCGTGCTGGG 0.699469 -185 CCCACATTCCCGGGGTCAGGCTGGTGCATAC 3 158 0 CGGGTCAGGC 0.68973 -143 CCGGGAATGTGGGGTGGCCGTTGCGCGACTA 3 176 1 GGGGGGCCGT 0.82847 -125 GTGACGAACCGGGGCTTCGGGCCGTCACAGT 3 218 0 GGGGTTCGGG 0.81664 -83 CGGTTCGTCACGGCAGCCCGGTCACCGCCCG 3 238 1 CGGCGCCCGG 0.956768 -63 GCCCGGTCACCGCCCGGCCGCCGCGCTGGCG 3 253 1 CGCCGGCCGC 0.994176 -48 CCCGGCCGCCGCGCTGGCGGCCCCGTACGAC 3 265 1 GCGCGGCGGC 0.997319 -36 GCTCCATGATCCGTCGTACGGGGCCGCCAGC 3 277 0 CCGTGTACGG 0.752384 -24 GCGTCTCCCCTTGCCGCGAGCGCGCGT 4 7 1 CCCCTGCCGC 0.98215 -109 GGGGCACCTCCCGCTTGCGGGGGAACACGCG 4 33 0 CCGCTGCGGG 0.96929 -83 CGGGAGGTGCCCCCAGTACGCCGACACACCG 4 51 1 CCCCGTACGC 0.971088 -65 ACTCCTTGCGCGAGGGTCCGCACTGGTACAT 4 88 0 CGAGGTCCGC 0.944559 -28 CCTCGCGCAAGGAGTGGCGGCC 4 104 1 GGAGGGCGGC 0.967707 -12 **** ****** Masking position 10 Map Score: 44.3462 Number of sites scoring better than the average of aligned sites = 96737 Number in coding regions = 90829 Number in noncoding regions = 5908 Number of orfs with sites within 600 bp upstream = 1576 Fraction of orfs with sites within 600 bp upstream = 0.253132 Motif number 2 GACTCGTTGCCACACGTGCGCCCAGTAGGCT 1 118 0 CACAGTGCGC 0.923771 -183 GTCCGCGGCCCAACGGCGGCATTTCGTGTGG 1 152 0 CAACGCGGCA 0.86293 -149 TGGGCTGTGTCACCACCCGGAAAATTCGGCT 1 184 0 CACCCCCGGA 0.935149 -117 AGTCCCATGCCAAATGTGGGCTGTGTCACCA 1 200 0 CAAAGTGGGC 0.914093 -101 CGGACAGGGCCGAAAGTCCCATGCCAAATGT 1 214 0 CGAAGTCCCA 0.484358 -87 CTGGCCGACACGGACGCGGACAGGGCCGAAA 1 230 0 CGGAGCGGAC 0.869736 -71 GGGCATTGGCCACAATCGGGCCACAATCGAA 1 270 1 CACATCGGGC 0.910324 -31 GGGCCACAATCGAAAGCCGAGCAG 1 287 1 CGAAGCCGAG 0.934167 -14 GCGTGCGGGCCGCCCGCGGCCAATCGG 2 7 0 CGCCGCGGCC 0.982808 -88 GCGGCCCGCACGCATCCGCACTATCTGATAA 2 25 1 CGCACCGCAC 0.914449 -70 GGCAAATGCCGAGATTAACAACA 3 3 1 CAAAGCCGAG 0.904781 -298 AGATTAACAACAAATGCTGCGCTTATCAGGG 3 22 1 CAAAGCTGCG 0.499506 -279 CTGGGGATTGCGCGTCCCGGCGAATTGTATG 3 68 0 CGCGCCCGGC 0.95057 -233 CGCTGCGAAGCAAAACTGGGGATTGCGCGTC 3 83 0 CAAACTGGGG 0.76046 -218 TCGCAGCGACCGACGCCGGACCCAGCCACGG 3 106 1 CGACCCGGAC 0.907438 -195 CACAGGTATGCACCAGCCTGACCCCGGGAAT 3 153 1 CACCGCCTGA 0.647566 -148 ACGGCCACCCCACATTCCCGGGGTCAGGCTG 3 166 0 CACATCCCGG 0.815398 -135 CATAGTCGCGCAACGGCCACCCCACATTCCC 3 178 0 CAACGCCACC 0.572132 -123 TGTGACGGCCCGAAGCCCCGGTTCGTCACGG 3 220 1 CGAACCCCGG 0.950053 -81 CGGTTCGTCACGGCAGCCCGGTCACCGCCCG 3 238 1 CGGCGCCCGG 0.933042 -63 GCAGCCCGGTCACCGCCCGGCCGCCGCGCTG 3 250 1 CACCCCCGGC 0.98178 -51 CGTACGGGGCCGCCAGCGCGGCGGCCGGGCG 3 263 0 CGCCGCGCGG 0.979391 -38 CTTGCGGGGGAACACGCGCGCTCGCGGCAAG 4 20 0 AACAGCGCGC 0.713901 -96 CGTGTTCCCCCGCAAGCGGGAGGTGCCCCCA 4 35 1 CGCAGCGGGA 0.978839 -81 ACTCCTTGCGCGAGGGTCCGCACTGGTACAT 4 88 0 CGAGGTCCGC 0.719981 -28 **** ****** Masking position 1 Map Score: 29.3904 Number of sites scoring better than the average of aligned sites = 69138 Number in coding regions = 64284 Number in noncoding regions = 4854 Number of orfs with sites within 600 bp upstream = 1556 Fraction of orfs with sites within 600 bp upstream = 0.24992 Motif number 3 CTCATGCGCTGCATCTGCTCGCCAACCTCGTA 1 32 1 GCACGCTCGC 0.988976 -269 CTGCGCAGAAGCTGAGGCTCGCTCTGGACATG 1 64 0 GCTAGCTCGC 0.991756 -237 GTGGCCAATGCCCAAAGCTTGTCTGGCCGACA 1 251 0 CCCAGCTTGT 0.84382 -50 TCTGATAAATTCTTCAACTCGTCAACCGATGT 2 48 1 TCTCACTCGT 0.617455 -47 CCGATGTAACGCTGAAGCTCTCAGGAGACGCG 2 73 1 GCTAGCTCTC 0.8976 -22 CACGGGTTCTGCTTCGACTCGCACAGGTATGC 3 132 1 GCTCACTCGC 0.986699 -169 ACGGCCCGAAGCCCCGGTTCGTCACGGCAGCC 3 224 1 GCCCGTTCGT 0.948781 -77 GCGTCTCCCCTTGCCGCGAGCGCG 4 3 1 GTCCCCTTGC 0.861146 -113 ACTGGGGGCACCTCCCGCTTGCGGGGGAACAC 4 36 0 CCTCGCTTGC 0.979416 -80 GCGGGAGGTGCCCCCAGTACGCCGACACACCG 4 50 1 CCCCGTACGC 0.79106 -66 ATGTACCAGTGCGGACCCTCGCGCAAGGAGTG 4 88 1 GCGACCTCGC 0.940603 -28 GGCCGCCACTCCTTGCGCGAGGGTCC 4 100 0 GCCCCCTTGC 0.988381 -16 *** * ****** Masking position 9 Map Score: 12.0497 Number of sites scoring better than the average of aligned sites = 8759 Number in coding regions = 7921 Number in noncoding regions = 838 Number of orfs with sites within 600 bp upstream = 551 Fraction of orfs with sites within 600 bp upstream = 0.0884998 Motif number 4 TTGGCGAGCAGATGCAGCGCATGAGGCTGG 1 27 0 GATGCAGCGC 0.97416 -274 TCGCTGCGCAGAAGCTGAGGCTCGCTCTGG 1 69 0 GAAGCTGAGG 0.958087 -232 GGCAGTTTCCGTCGCTGCGCAGAAGCTGAG 1 80 0 GTCGCTGCGC 0.974456 -221 ATCCACACGAAATGCCGCCGTTGGGCCGCG 1 150 1 AATGCCGCCG 0.831718 -151 GCCACAATCGAAAGCCGAGCAG 1 289 1 AAAGCCGAGC 0.96737 -12 CAACCGATGTAACGCTGAAGCTCTCAGGAG 2 70 1 AACGCTGAAG 0.797559 -25 GGCAAATGCCGAGATTAACAACAA 3 5 1 AATGCCGAGA 0.853756 -296 ATTAACAACAAATGCTGCGCTTATCAGGGG 3 24 1 AATGCTGCGC 0.97178 -277 TCCGGCGTCGGTCGCTGCGAAGCAAAACTG 3 96 0 GTCGCTGCGA 0.882516 -205 CGCAGCGACCGACGCCGGACCCAGCCACGG 3 107 1 GACGCCGGAC 0.922067 -194 TGTGCGAGTCGAAGCAGAACCCGTGGCTGG 3 127 0 GAAGCAGAAC 0.790224 -174 GTGACGGCCCGAAGCCCCGGTTCGTCACGG 3 221 1 GAAGCCCCGG 0.90363 -80 TCACCGCCCGGCCGCCGCGCTGGCGGCCCC 3 259 1 GCCGCCGCGC 0.983867 -42 ********** Masking position 5 Map Score: 12.9456 Number of sites scoring better than the average of aligned sites = 18326 Number in coding regions = 17057 Number in noncoding regions = 1269 Number of orfs with sites within 600 bp upstream = 765 Fraction of orfs with sites within 600 bp upstream = 0.122872 Motif number 5 TCGTTGCCACACGTGCGCCCAGTAGGCTTT 1 116 0 ACGTGCGCCC 0.893398 -185 AATTCGGCTAGTCCGCGGCCCAACGGCGGC 1 163 0 GTCCGCGGCC 0.678573 -138 CGTGCGGGCCGCCCGCGGCCAATCGG 2 7 0 GCCCGCGGCC 0.603175 -88 TAGTGCGGATGCGTGCGGGCCGCCCGCGGC 2 18 0 GCGTGCGGGC 0.736207 -77 TTCATACAATTCGCCGGGACGCGCAATCCC 3 66 1 TCGCCGGGAC 0.889427 -235 GCAGCGACCGACGCCGGACCCAGCCACGGG 3 108 1 ACGCCGGACC 0.891027 -193 CACCCCACATTCCCGGGGTCAGGCTGGTGC 3 162 0 TCCCGGGGTC 0.882473 -139 ACGGCCCGAAGCCCCGGTTCGTCACGGCAG 3 224 1 GCCCCGGTTC 0.731279 -77 TTCGTCACGGCAGCCCGGTCACCGCCCGGC 3 241 1 CAGCCCGGTC 0.893593 -60 AGCCCGGTCACCGCCCGGCCGCCGCGCTGG 3 252 1 CCGCCCGGCC 0.992158 -49 CGCCCGGCCGCCGCGCTGGCGGCCCCGTAC 3 263 1 CCGCGCTGGC 0.907951 -38 GCGGGGGAACACGCGCGCTCGCGGCAAGGG 4 18 0 ACGCGCGCTC 0.913136 -98 ********** Masking position 10 Map Score: 12.6411 Number of sites scoring better than the average of aligned sites = 15294 Number in coding regions = 14110 Number in noncoding regions = 1184 Number of orfs with sites within 600 bp upstream = 742 Fraction of orfs with sites within 600 bp upstream = 0.119178 Motif number 6 GAGCAGATGCAGCGCATGAGGCTGGGTCGT 1 22 0 AGCGCATGAG 0.923374 -279 TTTCCGTCGCTGCGCAGAAGCTGAGGCTCG 1 75 0 TGCGCAGAAG 0.901909 -226 AAGCCTACTGGGCGCACGTGTGGCAACGAG 1 117 1 GGCGCACGTG 0.974959 -184 CCGATTGGCCGCGGGCGGCCCGCACGC 2 8 1 GCCGCGGGCG 0.944132 -87 TTTATCAGATAGTGCGGATGCGTGCGGGCC 2 27 0 AGTGCGGATG 0.87535 -68 CGGGGCCGCCAGCGCGGCGGCCGGGCGGTG 3 260 0 AGCGCGGCGG 0.982765 -41 CCTTGCCGCGAGCGCGCGTGTTCCCCCGCA 4 19 1 AGCGCGCGTG 0.988697 -97 CGCCACTCCTTGCGCGAGGGTCCGCACTGG 4 93 0 TGCGCGAGGG 0.961912 -23 ********** Masking position 5 Map Score: 3.99508 Number of sites scoring better than the average of aligned sites = 6019 Number in coding regions = 5580 Number in noncoding regions = 439 Number of orfs with sites within 600 bp upstream = 370 Fraction of orfs with sites within 600 bp upstream = 0.0594282 Motif number 7 CGAGGTTGGCGAGCAGATGCAGCGCATGAG 1 32 0 GAGCAGATGC 0.74139 -269 CCGAATTTTCCGGGTGGTGACACAGCCCAC 1 186 1 CGGGTGGTGA 0.932017 -115 CGATTGGCCGCGGGCGGCCCGCACGCATCC 2 12 1 CGGGCGGCCC 0.977535 -83 CTGAAGCTCTCAGGAGACGCG 2 84 1 CAGGAGACGC 0.985083 -11 TACAATTCGCCGGGACGCGCAATCCCCAGT 3 70 1 CGGGACGCGC 0.995042 -231 GCGCGGCGGCCGGGCGGTGACCGGGCTGCC 3 249 0 CGGGCGGTGA 0.973954 -52 CTCGCGGCAAGGGGAGACGC 4 1 0 GGGGAGACGC 0.994228 -115 CCGCTTGCGGGGGAACACGCGCGCTCGCGG 4 24 0 GGGAACACGC 0.854616 -92 CCCCCGCAAGCGGGAGGTGCCCCCAGTACG 4 41 1 CGGGAGGTGC 0.997027 -75 ********** Masking position 3 Map Score: 12.3754 Number of sites scoring better than the average of aligned sites = 5777 Number in coding regions = 5309 Number in noncoding regions = 468 Number of orfs with sites within 600 bp upstream = 395 Fraction of orfs with sites within 600 bp upstream = 0.0634436 Motif number 8 ********** No masking Map Score: 5.63761e-13 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: 5.63761e-13 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: 5.63761e-13 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