AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i142_Cytochrome_Oxidase_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 ctaC 245 ctaC #2 ctaD 214 ctaD Motif number 1 GGCGCCCCAGTATGCCCCACTT 1 3 1 CGCCCCAGTA 0.607003 -243 GTCGTCGCGACCCGCCGGACGAGGCATCCA 1 44 0 CCCGCCGGAC 0.992881 -202 TCCGGCGGGTCGCGACGACCAGGCAGTCGC 1 55 1 CGCGACGACC 0.980245 -191 CGCCATCAGCCCCGCGGGCGACTGCCTGGT 1 72 0 CCCGCGGGCG 0.982259 -174 CGGGGCTGATGGCGCGGCTCCTCAGCGGGC 1 88 1 GGCGCGGCTC 0.941413 -158 GCGCGGCTCCTCAGCGGGCCGTTTCGGCCC 1 99 1 TCAGCGGGCC 0.944271 -147 CGCCCGCGCGGGCGACGATGCGGGCCGAAA 1 120 0 GGCGACGATG 0.866758 -126 CATCGTCGCCCGCGCGGGCGGCGTGGTCTA 1 130 1 CGCGCGGGCG 0.649471 -116 CACCGGCTGCGGCGAGAACCATCGGCTAAC 1 184 0 GGCGAGAACC 0.835028 -62 GGTTCTCGCCGCAGCCGGTGCTATCCCAGT 1 194 1 GCAGCCGGTG 0.979025 -52 CGGTGCTATCCCAGTCGGCCCAGCTTGTGA 1 209 1 CCAGTCGGCC 0.985141 -37 TGATACAGGAGGCGCCAACA 1 236 1 GGCGCCAACA 0.874576 -10 CCCGCCGGACAGCACGCGTT 2 1 1 CCCGCCGGAC 0.992881 -214 TTCGACGGTAGCACTCGGCCAGCCGTCGAC 2 29 1 GCACTCGGCC 0.962727 -186 CACTCGGCCAGCCGTCGACCCCGATTCGCG 2 40 1 GCCGTCGACC 0.98856 -175 GACCCCGATTCGCGCGGGCGGAAAGCGTTG 2 56 1 CGCGCGGGCG 0.649471 -159 TCTGCAACGGCCCGCCGGCGGAGTCTGGCA 2 87 1 CCCGCCGGCG 0.998272 -128 ACGGTTTGTAGGACCAGGCCTGCCGCCAGC 2 123 1 GGACCAGGCC 0.639942 -92 GACCAGGCCTGCCGCCAGCCTGATCGAGGG 2 134 1 GCCGCCAGCC 0.996174 -81 AGGCATCTTAGCCCTCGATCAGGCTGGCGG 2 145 0 GCCCTCGATC 0.864016 -70 CATCCAGCCCGGACCGGGCCAAAACCCAGT 2 181 0 GGACCGGGCC 0.555279 -34 ********** Masking position 7 Map Score: 49.251 Number of sites scoring better than the average of aligned sites = 73012 Number in coding regions = 68776 Number in noncoding regions = 4236 Number of orfs with sites within 600 bp upstream = 1434 Fraction of orfs with sites within 600 bp upstream = 0.230324 Motif number 2 AGGCATCCACAAGAGTCGCCAAGTGGGGCA 1 23 0 AAGAGTCGCC 0.925294 -223 GACCCGCCGGACGAGGCATCCACAAGAGTC 1 36 0 ACGAGGCATC 0.901845 -210 CCTGGTCGTCGCGACCCGCCGGACGAGGCA 1 48 0 GCGACCCGCC 0.996256 -198 GCGACGACCAGGCAGTCGCCCGCGGGGCTG 1 66 1 GGCAGTCGCC 0.712064 -180 GCCCGCTGAGGAGCCGCGCCATCAGCCCCG 1 88 0 GAGCCGCGCC 0.936359 -158 CGGCTCCTCAGCGGGCCGTTTCGGCCCGCA 1 102 1 GCGGGCCGTT 0.92627 -144 CGTAGACCACGCCGCCCGCGCGGGCGACGA 1 132 0 GCCGCCCGCG 0.874551 -114 CGGCTGCGGCGAGAACCATCGGCTAACTCA 1 181 0 GAGAACCATC 0.727426 -65 CTTGTGATACAGGAGGCGCCAACA 1 232 1 AGGAGGCGCC 0.958786 -14 ACCGTCGAACGCGTGCTGTCCGGCGGG 2 8 0 GCGTGCTGTC 0.938645 -207 ACGGCTGGCCGAGTGCTACCGTCGAACGCG 2 25 0 GAGTGCTACC 0.774793 -190 GTAGCACTCGGCCAGCCGTCGACCCCGATT 2 36 1 GCCAGCCGTC 0.862641 -179 TTGGTCTGCAACGGCCCGCCGGCGGAGTCT 2 83 1 ACGGCCCGCC 0.980704 -132 GTAGGACCAGGCCTGCCGCCAGCCTGATCG 2 130 1 GCCTGCCGCC 0.97683 -85 ACCCAGTATTGAGAGGCATCTTAGCCCTCG 2 158 0 GAGAGGCATC 0.938198 -57 ********** Masking position 7 Map Score: 21.465 Number of sites scoring better than the average of aligned sites = 31182 Number in coding regions = 28663 Number in noncoding regions = 2519 Number of orfs with sites within 600 bp upstream = 1166 Fraction of orfs with sites within 600 bp upstream = 0.187279 Motif number 3 AGTGGGGCATACTGGGGCGCC 1 2 0 ACTGGGGCGC 0.773566 -244 GACCCGCCGGACGAGGCATCCACAAGAGTC 1 36 0 ACGAGGCATC 0.595207 -210 GGTCGCGACGACCAGGCAGTCGCCCGCGGG 1 62 1 ACCAGGCAGT 0.716589 -184 AGCCGCGCCATCAGCCCCGCGGGCGACTGC 1 77 0 TCAGCCCCGC 0.949886 -169 GCGGCTCCTCAGCGGGCCGTTTCGGCCCGC 1 101 1 AGCGGGCCGT 0.722751 -145 AGCGGGCCGTTTCGGCCCGCATCGTCGCCC 1 111 1 TTCGGCCCGC 0.984163 -135 GCCCGCATCGTCGCCCGCGCGGGCGGCGTG 1 125 1 TCGCCCGCGC 0.908754 -121 CGCAGCGTAGACCACGCCGCCCGCGCGGGC 1 137 0 ACCACGCCGC 0.98297 -109 GACATCGAATACTACGCAGCGTAGACCACG 1 151 0 ACTACGCAGC 0.872325 -95 CCGATGGTTCTCGCCGCAGCCGGTGCTATC 1 189 1 TCGCCGCAGC 0.958641 -57 GCTATCCCAGTCGGCCCAGCTTGTGATACA 1 213 1 TCGGCCCAGC 0.8925 -33 TGTTGGCGCCTCCTGTATCACA 1 234 0 TTGGCGCCTC 0.759379 -12 GACGGTAGCACTCGGCCAGCCGTCGACCCC 2 32 1 CTCGGCCAGC 0.797236 -183 CGGCCAGCCGTCGACCCCGATTCGCGCGGG 2 44 1 TCGACCCCGA 0.749622 -171 GACCAACGCTTTCCGCCCGCGCGAATCGGG 2 59 0 TTCCGCCCGC 0.975306 -156 TAAATGCCAGACTCCGCCGGCGGGCCGTTG 2 91 0 ACTCCGCCGG 0.774669 -124 GGACCAGGCCTGCCGCCAGCCTGATCGAGG 2 133 1 TGCCGCCAGC 0.907154 -82 AATACTGGGTTTTGGCCCGGTCCGGGCTGG 2 178 1 TTTGGCCCGG 0.823328 -37 CCTCCAAACATCCAGCCCGGACCGGGCCAA 2 189 0 TCCAGCCCGG 0.96355 -26 ********** Masking position 9 Map Score: 26.2986 Number of sites scoring better than the average of aligned sites = 55545 Number in coding regions = 51748 Number in noncoding regions = 3797 Number of orfs with sites within 600 bp upstream = 1439 Fraction of orfs with sites within 600 bp upstream = 0.231128 Motif number 4 CGGCGGGTCGCGACGACCAGGCAGTCGCCCG 1 57 1 CGACGACCGG 0.915749 -189 ACGACCAGGCAGTCGCCCGCGGGGCTGATGG 1 69 1 AGTCGCCCCG 0.991042 -177 CGGCCCGCATCGTCGCCCGCGCGGGCGGCGT 1 123 1 CGTCGCCCCG 0.939211 -123 TACTACGCAGCGTAGACCACGCCGCCCGCGC 1 141 0 CGTAGACCCG 0.624957 -105 GTCTACGCTGCGTAGTATTCGATGTCTGAGT 1 155 1 CGTAGTATCG 0.806948 -91 CGATGGTTCTCGCCGCAGCCGGTGCTATCCC 1 190 1 CGCCGCAGCG 0.953272 -56 CGAGTGCTACCGTCGAACGCGTGCTGTCCGG 2 15 0 CGTCGAACCG 0.988187 -200 CTCGGCCAGCCGTCGACCCCGATTCGCGCGG 2 42 1 CGTCGACCCG 0.929034 -173 TCCTACAAACCGTCGTAAATGCCAGACTCCG 2 105 0 CGTCGTAATG 0.698575 -110 TGAGAGGCATCTTAGCCCTCGATCAGGCTGG 2 148 0 CTTAGCCCCG 0.972545 -67 ******** ** Masking position 5 Map Score: 22.4264 Number of sites scoring better than the average of aligned sites = 9343 Number in coding regions = 8871 Number in noncoding regions = 472 Number of orfs with sites within 600 bp upstream = 364 Fraction of orfs with sites within 600 bp upstream = 0.0584645 Motif number 5 ********** No masking Map Score: 6.06393e-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 6 ********** No masking Map Score: 6.06393e-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: 6.06393e-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