AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i010_Nucleotide_Metabolism_bbur_reg_100.orf -o010_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 RBB00545 300 3615 #2 RBB00736 178 3615 #3 RBB00735 61 3615 Motif number 1 ACACACCGCAAATAATAATACGTAAAGCTCAATT 1 26 1 AAAAAATATA 0.905702 -275 TATATATAAATACAACAAAACCTAATTTAACTTT 1 60 1 TAAAAAAATA 0.980205 -241 TGTTTTTTTATATAATAAATGTTATTAAGTTGGA 1 98 0 TAAAAAATTA 0.897593 -203 TATATAAAAAAACATGAAAAAATATAATTGATTT 1 118 1 AAATAAAATA 0.980844 -183 GCTTTTATTAAATAAATAGAATAAGCGTGATTAA 1 154 0 AAAATAGAAA 0.76828 -147 AAAAGAATGTTAAAATAAAACATAAATATGGGAA 1 196 1 TAAAAAAATA 0.979873 -105 TAAAAAGTCTAACAAAAAAATCTAAAATTAATAT 1 246 1 AAAAAAAATA 0.986828 -55 CCTAGACAAAAAAATATAAAATTAAGCAAAAACA 2 33 0 AAATTAAATA 0.94834 -146 TTTAATTATTAAGATAAAAACCTAGACAAAAAAA 2 53 0 AAATAAAATA 0.980844 -126 TTTTTATCTTAATAATTAAAATTATAAAATAAGT 2 67 1 AAAATAAATA 0.962377 -112 ATTAAAATTATAAAATAAGTTGTATAATGATGTT 2 81 1 TAAAAAGTTA 0.803941 -98 GTAAGGCAGCTAATTTAAAAATTAGCCACAAACA 2 111 0 TATTAAAATA 0.743075 -68 ATGAGTAATTTAAAAAAAGAGCTATAATTTGGTT 2 145 1 TAAAAAGATA 0.971287 -34 ATATTTTTCAAATATCAAGACCAAAAGCCAAAT 3 10 0 AAATAAGAAA 0.855011 -52 ATATTTGAAAAATATATAAACATATAGATGGGAT 3 29 1 AAATTAAATA 0.950586 -33 ** ** **** ** Masking position 8 Map Score: 23.2876 Number of sites scoring better than the average of aligned sites = 1570 Number in coding regions = 996 Number in noncoding regions = 574 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 AAAGCTCAATTTATATATAAATACAACAAA 1 49 1 TTATATATAA 0.43041 -252 TTTCATGTTTTTTTATATAATAAATGTTAT 1 107 0 TTTTATATAA 0.536717 -194 AAATCAATTATATTTTTTCATGTTTTTTTA 1 122 0 TATTTTTTCA 0.823623 -179 ATAATTGATTTTTTTAATCACGCTTATTCT 1 141 1 TTTTTAATCA 0.75193 -160 TTATTCTATTTATTTAATAAAAGCAGTTTT 1 164 1 TATTTAATAA 0.860988 -137 TTTAACATTCTTTTTTAAAACTGCTTTTAT 1 180 0 TTTTTTAAAA 0.576109 -121 ATTTATGTTTTATTTTAACATTCTTTTTTA 1 193 0 TATTTTAACA 0.946547 -108 TTTGTTAGACTTTTTAATAAGTTTTGTGTA 1 232 0 TTTTTAATAA 0.5273 -69 TTTATAATTTTAATTATTAAGATAAAAACC 2 65 0 TAATTATTAA 0.642498 -114 TTATACAACTTATTTTATAATTTTAATTAT 2 78 0 TATTTTATAA 0.951316 -101 GTAAGGCAGCTAATTTAAAAATTAGCCACA 2 115 0 TAATTTAAAA 0.861236 -64 CTTACATGAGTAATTTAAAAAAAGAGCTAT 2 140 1 TAATTTAAAA 0.861236 -39 TTGGTCTTGATATTTGAAAAATATATAAAC 3 20 1 TATTTGAAAA 0.862781 -42 ATTTGAAAAATATATAAACATATAGATGGG 3 31 1 TATATAAACA 0.541393 -31 ********** Masking position 10 Map Score: 15.0106 Number of sites scoring better than the average of aligned sites = 2930 Number in coding regions = 1815 Number in noncoding regions = 1115 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 3 AATAATACGTAAAGCTCAATTTATATATAAA 1 39 1 AAAGTCAATT 0.97131 -262 GTTGGATATTAAAGTTAAATTAGGTTTTGTT 1 73 0 AAAGTAAATT 0.968939 -228 GCGTGATTAAAAAAATCAATTATATTTTTTC 1 133 0 AAAATCAATT 0.955248 -168 TTTAAAAAAGAATGTTAAAATAAAACATAAA 1 191 1 AATGTAAAAT 0.814485 -110 TCTAACAAAAAAATCTAAAATTAATATAAAC 1 253 1 AAATTAAAAT 0.913483 -48 CAAAAACACAACAGGCCAATTAATTGTTAT 2 10 0 ACAGCCAATT 0.849227 -169 CTAGACAAAAAAATATAAAATTAAGCAAAAA 2 35 0 AAATTAAAAT 0.913483 -144 TTTTATCTTAATAATTAAAATTATAAAATAA 2 68 1 ATAATAAAAT 0.75645 -111 TCCTCCTTAAAACCAAATTATAGCTCTTT 2 160 0 AAAACAAATT 0.933458 -19 TATCAAGACCAAAAGCCAAAT 3 1 0 AAAACCAAAT 0.938258 -61 **** ****** Masking position 8 Map Score: 9.52583 Number of sites scoring better than the average of aligned sites = 973 Number in coding regions = 656 Number in noncoding regions = 317 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TATTATTTGCGGTGTGTTTGAGGTAGTTGA 1 13 0 GGTGTGTTTG 0.842817 -288 AGTTAAATTAGGTTTTGTTGTATTTATATA 1 62 0 GGTTTTGTTG 0.828607 -239 TATTTTTTCATGTTTTTTTATATAATAAAT 1 112 0 TGTTTTTTTA 0.956087 -189 AAATCAATTATATTTTTTCATGTTTTTTTA 1 122 0 TATTTTTTCA 0.806735 -179 AAATATAATTGATTTTTTTAATCACGCTTA 1 137 1 GATTTTTTTA 0.964245 -164 ACGCTTATTCTATTTATTTAATAAAAGCAG 1 160 1 TATTTATTTA 0.754017 -141 ATTAATTTTAGATTTTTTTGTTAGACTTTT 1 248 0 GATTTTTTTG 0.973863 -53 ATTGGCCTGTTGTGTTTTTGCTTAATTTTA 2 21 1 TGTGTTTTTG 0.968406 -158 CTTAATTTTATATTTTTTTGTCTAGGTTTT 2 41 1 TATTTTTTTG 0.973379 -138 TTTTTTTGTCTAGGTTTTTATCTTAATAAT 2 53 1 TAGGTTTTTA 0.809653 -126 GTTGTATAATGATGTTTGTGGCTAATTTTT 2 99 1 GATGTTTGTG 0.866983 -80 AAATTATAGCTCTTTTTTTAAATTACTCAT 2 145 0 TCTTTTTTTA 0.860793 -34 ATCCCATCTATATGTTTATATATTTTTCAA 3 33 0 TATGTTTATA 0.757492 -29 ********** Masking position 5 Map Score: 14.1395 Number of sites scoring better than the average of aligned sites = 1049 Number in coding regions = 689 Number in noncoding regions = 360 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 ********** No masking Map Score: 3.7902e-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: 3.7902e-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: 3.7902e-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