AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_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 moaA 148 moaA #2 moaB 50 moaB #3 Rv3115 161 hypothetical protein Rv3115 #4 moeB 77 moeB #5 cysA3 28 cysA3 Motif number 1 CGTGGCGCAGCGCATGAGCCTGCGTTTATGGCGC 1 15 0 CGCACCTGCG 0.565985 -134 CGAAATGCATCGGCGCATCGTGGCGCAGCGCATG 1 33 0 CGGCCGTGGC 0.958587 -116 GTTGATCAATCGACTGTTCGTTCGGC 2 3 0 CGACCGTTCG 0.964441 -48 CCTGCCCGTACACCACACCCCTGGACGTAACTCT 3 45 0 CACCCCCTGG 0.978052 -117 ACACGCCCACCGGCCTTACCTGCCCGTACACCAC 3 63 0 CGGCCCTGCC 0.993241 -99 ACGCGATGACCGCCCACTACTGGGCTACGACACG 3 92 0 CGCCACTGGG 0.981859 -70 GGGCGGTCATCGCGTGATCCTTCGAAACGACCAG 3 111 1 CGCGCCTTCG 0.879592 -51 TGCGTCATTTCCTTCGATTGACTTTT 3 146 0 CGTCCCTTCG 0.993872 -16 GAAGGTTCCTCGCGTGATCCTTCGGGTGGCAGT 4 10 0 CGCGCCTTCG 0.879592 -68 TTCACTCGTACACCACGTCCCTGGCCTTGGCCAG 4 41 1 CACCCCCTGG 0.978052 -37 GGCGGGAATCCTTTCGCATAGTTCGG 5 13 0 CGGGCTTTCG 0.966119 -16 **** ****** Masking position 1 Map Score: 19.4086 Number of sites scoring better than the average of aligned sites = 14347 Number in coding regions = 13749 Number in noncoding regions = 598 Number of orfs with sites within 600 bp upstream = 433 Fraction of orfs with sites within 600 bp upstream = 0.0695471 Motif number 2 TCTTTTCGATCCTCCACTTTGGACGCAGTCGG 1 117 0 CCTCCTTTGG 0.993993 -32 GGTTCCTTCCTCAACTGTGGAGTCGTTGAT 2 31 0 CCTCCTGTGG 0.809855 -20 TGGACGTAACTCTCCTCCTGGGTCAGTGAGGT 3 26 0 TCTCCCTGGG 0.992261 -136 TGCCCGTACACCACACCCCTGGACGTAACTCT 3 45 0 CCACCCCTGG 0.907635 -117 CGATGACCGCCCACTACTGGGCTACGACACGC 3 91 0 CCACCTGGGC 0.986292 -71 CACTCGTACACCACGTCCCTGGCCTTGGCCAG 4 43 1 CCACCCCTGG 0.842108 -35 GATTGCTCTCCTCCTGGCCAAGGCCAGG 4 60 0 TCTCCCTGGC 0.981857 -18 **** ****** Masking position 7 Map Score: 12.6874 Number of sites scoring better than the average of aligned sites = 1479 Number in coding regions = 1388 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 GTGGCGCAGCGCATGAGCCTGCGTTTATGGCGC 1 15 0 GAGAGCTGCG 0.796381 -134 AGCGCCTCAAGAGAGTTTCGTACAAGGGTTAAC 1 80 0 GGGTTCGTAC 0.970277 -69 TTTGGACGCAGTCGGTTAGAGCGCCTCAAGAGA 1 99 0 GCGTTGAGCG 0.842587 -50 TTGATCAATCGACTGTTCGTTCGGC 2 3 0 GCGTTGTTCG 0.983383 -48 CTCCTCCTGGGTCAGTGAGGTAGTCGGCAAGCC 3 14 0 GCGTGGGTAG 0.948513 -148 GACCCAGGAGGAGAGTTACGTCCAGGGGTGTGG 3 34 1 GGGTTCGTCC 0.989372 -128 TTACGTCCAGGGGTGTGGTGTACGGGCAGGTAA 3 49 1 GGGTGTGTAC 0.756107 -113 CACGCCCACCGGCCTTACCTGCCCGTACACCAC 3 63 0 GCTTACTGCC 0.578554 -99 TAAGGCCGGTGGGCGTGTCGTAGCCCAGTAGTG 3 79 1 GGGTGCGTAG 0.980245 -83 GGCGGTCATCGCGTGATCCTTCGAAACGACCAG 3 112 1 GGGATCTTCG 0.9867 -50 TGCGTCATTTCCTTCGATTGACTTTT 3 146 0 GCTTTCTTCG 0.936039 -16 AAGGTTCCTCGCGTGATCCTTCGGGTGGCAGT 4 10 0 GGGATCTTCG 0.9867 -68 CGTGGTGTACGAGTGAAGGTTCCTCGCGTGATC 4 25 0 GGGAAGTTCC 0.883727 -53 * * *** ***** Masking position 1 Map Score: 12.8857 Number of sites scoring better than the average of aligned sites = 13558 Number in coding regions = 12625 Number in noncoding regions = 933 Number of orfs with sites within 600 bp upstream = 654 Fraction of orfs with sites within 600 bp upstream = 0.105043 Motif number 4 GCGCCATAAACGCAGGCTCATGCGCTGCGC 1 15 1 CGCAGGCTCA 0.973162 -134 GCCGAACGAACAGTCGATTGAT 2 3 1 CGAACGAACA 0.980546 -48 AACGAACAGTCGATTGATCAACGACTCCAC 2 15 1 CGATTGATCA 0.909196 -36 CCACAGTTGAGGAAGGAACC 2 41 1 GGAAGGAACC 0.972425 -10 CTGGTCGTTTCGAAGGATCACGCGATGACC 3 115 0 CGAAGGATCA 0.997196 -47 AAAAGTCAATCGAAGGAAATGACGCA 3 146 1 CGAAGGAAAT 0.88401 -16 ACTGCCACCCGAAGGATCACGCGAGGAAC 4 10 1 CGAAGGATCA 0.997196 -68 GGTGTACGAGTGAAGGTTCCTCGCGTGATC 4 25 0 TGAAGGTTCC 0.829241 -53 ********** Masking position 6 Map Score: 10.4237 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 440 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 ATCGGCGCATCGTGGCGCAGCGCATGAGCC 1 29 0 CGTGGCGCAG 0.9922 -120 GCCTCAAGAGAGTTTCGTACAAGGGTTAAC 1 80 0 AGTTTCGTAC 0.856395 -69 CTCCTGGGTCAGTGAGGTAGTCGGCAAGCC 3 14 0 AGTGAGGTAG 0.945383 -148 GGCCGGTGGGCGTGTCGTAGCCCAGTAGTG 3 82 1 CGTGTCGTAG 0.994637 -80 TTTTGCTGGTCGTTTCGAAGGATCACGCGA 3 120 0 CGTTTCGAAG 0.957867 -42 CGTGATCCTTCGGGTGGCAGT 4 2 0 CGGGTGGCAG 0.972987 -76 CGAAGGATCACGCGAGGAACCTTCACTCGT 4 20 1 CGCGAGGAAC 0.884672 -58 AGGCCAGGGACGTGGTGTACGAGTGAAGGT 4 38 0 CGTGGTGTAC 0.947669 -40 ********** Masking position 9 Map Score: 7.03331 Number of sites scoring better than the average of aligned sites = 2513 Number in coding regions = 2255 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 6 GGCGCATCGTGGCGCAGCGCATGAGCCTGC 1 26 0 GGCGCAGCGC 0.961889 -123 GAAATGCATCGGCGCATCGTGGCGCAGCGC 1 36 0 GGCGCATCGT 0.993516 -113 GCGCCTCAAGAGAGTTTCGTACAAGGGTTA 1 82 0 AGAGTTTCGT 0.960649 -67 CGTCCAAAGTGGAGGATCGAAAAGATGATA 1 124 1 GGAGGATCGA 0.955765 -25 ACCCAGGAGGAGAGTTACGTCCAGGGGTGT 3 35 1 AGAGTTACGT 0.857602 -127 AAGGCCGGTGGGCGTGTCGTAGCCCAGTAG 3 80 1 GGCGTGTCGT 0.99086 -82 ACTTTTGCTGGTCGTTTCGAAGGATCACGC 3 122 0 GTCGTTTCGA 0.927793 -40 ********** Masking position 4 Map Score: 4.58652 Number of sites scoring better than the average of aligned sites = 3393 Number in coding regions = 3021 Number in noncoding regions = 372 Number of orfs with sites within 600 bp upstream = 312 Fraction of orfs with sites within 600 bp upstream = 0.0501124 Motif number 7 ********** No masking Map Score: -3.81261e-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 8 ********** No masking Map Score: -3.81261e-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: -3.81261e-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