AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_bbur_reg_100.orf -o207_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RBB00708 44 3615 #2 RBB00707 79 3615 #3 RBB00462 198 3615 #4 RBB00392 26 3615 Motif number 1 TTATTAGTTTTTTATAGTTATAAA 1 5 1 TAGTTTTTTA 0.965117 -40 TAGTTTTTTATAGTTATAAAATAGTTTTTA 1 15 1 TAGTTATAAA 0.9044 -30 AGTTATAAAATAGTTTTTAAGGAATATTT 1 26 1 TAGTTTTTAA 0.985046 -19 CTTAAGGCTTTTGCTTTAAATTGTTGAATG 2 28 1 TTGCTTTAAA 0.85826 -52 CTGTGTAATATAATTTATAATTTAATTAT 2 61 1 TAATTTATAA 0.932877 -19 ATGTCATAATATATTTATAA 3 1 0 ATATTTATAA 0.698722 -198 TATGACATTTTAATTTTATATTTGTTTTTT 3 23 1 TAATTTTATA 0.945426 -176 AATTATTAAATTGTTTAAAAAAACAAATAT 3 40 0 TTGTTTAAAA 0.956197 -159 AACAATTTAATAATTTATTATTAAAAATAA 3 55 1 TAATTTATTA 0.884464 -144 CCTTTTCGGGTTATTTTTAATAATAAATTA 3 65 0 TTATTTTTAA 0.966707 -134 ATTGCTTTTGTTATTTTTAAGAAAAAATAT 3 99 1 TTATTTTTAA 0.966707 -100 ACTACTACGATAGATTATAATATTTTTTCT 3 118 0 TAGATTATAA 0.799541 -81 ATCGTAGTAGTTATTTTAAATTATGGCAAG 3 137 1 TTATTTTAAA 0.968944 -62 ATATCCCAAATAATTATATATA 4 3 0 TAATTATATA 0.758164 -24 ********** Masking position 10 Map Score: 23.2717 Number of sites scoring better than the average of aligned sites = 1604 Number in coding regions = 1003 Number in noncoding regions = 601 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 2 TTATAACTATAAAAAACTAATAA 1 4 0 AAAAAACTAA 0.706721 -41 AAATATTCCTTAAAAACTATTTTATAACTA 1 25 0 TAAAAACTAT 0.96368 -20 ATAATTAAATTATAAATTATATTACACAGA 2 60 0 TATAAATTAT 0.959186 -20 AAAACAAATATAAAATTAAAATGTCATAAT 3 21 0 TAAAATTAAA 0.743163 -178 TATTTGTTTTTTTAAACAATTTAATAATTT 3 41 1 TTTAAACAAT 0.867701 -158 TATTTTTAATAATAAATTATTAAATTGTTT 3 54 0 AATAAATTAT 0.854096 -145 AATTTATTATTAAAAATAACCCGAAAAGGA 3 66 1 TAAAAATAAC 0.965243 -133 TATTTTTTCTTAAAAATAACAAAAGCAATT 3 98 0 TAAAAATAAC 0.965243 -101 GAAAAAATATTATAATCTATCGTAGTAGTT 3 119 1 TATAATCTAT 0.847031 -80 TTGCCATAATTTAAAATAACTACTACGATA 3 136 0 TTAAAATAAC 0.871484 -63 TATATATAATTATTTGGGAT 4 1 1 TATATATAAT 0.781177 -26 ********** Masking position 4 Map Score: 10.2655 Number of sites scoring better than the average of aligned sites = 1776 Number in coding regions = 1062 Number in noncoding regions = 714 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 3 TTTACTTAAGGCTTTTGCTTTAAATTGTTGA 2 24 1 GCTTTGCTTT 0.979261 -56 TTTTAATTTTATATTTGTTTTTTTAAACAAT 3 30 1 ATTTTGTTTT 0.924463 -169 AGGATAAATTGCTTTTGTTATTTTTAAGAAA 3 92 1 GCTTTGTTAT 0.980737 -107 ATAATCTATCGTAGTAGTTATTTTAAATTAT 3 130 1 GTGTAGTTAT 0.82132 -69 TTATGGCAAGAGGTTTGTTAGAGCTTTGCTA 3 157 1 AGTTTGTTAG 0.917003 -42 GGTTTGTTAGAGCTTTGCTATAATGGTATAG 3 168 1 AGTTTGCTAT 0.977457 -31 TAATGGTATAGGAGTTGCTTT 3 188 1 GGGTTGCTTT 0.978849 -11 ** ******** Masking position 5 Map Score: 3.64951 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 267 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 GAAACATTCAACAATTTAAAGCAAAAGCCT 2 32 0 ACAATTTAAA 0.943269 -48 ATGTTTCTGTGTAATATAATTTATAATTTA 2 55 1 GTAATATAAT 0.927163 -25 AATATAATTTATAATTTAATTAT 2 67 1 ATAATTTAAT 0.978943 -13 TTAAAATGTCATAATATATTTATAA 3 6 0 ATAATATATT 0.936205 -193 ATATATTATGACATTTTAATTTTATATTTG 3 17 1 ACATTTTAAT 0.936001 -182 GTTTTTTTAAACAATTTAATAATTTATTAT 3 46 1 ACAATTTAAT 0.981312 -153 GTTATTTTTAATAATAAATTATTAAATTGT 3 56 0 ATAATAAATT 0.678549 -143 AATAACAAAAGCAATTTATCCTTTTCGGGT 3 84 0 GCAATTTATC 0.731256 -115 TTAAGAAAAAATATTATAATCTATCGTAGT 3 115 1 ATATTATAAT 0.898393 -84 ACCTCTTGCCATAATTTAAAATAACTACTA 3 141 0 ATAATTTAAA 0.938796 -58 ********** Masking position 5 Map Score: 14.1163 Number of sites scoring better than the average of aligned sites = 877 Number in coding regions = 528 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 5 ********** No masking Map Score: -4.94948e-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: -4.94948e-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: -4.94948e-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