AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i225_Glutamyl_tRNA_synthase_hpyl_reg_100.orf -o225_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RHP00088 297 AE000511 #2 RHP00089 82 AE000511 #3 RHP00253 58 AE000511 #4 RHP00255 91 AE000511 #5 RHP00256 76 AE000511 Motif number 1 GTATGAAAATTTTTAAAAATTTACAAAAATGAGAA 1 82 1 TTTTAATTCA 0.95929 -216 AAAGCTTAGATTTTATCATAAAAATCTATTTAATG 1 140 1 TTTTACAAAT 0.83618 -158 CAACCCCTTTTTTTTACCTAATTCTCATTAAATAG 1 165 0 TTTTTCAACT 0.677431 -133 TAAGAATGCTTTTTACATATTATATAAAAATATCC 1 222 0 TTTTAATTAT 0.917909 -76 ATTGTAGCATTTTTAGATTTAAGAATGCTTTTTAC 1 241 0 TTTTAATAAA 0.96871 -57 TGCCCTTTCGTTTTAAAGATAAACATTGTAGCATT 1 265 0 TTTTAATACA 0.970713 -33 TAATTTTTAGCGTTTTTAAGAATGATTAG 2 5 1 TTTTACTTAA 0.968973 -78 TTAGTAGCGTTATTATAACTAATCATTCTTAAAAA 2 23 0 TATTAATACA 0.886877 -60 GCTCGTTTTATCTCTAAGCATGTTAAACTA 3 6 1 TTTTACTACA 0.98528 -53 GTTTTTAGCCTTACAAAAAATTTAATG 3 42 0 TTTTACTAAA 0.979141 -17 ATAATTTAGATTTTTTAGCTAGCATGTTAGCAATT 4 23 1 TTTTTATAAT 0.851592 -69 TTAGCTTACTTTTTAACAATATCCATGCCTTAATG 4 58 0 TTTTACTACA 0.985302 -34 CTTTTTTATCGCTTCAATTTAATCAAAA 5 4 1 TTTTACTTAT 0.94715 -73 GCTAGACCCTTATTTAAGCTTTAAATAACTATAAT 5 51 0 TATTTATTAA 0.517878 -26 ***** * ** ** Masking position 4 Map Score: 17.6787 Number of sites scoring better than the average of aligned sites = 948 Number in coding regions = 795 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 2 TTTTTAAAAATTTACAAAAATGAGAAAGAACACC 1 91 1 TTAAAATGAG 0.896563 -207 GGCTAATGGCTTGATAAAGCTTAGATTTTATCAT 1 125 1 TTAAAGTTAG 0.984741 -173 AAAAATCTATTTAATGAGAATTAGGTAAAAAAAA 1 159 1 TTAAGATTAG 0.949294 -139 AGATAAACATTGTAGCATTTTTAGATTTAAGAAT 1 250 0 TGAATTTTAG 0.933002 -48 TTTAGCGTTTTTAAGAATGATTAGTTATAATAAC 2 16 1 TTAATGTTAG 0.95335 -67 AGATTTTAGCTTGAGTGTTGTTAGTAGCGTTATT 2 44 0 TTAGTTTTAG 0.970239 -39 ACTGATTTCCTTAATAGATTTTAGCTTGAGTGTT 2 59 0 TTAGATTTAG 0.963273 -24 TTAATGGTAGTTTAACATGCTTAGAGATAAAACG 3 14 0 TTAATGTTAG 0.986275 -45 GTTACAATAATTTAGATTTTTTAGCTAGCATGTT 4 17 1 TTATTTTTAG 0.921994 -75 TCGCTTCAATTTAATCAAAATTAGATTACAATAT 5 19 1 TTAAAATTAG 0.968765 -58 ** * *** **** Masking position 4 Map Score: 12.2051 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 146 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 CATTATCATTTATGCTATAATTATGGGACA 1 37 0 TATGCTATAA 0.862445 -261 TAAGCTTTATCAAGCCATTAGCCGGTGTTC 1 118 0 CAAGCCATTA 0.51821 -180 ATGGCTTGATAAAGCTTAGATTTTATCATA 1 130 1 AAAGCTTAGA 0.85026 -168 ATGTAAAAAGCATTCTTAAATCTAAAAATG 1 239 1 CATTCTTAAA 0.870212 -59 TAAATCTAAAAATGCTACAATGTTTATCTT 1 255 1 AATGCTACAA 0.840507 -43 CATTCTTAAAAACGCTAAAAATTA 2 5 0 AACGCTAAAA 0.874058 -78 TATAACTAATCATTCTTAAAAACGCTAAAA 2 15 0 CATTCTTAAA 0.870212 -68 TAACAACACTCAAGCTAAAATCTATTAAGG 2 55 1 CAAGCTAAAA 0.981011 -28 GGTAGTTTAACATGCTTAGAGATAAAACGA 3 13 0 CATGCTTAGA 0.948363 -46 AATTTTTTGTAAGGCTAAAAAC 3 47 1 AAGGCTAAAA 0.874058 -12 TGCTAACATGCTAGCTAAAAAATCTAAATT 4 25 0 CTAGCTAAAA 0.8461 -67 TAACAATATCCATGCCTTAATGAATTGCTA 4 50 0 CATGCCTTAA 0.896729 -42 GACCCTTATTTAAGCTTTAAATAACTATAA 5 52 0 TAAGCTTTAA 0.819963 -25 ********** Masking position 10 Map Score: 9.96887 Number of sites scoring better than the average of aligned sites = 2259 Number in coding regions = 2015 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 4 TAAACCAACACAAAGGAGATACT 1 4 0 CAAAGGAGAT 0.969315 -294 ATGATAATGAAAAAGTAAATGAGAGTATGA 1 58 1 AAAAGTAAAT 0.78414 -240 AAAATTTACAAAAATGAGAAAGAACACCGG 1 97 1 AAAATGAGAA 0.853248 -201 TTAGGTAAAAAAAAGGGGTTGGCATCAATA 1 179 1 AAAAGGGGTT 0.968339 -119 GGTTGGCATCAATAGGGGGTTAAAAGGGGA 1 195 1 AATAGGGGGT 0.903948 -103 ATAGGGGGTTAAAAGGGGATATTTTTATAT 1 206 1 AAAAGGGGAT 0.991998 -92 CAATTTAATCAAAATTAGATTACAATATTA 5 25 1 AAAATTAGAT 0.884257 -52 ********** Masking position 4 Map Score: 3.42851 Number of sites scoring better than the average of aligned sites = 643 Number in coding regions = 497 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 5 TAAATGAGAGTATGAAAATTTTTAAAAATTT 1 73 1 TATGAAAATT 0.915162 -225 TTTAAAAATTTACAAAAATGAGAAAGAACAC 1 93 1 TACAAAAATA 0.937625 -205 TAGATTTTATCATAAAAATCTATTTAATGAG 1 146 1 CATAAAAATT 0.915162 -152 TTACATATTATATAAAAATATCCCCTTTTAA 1 214 0 TATAAAAATT 0.972266 -84 TTTTTAGCCTTACAAAAAATTTAATGGTAGT 3 37 0 TACAAAAAAT 0.937624 -22 GCTTTTGTTACAATAATTTAGATTTTTTA 4 9 1 TACAATAATT 0.969229 -83 AAAATTAGATTACAATATTATAGTTATTTAA 5 35 1 TACAATATTT 0.867362 -42 ********* * Masking position 5 Map Score: 3.30395 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 78 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 ********** No masking Map Score: 1.44541e-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: 1.44541e-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 8 ********** No masking Map Score: 1.44541e-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