AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00930_mtub_reg_300.orf -o00930_mtub_300.ace -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -x5 -e 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 = 1 Input sequences: #1 lipW 92 lipW #2 mmpS2 173 mmpS2 #3 hemA 49 hemA #4 fecB 214 fecB #5 adhC 69 adhC Motif number 1 CGATGGCTTTGGCAGGCTGCGGTTAGTCGAA 1 33 0 GGCAGGCGCG 0.9208 -60 CGGTCCAGTATGCGTCGGCGCA 1 81 0 GGTCCAGATG 0.545429 -12 ACCGGTACGCGCAAAGCTGGGTACGTGA 2 8 1 CGCGCAAGCT 0.964105 -166 TTCCGCCCATCGCGCGGACCTAGTGACCCTT 2 146 0 CGCGCGGCCT 0.960646 -28 CCGCGCGATGGGCGGAACACGAGG 2 160 1 GGCGGAAACG 0.965758 -14 CTGGGGTAGTCGAGGGAGCTGGCCAGGTGGT 3 23 1 CGAGGGACTG 0.579693 -27 CTGGATGTTTGGAGGAGTGCG 4 1 0 GGAGGAGGCG 0.986974 -214 GCCCGGTCCGGGCTGGATGTTTGGAGGAGTG 4 13 0 GGCTGGAGTT 0.683094 -202 ACTGGGTTTTGGCCCGGTCCGGGCTGGATGT 4 24 0 GGCCCGGCCG 0.988225 -191 CCGCCAGCCTGATCGAGGGCTAAGATGCCTC 4 60 0 GATCGAGGCT 0.634061 -155 ACGGTTTGTAGGACCAGGCCTGCCGCCAGCC 4 82 0 GGACCAGCCT 0.891861 -133 ACGGCCCGCCGGCGGAGTCTGGCATTTACGA 4 112 0 GGCGGAGCTG 0.979907 -103 AGACTCCGCCGGCGGGCCGTTGCAGACCAAC 4 123 1 GGCGGGCGTT 0.951125 -92 GATTCGCGCGGGCGGAAAGCGTTGGTCTGCA 4 143 0 GGCGGAAGCG 0.995513 -72 GCTTTCCGCCCGCGCGAATCGGGGTCGACGG 4 154 1 CGCGCGATCG 0.766625 -61 CGCGAATCGGGGTCGACGGCTGGCCGAGTGC 4 166 1 GGTCGACGCT 0.931547 -49 GTCGACGGCTGGCCGAGTGCTACCGTCGAAC 4 177 1 GGCCGAGGCT 0.994464 -38 CGAGTGCTACCGTCGAACGCGTGCTGTCCGG 4 190 1 CGTCGAAGCG 0.923266 -25 TGAGGCGCAGCGCTAGGCTTTGGG 5 4 1 GGCGCAGGCT 0.991756 -66 ******* *** Masking position 2 Map Score: 26.8946 Number of sites scoring better than the average of aligned sites = 42285 Number in coding regions = 39328 Number in noncoding regions = 2957 Number of orfs with sites within 600 bp upstream = 1289 Fraction of orfs with sites within 600 bp upstream = 0.207035 Motif number 2 ACTAACCGCAGCCTGCCAAAGCCATCGCTGTAC 1 37 1 GCCTCAAGCC 0.860189 -56 GCGCAATTTCGCCTCGGTACAGCGATGGCTTTG 1 53 0 GCCTGACAGC 0.947878 -40 GCGAAATTGCGCCGACGCATACTGGACCG 1 74 1 GCCGGATACT 0.970843 -19 GAATTCTTCAGCCTGTCAACGGTAGCGTCTACG 2 45 1 GCCTCACGGT 0.811801 -129 TGACCCTTAGGCCTCCCGATACCTCCTGAAATG 2 121 0 GCCTCATACC 0.993012 -53 GGGCTAAGATGCCTCTCAATACTGGGTTTTGGC 4 42 0 GCCTCATACT 0.966385 -173 GTAGGACCAGGCCTGCCGCCAGCCTGATCGAGG 4 73 0 GCCTCCCAGC 0.678239 -142 CGTCGTAAATGCCAGACTCCGCCGGCGGGCCGT 4 110 1 GCCACCCGCC 0.717414 -105 CCGCCGGCGGGCCGTTGCAGACCAACGCTTTCC 4 128 1 GCCGGAGACC 0.980757 -87 CCCGATTCGCGCGGGCGGAAAGCGTTGGTCTGC 4 144 0 GCGGGAAAGC 0.732857 -71 TCGACGGCTGGCCGAGTGCTACCGTCGAACGCG 4 178 1 GCCGTCTACC 0.916333 -37 CCCGCCGGACAGCACGCGTTCGA 4 202 0 CCCGGACAGC 0.939652 -13 GCAGCGCTAGGCTTTGGGATACCCACAGCTAAA 5 17 1 GCTTGATACC 0.905362 -53 **** * ***** Masking position 2 Map Score: 16.7064 Number of sites scoring better than the average of aligned sites = 9354 Number in coding regions = 8778 Number in noncoding regions = 576 Number of orfs with sites within 600 bp upstream = 475 Fraction of orfs with sites within 600 bp upstream = 0.076293 Motif number 3 AGGCCACCATCCCGATCCTCGTTCGACTAAC 1 12 1 CCGATCCTCG 0.873489 -81 CGCAGCCTGCCAAAGCCATCGCTGTACCGAG 1 43 1 CAAGCCATCG 0.882506 -50 ACCGGTACGCGCAAAGCTGGG 2 1 1 ACGGTACGCG 0.835207 -173 GTCTCGTTGCGTTAGCTAGCGTAGACGCTAC 2 66 0 GTAGCTAGCG 0.786101 -108 TCCTAACGTGCGTAGTAATCGGATGTCTCGT 2 90 0 CTAGTAATCG 0.720139 -84 CTAAGGGTCACTAGGTCCGCGCGATGGGCGG 2 144 1 CAGGTCCGCG 0.820057 -30 GGCAGCACCACCTGGCCAGCTCCCTCGACTA 3 29 0 CTGGCCAGCT 0.832985 -21 TGGGTTTTGGCCCGGTCCGGGCTGGATGTTT 4 22 0 CCGGTCCGGG 0.548837 -193 TGAGAGGCATCTTAGCCCTCGATCAGGCTGG 4 57 1 CTAGCCCTCG 0.979895 -158 AAATGCCAGACTCCGCCGGCGGGCCGTTGCA 4 116 1 CCCGCCGGCG 0.936412 -99 GATTCGCGCGGGCGGAAAGCGTTGGTCTGCA 4 143 0 GCGGAAAGCG 0.745694 -72 AGCCGTCGACCCCGATTCGCGCGGGCGGAAA 4 156 0 CCGATTCGCG 0.753912 -59 GTAGCACTCGGCCAGCCGTCGACCCCGATTC 4 169 0 GCAGCCGTCG 0.956703 -46 CGCGTTCGACGGTAGCACTCGGCCAGCCGTC 4 180 0 GTAGCACTCG 0.920822 -35 CCCGCCGGACAGCACGCGTTCGACGGTA 4 197 0 GCAGCACGCG 0.985371 -18 GGCAACCCTCTTCGTTTCTTT 5 59 0 GCAACCCTCT 0.587299 -11 * ********* Masking position 10 Map Score: 15.4695 Number of sites scoring better than the average of aligned sites = 41336 Number in coding regions = 38446 Number in noncoding regions = 2890 Number of orfs with sites within 600 bp upstream = 1262 Fraction of orfs with sites within 600 bp upstream = 0.202698 Motif number 4 ACCGGTACGCGCAAAGCTGGGTACGTGAAAT 2 11 1 GCAAGCTGGG 0.951551 -163 ATTTCAGGAGGTATCGGGAGGCCTAAGGGTC 2 122 1 GTACGGGAGG 0.922481 -52 GGAGGCCTAAGGGTCACTAGGTCCGCGCGAT 2 138 1 GGGCACTAGG 0.954315 -36 CGTGTTCCGCCCATCGCGCGGACCTAGTGAC 2 150 0 CCACGCGCGG 0.953322 -24 CGCGATGGGCGGAACACGAGG 2 163 1 GGACACGAGG 0.987189 -11 GGCAGCACCACCTGGCCAGCTCCCT 3 35 0 GCACACCTGG 0.958712 -15 ACGACGGTTTGTAGGACCAGGCCTGCCGCCA 4 85 0 GTAGACCAGG 0.860627 -130 TTCCGCCCGCGCGAATCGGGGTCGACGGCTG 4 157 1 GCGATCGGGG 0.719623 -58 GCGTTCGACGGTAGCACTCGGCCAGCCGTCG 4 179 0 GTACACTCGG 0.968032 -36 TGAGGCGCAGCGCTAGGCTTTGGGATA 5 7 1 GCACGCTAGG 0.993296 -63 *** ******* Masking position 10 Map Score: 6.63054 Number of sites scoring better than the average of aligned sites = 6269 Number in coding regions = 5740 Number in noncoding regions = 529 Number of orfs with sites within 600 bp upstream = 449 Fraction of orfs with sites within 600 bp upstream = 0.0721169 Motif number 5 GAAGAATTCAGGATTTCACGTACCCAGCTT 2 24 0 GGATTTCACG 0.969312 -150 CGTAGTAATCGGATGTCTCGTTGCGTTAGC 2 81 0 GGATGTCTCG 0.996262 -93 GGACATTTCAGGAGGTATCGGGAGGCCTAA 2 118 1 GGAGGTATCG 0.982826 -56 GGTCCGGGCTGGATGTTTGGAGGAGTGCG 4 10 0 GGATGTTTGG 0.977487 -205 ********** Masking position 6 Map Score: 1.71926 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 155 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ********** No masking Map Score: 9.90086e-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: 9.90086e-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: 9.90086e-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