AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i063_Glycine_Catabolism_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 pgsA2 196 pgsA2 #2 Rv1824 28 hypothetical protein Rv1824 #3 gcvH 37 gcvH #4 Rv1830 300 hypothetical protein Rv1830 #5 Rv1831 52 hypothetical protein Rv1831 #6 gcvB 48 gcvB Motif number 1 CTCGGCGCTTACGCTGGGCAGC 1 3 0 ACGCTGGGCA 0.915846 -194 CCCAGCGTAAGCGCCGAGCGTAACGCCACT 1 15 1 GCGCCGAGCG 0.99694 -182 GGCACCCCTAGCCGCGAGCGTAACGCCACT 1 69 0 GCCGCGAGCG 0.957652 -128 GCGCGCCGAAACGGCGGGCTGTGGGGGCAC 1 94 0 ACGGCGGGCT 0.997702 -103 GCCCGCCGTTTCGGCGCGCATCGTCGCCAG 1 105 1 TCGGCGCGCA 0.997504 -92 GCGCGCATCGTCGCCAGGCTAGATCCGATT 1 118 1 TCGCCAGGCT 0.979966 -79 GCGGGCTGAGGAGCCGGGCAATCGGATCTA 1 137 0 GAGCCGGGCA 0.977042 -60 GCGCGCCGAAACGGCGGGCTGAGGAGCCGG 1 150 0 ACGGCGGGCT 0.997702 -47 GCCCGCCGTTTCGGCGCGCATCGTCGCCAG 1 161 1 TCGGCGCGCA 0.997504 -36 GCGCGCATCGTCGCCAGGCTAAGGTCACGG 1 174 1 TCGCCAGGCT 0.979966 -23 GCGCGCATCGTCGCCGCGCTCGGCCTT 4 8 0 TCGCCGCGCT 0.99712 -293 GCCCGCCGTCCCGGCGCGCATCGTCGCCGC 4 21 0 CCGGCGCGCA 0.994919 -280 GCGCGCCGGGACGGCGGGCTGAGGAGGCGC 4 32 1 ACGGCGGGCT 0.997702 -269 GCGGGCTGAGGAGGCGCGCGATAAGGCCGA 4 45 1 GAGGCGCGCG 0.983516 -256 GCGCGCATCGTCGCCGCGCTCGGCCTTATC 4 64 0 TCGCCGCGCT 0.99712 -237 GCTCGCCGTCGCGGCGCGCATCGTCGCCGC 4 77 0 GCGGCGCGCA 0.99864 -224 GCGCGCCGCGACGGCGAGCATCCATTATTT 4 88 1 ACGGCGAGCA 0.993933 -213 CCATTATTTGCCGGCCAGCAACGTCACGGC 4 109 1 CCGGCCAGCA 0.948135 -192 AATTGTCGACACGCCTAGCGGTTAGTGCCT 4 159 1 ACGCCTAGCG 0.884113 -142 AGTATCGCGGTCGCCGGGCGCATTAGGCAC 4 183 0 TCGCCGGGCG 0.997638 -118 CGGGAGCATCGCGCCCATCGAACAGCGTAT 4 236 1 GCGCCCATCG 0.810921 -65 AGAATCGCACGCGGCAGGCTCCTCGG 5 37 1 GCGGCAGGCT 0.991434 -16 CAGAGGACTAGCGGCCCTCTCCCTCTGTCT 6 11 0 GCGGCCCTCT 0.915521 -38 ********** Masking position 9 Map Score: 78.9149 Number of sites scoring better than the average of aligned sites = 11241 Number in coding regions = 10335 Number in noncoding regions = 906 Number of orfs with sites within 600 bp upstream = 592 Fraction of orfs with sites within 600 bp upstream = 0.0950851 Motif number 2 CCGAGCGTAACGCCACTGCGAAATTTCGGG 1 28 1 CGCCACTGCG 0.638857 -169 GCGAGCGTAACGCCACTGCGATTTTCTGCC 1 56 0 CGCCACTGCG 0.638857 -141 TGGGGGCACCCCTAGCCGCGAGCGTAACGC 1 73 0 CCTAGCCGCG 0.912765 -124 CGATGCGCGCCGAAACGGCGGGCTGTGGGG 1 98 0 CGAAACGGCG 0.959025 -99 CGGCGCGCATCGTCGCCAGGCTAGATCCGA 1 116 1 CGTCGCCAGG 0.834601 -81 CGATGCGCGCCGAAACGGCGGGCTGAGGAG 1 154 0 CGAAACGGCG 0.959025 -43 CGGCGCGCATCGTCGCCAGGCTAAGGTCAC 1 172 1 CGTCGCCAGG 0.834601 -25 GCCAGGCTAAGGTCACGGCTC 1 186 1 GGTCACGGCT 0.967494 -11 CGGCGCGCATCGTCGCCGCGCTCGGCCTT 4 10 0 CGTCGCCGCG 0.70476 -291 CTCAGCCCGCCGTCCCGGCGCGCATCGTCG 4 25 0 CGTCCCGGCG 0.737239 -276 CGGCGCGCATCGTCGCCGCGCTCGGCCTTA 4 66 0 CGTCGCCGCG 0.70476 -235 GGATGCTCGCCGTCGCGGCGCGCATCGTCG 4 81 0 CGTCGCGGCG 0.5052 -220 CGGCCAGCAACGTCACGGCTGCGTCTCATC 4 120 1 CGTCACGGCT 0.980424 -181 AAAGTATCGCGGTCGCCGGGCGCATTAGGC 4 185 0 GGTCGCCGGG 0.995212 -116 CGACCTGATAGTTAACCGGGAGCATCGCGC 4 220 1 GTTAACCGGG 0.763567 -81 TTCTGTGTCTGTTCGCGGGGGAACTCTCGG 5 11 0 GTTCGCGGGG 0.963682 -42 ********** Masking position 6 Map Score: 47.4612 Number of sites scoring better than the average of aligned sites = 12426 Number in coding regions = 11531 Number in noncoding regions = 895 Number of orfs with sites within 600 bp upstream = 612 Fraction of orfs with sites within 600 bp upstream = 0.0982975 Motif number 3 CACTGCGAAATTTCGGGCAGAAAATCGCAG 1 41 1 TTTCGGGCAG 0.776944 -156 AACGGCGGGCTGTGGGGGCACCCCTAGCCG 1 85 0 TGTGGGGGCA 0.896091 -112 CAGCCCGCCGTTTCGGCGCGCATCGTCGCC 1 103 1 TTTCGGCGCG 0.990081 -94 AACGGCGGGCTGAGGAGCCGGGCAATCGGA 1 141 0 TGAGGAGCCG 0.72854 -56 CAGCCCGCCGTTTCGGCGCGCATCGTCGCC 1 159 1 TTTCGGCGCG 0.990081 -38 TCGGCTCGGAGTTGGGCTAGT 3 2 0 GTTGGGCTAG 0.555063 -36 ATCCTATTCTGGTCGGCTCGGAGTTGGGCT 3 14 0 GGTCGGCTCG 0.98107 -24 CGGCGCGCATCGTCGCCGCGCTCGGCCTT 4 10 0 CGTCGCCGCG 0.871986 -291 ATGCGCGCCGGGACGGCGGGCTGAGGAGGC 4 30 1 GGACGGCGGG 0.980583 -271 GACGGCGGGCTGAGGAGGCGCGCGATAAGG 4 41 1 TGAGGAGGCG 0.876584 -260 CGGCGCGCATCGTCGCCGCGCTCGGCCTTA 4 66 0 CGTCGCCGCG 0.871986 -235 ATGCGCGCCGCGACGGCGAGCATCCATTAT 4 86 1 CGACGGCGAG 0.962025 -215 ATCCATTATTTGCCGGCCAGCAACGTCACG 4 107 1 TGCCGGCCAG 0.874501 -194 TGGCTGCAATTGTCGACACGCCTAGCGGTT 4 152 1 TGTCGACACG 0.855812 -149 AAAGTATCGCGGTCGCCGGGCGCATTAGGC 4 185 0 GGTCGCCGGG 0.968369 -116 TACGCTGTTCGATGGGCGCGATGCTCCCGG 4 235 0 GATGGGCGCG 0.92698 -66 CAGCCATTACTGAGGGCCCGAGTGTTAGAG 4 269 0 TGAGGGCCCG 0.976102 -32 CAGTAATGGCTGTCGGGGGAGCCA 4 287 1 TGTCGGGGGA 0.830649 -14 ********** Masking position 5 Map Score: 31.2988 Number of sites scoring better than the average of aligned sites = 26543 Number in coding regions = 24578 Number in noncoding regions = 1965 Number of orfs with sites within 600 bp upstream = 1087 Fraction of orfs with sites within 600 bp upstream = 0.17459 Motif number 4 GCTGCCCAGCGTAAGCGCCGAGCGTAACGC 1 7 1 CAGCGACGCG 0.523159 -190 CCCTAGCCGCGAGCGTAACGCCACTGCGATTTTC 1 60 0 GAGCGAGCCC 0.91219 -137 GGCGGGCTGTGGGGGCACCCCTAGCCGCGAGCGT 1 78 0 GGGGGACCTG 0.865998 -119 CCGAAACGGCGGGCTGAGGAGCCGGGCAATCGGA 1 141 0 GGGCTAAGCG 0.810115 -56 TGAGAGAAGTCCTGGTGAATAGGAA 2 2 1 GAGAGACCTG 0.977519 -27 GGACGGCGGGCTGAGGAGGCGCGCGATAAGGCCG 4 40 1 CTGAGACGCC 0.91715 -261 ATTGCAGCCAGAGATGAGACGCAGCCGTGACGTT 4 128 0 GAGATACGCG 0.982548 -173 CCGAGTGTTAGAGAGCATACGCTGTTCGATGGGC 4 248 0 GAGAGACGCG 0.605018 -53 CCGAGAGTTCCCCCGCGAACAGACAC 5 3 1 GAGAGTCCCC 0.938115 -50 CCTGACAAAGCAGAGGACTAGCGGCCCTCTCCCT 6 17 0 CAGAGAAGCG 0.969153 -32 ***** * *** * Masking position 3 Map Score: 7.46194 Number of sites scoring better than the average of aligned sites = 3662 Number in coding regions = 3308 Number in noncoding regions = 354 Number of orfs with sites within 600 bp upstream = 299 Fraction of orfs with sites within 600 bp upstream = 0.0480244 Motif number 5 CGTAAGCGCCGAGCGTAACGCCACTGCGAAA 1 20 1 GAGCGAACGC 0.865261 -177 ATTTTCTGCCCGAAATTTCGCAGTGGCGTTA 1 35 0 CGAAATTCGC 0.650652 -162 AAATTTCGGGCAGAAAATCGCAGTGGCGTTA 1 48 1 CAGAAATCGC 0.95342 -149 CCCTAGCCGCGAGCGTAACGCCACTGCGATT 1 63 0 GAGCGAACGC 0.865261 -134 CGTTTCGGCGCGCATCGTCGCCAGGCTAGAT 1 111 1 CGCATGTCGC 0.991803 -86 CGTTTCGGCGCGCATCGTCGCCAGGCTAAGG 1 167 1 CGCATGTCGC 0.991803 -30 CGTCCCGGCGCGCATCGTCGCCGCGCTCGGC 4 14 0 CGCATGTCGC 0.991803 -287 CGCCGCGCTCGGCCTTATCGCGCGCCTCCTC 4 52 0 GGCCTATCGC 0.970933 -249 CGTCGCGGCGCGCATCGTCGCCGCGCTCGGC 4 70 0 CGCATGTCGC 0.991803 -231 AGGTCGTGATCAAAGTATCGCGGTCGCCGGG 4 195 0 CAAAGATCGC 0.960693 -106 ATAGTTAACCGGGAGCATCGCGCCCATCGAA 4 227 1 GGGAGATCGC 0.989729 -74 CGCGAACAGACACAGAATCGCACGCGGCAGG 5 24 1 CACAGATCGC 0.990728 -29 AGACAGAGGGAGAGGGCCGCTAGTCCTCTG 6 10 1 GAGAGGCCGC 0.925291 -39 ***** ***** Masking position 9 Map Score: 25.6934 Number of sites scoring better than the average of aligned sites = 4103 Number in coding regions = 3648 Number in noncoding regions = 455 Number of orfs with sites within 600 bp upstream = 365 Fraction of orfs with sites within 600 bp upstream = 0.0586251 Motif number 6 ********** No masking Map Score: -4.16788e-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 7 ********** No masking Map Score: -4.16788e-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: -4.16788e-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