AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i010_Nucleotide_Metabolism_bbur_reg_300.orf -o010_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 RBB00545 300 3615 #2 RBB00736 178 3615 #3 RBB00735 61 3615 Motif number 1 CACACCGCAAATAATAATACGTAAAGCTCAATTTA 1 27 1 AAAAAATAAA 0.991064 -274 ATATATAAATACAACAAAACCTAATTTAACTTTAA 1 61 1 AAAAAATAAT 0.947105 -240 AATATCCAACTTAATAACATTTATTATATAAAAAA 1 94 1 TAAAAATATT 0.745451 -207 TTTATTATATAAAAAAACATGAAAAAATATAATTG 1 113 1 AAAAAAAAAA 0.974892 -188 AGCGTGATTAAAAAAATCAATTATATTTTTTCATG 1 130 0 AAAATATATA 0.826609 -171 CTGCTTTTATTAAATAAATAGAATAAGCGTGATTA 1 155 0 TAAAATAATA 0.690889 -146 TTTATTTAATAAAAGCAGTTTTAAAAAAGAATGTT 1 172 1 AAACATTAAA 0.830917 -129 AAAGAATGTTAAAATAAAACATAAATATGGGAATC 1 197 1 AAAAAATAAA 0.991064 -104 GGGAATCTACACAAAACTTATTAAAAAGTCTAACA 1 225 1 AAAACTTAAA 0.840491 -76 AAAAAGTCTAACAAAAAAATCTAAAATTAATATAA 1 247 1 AAAAAATAAA 0.991063 -54 AAAAACCTAGACAAAAAAATATAAAATTAAGCAAA 2 37 0 AAAAAATAAA 0.991063 -142 ATAATTTTAATTATTAAGATAAAAACCTAGACAAA 2 57 0 TATAAAAAAA 0.686989 -122 TTAAAATTATAAAATAAGTTGTATAATGATGTTTG 2 82 1 AAAAATTATA 0.947654 -97 TGAGTAATTTAAAAAAAGAGCTATAATTTGGTTTT 2 146 1 AAAAAATATA 0.981155 -33 TATTTTTCAAATATCAAGACCAAAAGCCAAAT 3 8 0 AATAAAAAAA 0.862431 -54 TCTTGATATTTGAAAAATATATAAACATATAGATG 3 24 1 TAAAAATAAA 0.974885 -38 * ** ** * **** Masking position 3 Map Score: 24.7412 Number of sites scoring better than the average of aligned sites = 2595 Number in coding regions = 1638 Number in noncoding regions = 957 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 2 ATAAATACAACAAAACCTAATTTAACTTTA 1 65 1 CAAAACCTAA 0.934664 -236 AATTTAACTTTAATATCCAACTTAATAACA 1 83 1 TAATATCCAA 0.616846 -218 TATTATATAAAAAAACATGAAAAAATATAA 1 115 1 AAAAACATGA 0.860824 -186 AAAAACATGAAAAAATATAATTGATTTTTT 1 125 1 AAAAATATAA 0.969962 -176 AATGTTAAAATAAAACATAAATATGGGAAT 1 201 1 TAAAACATAA 0.930259 -100 AAACTTATTAAAAAGTCTAACAAAAAAATC 1 238 1 AAAAGTCTAA 0.944856 -63 AGTCTAACAAAAAAATCTAAAATTAATATA 1 251 1 AAAAATCTAA 0.983342 -50 AAAATTAAGCAAAAACACAACAGGCCAATT 2 20 0 AAAAACACAA 0.940473 -159 ACCTAGACAAAAAAATATAAAATTAAGCAA 2 38 0 AAAAATATAA 0.969962 -141 TTATTAAGATAAAAACCTAGACAAAAAAAT 2 52 0 AAAAACCTAG 0.957212 -127 CTTAATAATTAAAATTATAAAATAAGTTGT 2 74 1 AAAATTATAA 0.774596 -105 TCCTCCTTAAAACCAAATTATAGCTCT 2 162 0 TAAAACCAAA 0.886746 -17 TATCAAGACCAAAAGCCAAAT 3 2 0 AAAAGCCAAA 0.885918 -60 TATATTTTTCAAATATCAAGACCAAAAGCC 3 15 0 AAATATCAAG 0.577705 -47 GATATTTGAAAAATATATAAACATATAGAT 3 28 1 AAATATATAA 0.896703 -34 ********** Masking position 3 Map Score: 19.5109 Number of sites scoring better than the average of aligned sites = 1604 Number in coding regions = 1025 Number in noncoding regions = 579 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 ATAATACGTAAAGCTCAATTTATATATAAAT 1 40 1 AAGCTAATTT 0.829486 -261 AATACAACAAAACCTAATTTAACTTTAATAT 1 68 1 AACCTATTTA 0.945401 -233 CGTGATTAAAAAAATCAATTATATTTTTTCA 1 132 0 AAAATAATTA 0.67028 -169 TTCTTTTTTAAAACTGCTTTTATTAAATAAA 1 172 0 AAACTCTTTT 0.924166 -129 GTTTTATTTTAACATTCTTTTTTAAAACTGC 1 186 0 AACATCTTTT 0.918009 -115 GTTAAAATAAAACATAAATATGGGAATCTAC 1 204 1 AACATAATAT 0.919583 -97 AATCTACACAAAACTTATTAAAAAGTCTAAC 1 228 1 AAACTATTAA 0.901248 -73 AAAAAAATCTAAAATTAATATAAACTATTAC 1 259 1 AAAATAATAT 0.843873 -42 CATCATTATACAACTTATTTTATAATTTTAA 2 82 0 CAACTATTTT 0.804065 -97 ATTAGCCACAAACATCATTATACAACTTATT 2 94 0 AACATATTAT 0.949868 -85 TCCTCCTTAAAACCAAATTATAGCTCTTTTT 2 158 0 AACCAATTAT 0.850118 -21 AACCTACTTATCCCATCTATA 3 51 0 AACCTCTTAT 0.964754 -11 ***** ***** Masking position 2 Map Score: 10.1433 Number of sites scoring better than the average of aligned sites = 800 Number in coding regions = 529 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 GGTTTTGTTGTATTTATATATAAATTGAGC 1 52 0 TATTTATATA 0.753295 -249 TTTTCATGTTTTTTTATATAATAAATGTTA 1 108 0 TTTTTATATA 0.957657 -193 TTAATCACGCTTATTCTATTTATTTAATAA 1 154 1 TTATTCTATT 0.649726 -147 AAAACTGCTTTTATTAAATAAATAGAATAA 1 164 0 TTATTAAATA 0.687573 -137 GTTTATATTAATTTTAGATTTTTTTGTTAG 1 254 0 ATTTTAGATT 0.850425 -47 AGATAGTAATAGTTTATATTAATTTTAGAT 1 265 0 AGTTTATATT 0.904783 -36 TTTTTGCTTAATTTTATATTTTTTTGTCTA 2 35 1 ATTTTATATT 0.957657 -144 TTTGTCTAGGTTTTTATCTTAATAATTAAA 2 57 1 TTTTTATCTT 0.892171 -122 TATACAACTTATTTTATAATTTTAATTATT 2 77 0 ATTTTATAAT 0.723174 -102 TTGTGGCTAATTTTTAAATTAGCTGCCTTA 2 114 1 TTTTTAAATT 0.882265 -65 TATAGCTCTTTTTTTAAATTACTCATGTAA 2 141 0 TTTTTAAATT 0.882265 -38 CCCATCTATATGTTTATATATTTTTCAAAT 3 31 0 TGTTTATATA 0.904783 -31 ********** Masking position 5 Map Score: 13.1071 Number of sites scoring better than the average of aligned sites = 1700 Number in coding regions = 1034 Number in noncoding regions = 666 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 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