AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_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 Rv3108 98 hypothetical protein Rv3108 #2 moaA 148 moaA #3 moaB 50 moaB #4 Rv3113 122 hypothetical protein Rv3113 #5 Rv3115 161 hypothetical protein Rv3115 #6 moeB 77 moeB #7 cysA3 28 cysA3 Motif number 1 GTCAGCGTTTGAGGACGATCATGGCTCCGCCGACGACCA 1 20 1 GGGCGCACCG 0.988385 -79 TGGCTCCGCCGACGACCACCAGCACCAGGGCCGCGACGA 1 41 1 GCGCCCACAG 0.879094 -58 GTGGTGGCTAGCCGGTGCTGGATGGGCTATCGTCGCGGC 1 70 0 GCGTGGGGCA 0.958006 -29 GGCGCATCGTGGCGCAGCGCATGAGCCTGCGTTTATGGC 2 17 0 GCGAGCAGCG 0.98182 -132 CTCCACTTTGGACGCAGTCGGTTAGAGCGCCTCAAGAGA 2 99 0 GCGAGGGGGG 0.986887 -50 CAACTGTGGAGTCGTTGATCAATCGACTGTTCGTTCGGC 3 11 0 GCGTGCAGCG 0.996027 -40 ACAAGGGGATGACCGGCCGTGAATGCGCTCTCA 4 5 1 GGGTGCGGGA 0.886898 -118 GTTGCCGAACAGCGGCGACGATGAGAGCGCATTCACGGC 4 26 0 ACGCGGAGGG 0.939262 -97 GTTCGGCAACGTGGGAGTTCCAGTGCCGGCGTGCAGAAC 4 55 1 GGGAGCCGCG 0.916927 -68 ACCGAAATTCGCCGCACCCGAATAGTCGGGTCGCATAG 4 95 1 GCGACGAGCG 0.994635 -28 CTGGGTCAGTGAGGTAGTCGGCAAGCCGAG 5 2 0 GGGAGGGGCA 0.960518 -160 GCCTTACCTGCCCGTACACCACACCCCTGGACGTAACTC 5 46 0 CCGACCACCG 0.951068 -116 CGGTGGGCGTGTCGTAGCCCAGTAGTGGGCGGTCATCGC 5 85 1 GCGAGCAGGG 0.994016 -77 GGTCGTTTCGAAGGATCACGCGATGACCGCCCACTACTG 5 104 0 AGGTCGCGCG 0.757418 -58 GATCCTTCGAAACGACCAGCAAAAGTCAATCGAAGGAAA 5 126 1 ACGCCCAGCA 0.920539 -36 GGTTCCTCGCGTGATCCTTCGGGTGGCAGT 6 2 0 GGACCCGGCG 0.886728 -76 GGAACCTTCACTCGTACACCACGTCCCTGGCCTTGGCCA 6 35 1 CCGACCACCG 0.888421 -43 * ** ** ** * * * Masking position 4 Map Score: 24.7033 Number of sites scoring better than the average of aligned sites = 41130 Number in coding regions = 38795 Number in noncoding regions = 2335 Number of orfs with sites within 600 bp upstream = 1066 Fraction of orfs with sites within 600 bp upstream = 0.171217 Motif number 2 GCTGATGGTGTCAGCGTTTGAGGACG 1 4 1 GATGTGCGCG 0.925436 -95 CGACCACCAGCACCAGGGCCGCGACGATAGCCC 1 53 1 CACAGGCGCG 0.940596 -46 GTGGCGCAGCGCATGAGCCTGCGTTTATGGCGC 2 15 0 GCAGAGCGCG 0.896525 -134 TTTGGACGCAGTCGGTTAGAGCGCCTCAAGAGA 2 99 0 GTCGTTGGCG 0.963832 -50 TTGATCAATCGACTGTTCGTTCGGC 3 3 0 GACGTTGTCG 0.788532 -48 GAACAGCGGCGACGATGAGAGCGCATTCACGGC 4 26 0 GACATGGGCG 0.990808 -97 ACGTGGGAGTTCCAGTGCCGGCGTGCAGAACGA 4 63 1 TCCGTGCGCG 0.979614 -60 TATGCGACCCGACTATTCGGGTGCGGCGAATTT 4 99 0 GACATTGGTG 0.945288 -24 GTAACTCTCCTCCTGGGTCAGTGAGGTAGTCGG 5 20 0 TCCGGGCGTG 0.967718 -142 GGAGAGTTACGTCCAGGGGTGTGGTGTACGGGC 5 43 1 GTCAGGGGTG 0.967023 -119 GGCAGGTAAGGCCGGTGGGCGTGTCGTAGCCCA 5 73 1 GCCGTGGGTG 0.99425 -89 GCGTGTCGTAGCCCAGTAGTGGGCGGTCATCGC 5 91 1 GCCAGTGGGG 0.972591 -71 TCTCCTCCTGGCCAAGGCCAGGGACGTGGTGTA 6 49 0 GCCAGGCGGG 0.989996 -29 GAATCCTTTCGCATAGTTCGGTG 7 1 0 GCAAGTCGTG 0.869665 -28 *** *** * *** Masking position 13 Map Score: 17.4224 Number of sites scoring better than the average of aligned sites = 23070 Number in coding regions = 21719 Number in noncoding regions = 1351 Number of orfs with sites within 600 bp upstream = 857 Fraction of orfs with sites within 600 bp upstream = 0.137649 Motif number 3 GCTATCGTCGCGGCCCTGGTGCTGGTGGTCG 1 53 0 CGGCCCTGGG 0.974789 -46 CCGCGACGATAGCCCATCCAGCACCGGCTAG 1 71 1 AGCCCATCCG 0.899762 -28 CATAAACGCAGGCTCATGCGCTGCGCCACGA 2 19 1 GGCTCATGCC 0.935027 -130 GAAATGCATCGGCGCATCGTGGCGCAGCGCA 2 35 0 GGCGCATCGG 0.915359 -114 ATCATCTTTTCGATCCTCCACTTTGGACGCA 2 122 0 CGATCCTCCC 0.946204 -27 CATTCACGGCCGGTCATCCCCTTGT 4 5 0 CGGTCATCCC 0.97755 -118 CGTGAATGCGCTCTCATCGTCGCCGCTGTTC 4 28 1 CTCTCATCGC 0.967158 -95 CTGGACGTAACTCTCCTCCTGGGTCAGTGAG 5 28 0 CTCTCCTCCG 0.972766 -134 CCGTACACCACACCCCTGGACGTAACTCTCC 5 43 0 CACCCCTGGC 0.886794 -119 GGCTACGACACGCCCACCGGCCTTACCTGCC 5 73 0 CGCCCACCGC 0.956497 -89 CAGTAGTGGGCGGTCATCGCGTGATCCTTCG 5 104 1 CGGTCATCGG 0.982933 -58 TACGAGTGAAGGTTCCTCGCGTGATCCTTCG 6 20 0 GGTTCCTCGG 0.927779 -58 TCGTACACCACGTCCCTGGCCTTGGCCAGGA 6 46 1 CGTCCCTGGC 0.945032 -32 GATTGCTCTCCTCCTGGCCAAGGCCA 6 62 0 CTCTCCTCCG 0.972766 -16 ********* * Masking position 5 Map Score: 20.0383 Number of sites scoring better than the average of aligned sites = 7916 Number in coding regions = 7231 Number in noncoding regions = 685 Number of orfs with sites within 600 bp upstream = 540 Fraction of orfs with sites within 600 bp upstream = 0.0867331 Motif number 4 GTGGTGGCTAGCCGGTGCTGGA 1 87 0 GGTGGCTAGC 0.9617 -12 TTTGGACGCAGTCGGTTAGAGCGCCTCAAG 2 102 0 GTCGGTTAGA 0.931876 -47 CACCCGAATAGTCGGGTCGCATAG 4 109 1 GTCGGGTCGC 0.98862 -14 CAGTGAGGTAGTCGGCAAGCCGAG 5 5 0 GTCGGCAAGC 0.988452 -157 CCCAGTAGTGGGCGGTCATCGCGTGATCCT 5 102 1 GGCGGTCATC 0.939713 -60 CGCGTGATCCTTCGGGTGGCAGT 6 4 0 TTCGGGTGGC 0.918492 -74 GGCGGGAATCCTTTCGCATA 7 19 0 GGCGGGAATC 0.976713 -10 ********** Masking position 5 Map Score: 4.35177 Number of sites scoring better than the average of aligned sites = 6690 Number in coding regions = 6231 Number in noncoding regions = 459 Number of orfs with sites within 600 bp upstream = 398 Fraction of orfs with sites within 600 bp upstream = 0.0639255 Motif number 5 CGTCGCGGCCCTGGTGCTGGTGGTCGTCGG 1 49 0 CTGGTGCTGG 0.950243 -50 TGGTGGCTAGCCGGTGCTGGATGGGCTATC 1 78 0 CCGGTGCTGG 0.615347 -21 AAGGGGATGACCGGCCGTGAATGCGCTCTC 4 13 1 CCGGCCGTGA 0.974836 -110 GTTCTGCACGCCGGCACTGGAACTCCCACG 4 64 0 CCGGCACTGG 0.643751 -59 GACTACCTCACTGACCCAGGAGGAGAGTTA 5 22 1 CTGACCCAGG 0.881923 -140 GTGTCGTAGCCCAGTAGTGGGCGGTCATCG 5 93 1 CCAGTAGTGG 0.678299 -69 CACCACGTCCCTGGCCTTGGCCAGGAGGAG 6 51 1 CTGGCCTTGG 0.981171 -27 ********** Masking position 9 Map Score: 8.23594 Number of sites scoring better than the average of aligned sites = 5359 Number in coding regions = 5060 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 6 AACAATCGTTACCGAAATGCATCGGCGCAT 2 49 0 ACCGAAATGC 0.978892 -100 GCCGAACGAACAGTCGATTGATCA 3 5 1 AACGAACAGT 0.959311 -46 CTCCCACGTTGCCGAACAGCGGCGACGATG 4 42 0 GCCGAACAGC 0.984675 -81 GTGCAGAACGACCGAAATTCGCCGCACCCG 4 85 1 ACCGAAATTC 0.877681 -38 ATTCGCCGCACCCGAATAGTCGGGTCGCAT 4 101 1 CCCGAATAGT 0.858427 -22 GATCCTTCGAAACGACCAGCAAAAGTCAAT 5 126 1 AACGACCAGC 0.937493 -36 CACCGAACTATGCGAAAGGAT 7 2 1 ACCGAACTAT 0.911349 -27 ********** Masking position 5 Map Score: 3.08415 Number of sites scoring better than the average of aligned sites = 2986 Number in coding regions = 2821 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 7 ********** No masking Map Score: 1.69352e-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: 1.69352e-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: 1.69352e-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