AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i334_1_bbur_reg_300.orf -o334_borburg_300.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 RBB01728 300 4077 #2 RBB01729 85 4077 #3 RBB00545 300 3615 #4 RBB00031 66 3615 Motif number 1 AAATAAAACTTAAACTGGGAAAAT 1 2 1 AATAAACTAA 0.984952 -299 TAAACTGGGAAAATTAGTGTTACATAAAATGAA 1 21 1 AAATAGTTAC 0.713764 -280 GTGATCGTGAAATAGGGCTTAAAGCAAGTTTTT 1 79 0 AATAGGCTAA 0.778144 -222 TTATAGTATAACAAAAATTAAACCATAGTCAAG 1 143 1 ACAAAATAAC 0.533479 -158 ATTTATTTAAAATACAACTTGACTATGGTTTAA 1 160 0 AATAAACTAC 0.981719 -141 GTTGTATTTTAAATAAATTTTAATCTCAATTAC 1 175 1 AAATAATTAA 0.864171 -126 AATCTCAATTACTAAAACTTTACAATATAACTA 1 196 1 ACTAAACTAC 0.92166 -105 AAAACTTTACAATATAACTAAAATTGCTATAAG 1 209 1 AATAAACAAA 0.951725 -92 ATCATTTTACAATATAACTAAAATTGCTATAAA 1 252 0 AATAAACAAA 0.951725 -49 TTTATATATAAATTGAGCTTTACGTATTATTAT 3 37 0 AATTAGCTAC 0.885413 -264 TTTATATATAAATACAACAAAACCTAATTTAAC 3 58 1 AATAAACAAC 0.941774 -243 AACAAAACCTAATTTAACTTTAATATCCAACTT 3 73 1 AATTAACTAA 0.951725 -228 TTTATTATATAAAAAAACATGAAAAAATATAAT 3 113 1 AAAAAACTAA 0.981398 -188 GCAGTTTTAAAAAAGAATGTTAAAATAAAACAT 3 186 1 AAAAAATTAA 0.9548 -115 AGAATGTTAAAATAAAACATAAATATGGGAATC 3 199 1 AATAAACTAA 0.984952 -102 AAAGTCTAACAAAAAAATCTAAAATTAATATAA 3 249 1 AAAAAATTAA 0.9548 -52 AATTAAATCAAAAAAAATGTAAATAAGCAATTT 4 21 0 AAAAAATTAA 0.9548 -46 TTATAAAAAGAAAAAAGTCTAAAAA 4 52 1 AAAAAGTTAA 0.90984 -15 **** *** * ** Masking position 12 Map Score: 29.2325 Number of sites scoring better than the average of aligned sites = 1278 Number in coding regions = 818 Number in noncoding regions = 460 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 2 AAATAAAACTTAAACTGGGAAA 1 2 1 AATAAAACTA 0.9156 -299 AGACAAATTCTTTATAAAAAACTTGCTTTAA 1 63 1 TTTATAAAAA 0.635374 -238 GAGAGTTCGAATTACAAAGAAGTGATCGTGA 1 102 0 ATTACAAAAA 0.747891 -199 AACTATTTATAGTATAACAAAAATTAAACCA 1 137 1 AGTATAACAA 0.918538 -164 ATTTATTTAAAATACAACTTGACTATGGTTT 1 162 0 AATACAACTG 0.800634 -139 AAAACTTTACAATATAACTAAAATTGCTATA 1 209 1 AATATAACAA 0.976745 -92 ATCATTTTACAATATAACTAAAATTGCTATA 1 254 0 AATATAACAA 0.976745 -47 TTTCTGCACTAATCTAAATAAACTTTTCATA 2 20 0 AATCTAAAAA 0.922816 -66 GTTGTATTTATATATAAATTGAGCTTTACGT 3 45 0 TATATAAATG 0.566621 -256 TTTATATATAAATACAACAAAACCTAATTTA 3 58 1 AATACAACAA 0.968595 -243 TTAACTTTAATATCCAACTTAATAACATTTA 3 86 1 TATCCAACTA 0.792199 -215 TAACATTTATTATATAAAAAAACATGAAAAA 3 108 1 TATATAAAAA 0.909415 -193 AGAATGTTAAAATAAAACATAAATATGGGAA 3 199 1 AATAAAACTA 0.9156 -102 CTTATTAAAAAGTCTAACAAAAAAATCTAAA 3 241 1 AGTCTAACAA 0.852755 -60 ATCTAAAATTAATATAAACTATTACTATCTT 3 265 1 AATATAAATA 0.928505 -36 TTTATAATTAAATCAAAAAAAATGTAAATAA 4 28 0 AATCAAAAAA 0.846977 -39 TTGATTTAATTATAAAAAGAAAAAAGTCTAA 4 43 1 TATAAAAAAA 0.82296 -24 ******** ** Masking position 6 Map Score: 19.6834 Number of sites scoring better than the average of aligned sites = 1058 Number in coding regions = 641 Number in noncoding regions = 417 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 3 TTCCCAGTTTAAGTTTTATTT 1 2 0 AAGTTTTATT 0.69559 -299 CATTTTATGTAACACTAATTTTCCCAGTTT 1 22 0 AACACTAATT 0.849593 -279 AATTTGTCTTAAGCCCTATTCATTTTATGT 1 42 0 AAGCCCTATT 0.967322 -259 AATAGGGCTTAAGACAAATTCTTTATAAAA 1 52 1 AAGACAAATT 0.705579 -249 AACTTGCTTTAAGCCCTATTTCACGATCAC 1 82 1 AAGCCCTATT 0.967322 -219 AATTGAGATTAAAATTTATTTAAAATACAA 1 176 0 AAAATTTATT 0.891183 -125 AATAAATTTTAATCTCAATTACTAAAACTT 1 186 1 AATCTCAATT 0.790204 -115 TAAAATATGAAAAGTTTATTTAGATTAGTG 2 15 1 AAAGTTTATT 0.716362 -71 TCGTATTTTTGAACTCAATTTTCTGCACTA 2 40 0 GAACTCAATT 0.725862 -46 ATAATACGTAAAGCTCAATTTATATATAAA 3 40 1 AAGCTCAATT 0.960564 -261 AAATACAACAAAACCTAATTTAACTTTAAT 3 67 1 AAACCTAATT 0.941062 -234 CCAACTTAATAACATTTATTATATAAAAAA 3 99 1 AACATTTATT 0.822748 -202 CGTGATTAAAAAAATCAATTATATTTTTTC 3 133 0 AAAATCAATT 0.91892 -168 GAATCTACACAAAACTTATTAAAAAGTCTA 3 227 1 AAAACTTATT 0.908839 -74 ********** Masking position 8 Map Score: 12.6484 Number of sites scoring better than the average of aligned sites = 906 Number in coding regions = 618 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 CTTAAAGCAAGTTTTTTATAAAGAATTTGT 1 65 0 GTTTTTTATA 0.862387 -236 TAAAAGTAAATACTCTTATAGCAATTTTAG 1 226 0 TACTCTTATA 0.751611 -75 TAAGAGTATTTACTTTTATAGCAATTTTAG 1 238 1 TACTTTTATA 0.94631 -63 GGTTTTGTTGTATTTATATATAAATTGAGC 3 52 0 TATTTATATA 0.771543 -249 TTTTTTCATGTTTTTTTATATAATAAATGT 3 110 0 TTTTTTTATA 0.843985 -191 AAATCAATTATATTTTTTCATGTTTTTTTA 3 122 0 TATTTTTTCA 0.79777 -179 AAATATAATTGATTTTTTTAATCACGCTTA 3 137 1 GATTTTTTTA 0.96042 -164 ACGCTTATTCTATTTATTTAATAAAAGCAG 3 160 1 TATTTATTTA 0.824283 -141 TATTTTAACATTCTTTTTTAAAACTGCTTT 3 183 0 TTCTTTTTTA 0.896128 -118 TTTTTTGTTAGACTTTTTAATAAGTTTTGT 3 235 0 GACTTTTTAA 0.781259 -66 ATTAATTTTAGATTTTTTTGTTAGACTTTT 3 248 0 GATTTTTTTG 0.820458 -53 TTTTTAGACTTTTTTCTTTTTATAAT 4 51 0 GACTTTTTTC 0.841107 -16 ********** Masking position 4 Map Score: 7.91351 Number of sites scoring better than the average of aligned sites = 1312 Number in coding regions = 828 Number in noncoding regions = 484 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 ********** No masking Map Score: 1.40931e-12 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: 1.40931e-12 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: 1.40931e-12 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