AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00580_bsub_reg_300.orf -o00580_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 glpQ 98 glycerophosphoryl diester phosphodiesterase #2 glpT 296 glycerol-3-phosphate permease #3 yhdW 233 similar to glycerophosphodiester phosphodiesterase Motif number 1 GATTTCTCCTCCTTATAGATAAGC 1 85 0 GATCCCTCTT 0.956249 -14 TTAGGGAAGTGAATATTATCCTTTTACTAAATGC 2 63 0 GAATATCCTT 0.961697 -234 GGCCCAATTTGAAAATTACCCGTTTACATTCGCT 2 97 1 GAATACCCTT 0.992227 -200 GGAGAGCCAGGAATCCAACCCCTTTTGACAAGGG 2 192 1 GAACACCCTT 0.993952 -105 AAAAGAGCCAGAAAACACCCCTTGTCAAAAGGGG 2 210 0 GAACCCCCTG 0.980174 -87 TAATAATTATCCCCCTTTGCTGTTTGTG 2 279 0 AATTCCCCTT 0.965749 -18 GATCTCGCCTCCTTTTTTGCTATT 3 1 1 GATCCCTCTT 0.956249 -233 GTTCACAACAAAATATGATCCTTTATAATAGCAA 3 27 0 AAATATCCTT 0.890335 -207 TATGGCAGAAAAAATTCACCAGTTTGTATCGCGG 3 154 1 AAATACCATT 0.803988 -80 *** * **** ** Masking position 2 Map Score: 7.31377 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 445 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 2 AAACGGATGTAAACGGCGTGTTGGAAAACT 1 33 0 AAACGGCGTG 0.927577 -66 TGCTTATCTATAAGGAGGAGAAATC 1 84 1 TAAGGAGGAG 0.963693 -15 GAGCGAATGTAAACGGGTAATTTTCAAATT 2 102 0 AAACGGGTAA 0.900015 -195 CCCCTTGTCAAAAGGGGTTGGATTCCTGGC 2 197 0 AAAGGGGTTG 0.966423 -100 GTTTTTCGGGAAAGGAGGCACGCCACACAT 2 245 1 AAAGGAGGCA 0.971012 -52 CACAAACAGCAAAGGGGGATAATTATTA 2 279 1 AAAGGGGGAT 0.973219 -18 TAATAGCAAAAAAGGAGGCGAGATC 3 6 0 AAAGGAGGCG 0.991922 -228 AGAAATGCCCATACGAGGAGCTGACTTAGC 3 214 1 ATACGAGGAG 0.942244 -20 ********** Masking position 3 Map Score: 6.92984 Number of sites scoring better than the average of aligned sites = 993 Number in coding regions = 602 Number in noncoding regions = 391 Number of orfs with sites within 600 bp upstream = 441 Fraction of orfs with sites within 600 bp upstream = 0.070832 Motif number 3 CCTGTCTTTCATAATAAAAAACGGATGTAA 1 51 0 ATAATAAAAA 0.935623 -48 TTTTATGTTACTAGTAAAAAAATATAATTG 2 34 1 CTAGTAAAAA 0.843757 -263 CCTTTCCCGAAAAACAAAAAGAGCCAGAAA 2 230 0 AAAACAAAAA 0.917085 -67 ATCCTTTATAATAGCAAAAAAGGAGGCGAG 3 14 0 ATAGCAAAAA 0.984695 -220 AGGAATGCGTATAACTAAAAAAAGACACTC 3 106 0 ATAACTAAAA 0.917085 -128 CCATTCCGATATGGCAGAAAAAATTCACCA 3 145 1 ATGGCAGAAA 0.930173 -89 ATTTGATACAATAACAGAAATGCCCATACG 3 199 1 ATAACAGAAA 0.972863 -35 ********** Masking position 8 Map Score: 5.21906 Number of sites scoring better than the average of aligned sites = 495 Number in coding regions = 397 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 4 GATTTCTCCTCCTTATAGATAA 1 87 0 TTTCTCCTCC 0.935125 -12 CTTTAAACAGCCTCCCTCCAGATTTTTAT 2 10 1 GCCTCCCTCC 0.983697 -287 TGGATTCCTGGCTCTCCTCATCTCCATCCA 2 179 0 GCTCTCCTCA 0.989381 -118 TGGATGTGTGGCGTGCCTCCTTTCCCGAAA 2 248 0 GCGTGCCTCC 0.991063 -49 GATCTCGCCTCCTTTTTTGCTA 3 3 1 TCTCGCCTCC 0.990152 -231 TTAGTTATACGCATTCCTCAGCCCGGACCA 3 118 1 GCATTCCTCA 0.959101 -116 ********** Masking position 8 Map Score: 4.28164 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 286 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 TGTTGGAAAACTATTAATCTTTTATGTGTCTT 1 13 0 CTATTAATTT 0.963613 -86 TTACTAAATGCAATTATATTTTTTTACTAGTA 2 42 0 CAATTATTTT 0.921015 -255 AGGGAAGTGAATATTATCCTTTTACTAAATGC 2 63 0 ATATTATTTT 0.906108 -234 TCGCTCCGGACTATGATAATTTAAGAAAGCGC 2 126 1 CTATGATTTT 0.92116 -171 TCCATCCAAGCTATTAACTTATCATGATAGCG 2 155 0 CTATTAATAT 0.919804 -142 TCACAACAAAATATGATCCTTTATAATAGCAA 3 27 0 ATATGATTTT 0.88181 -207 ATGGGCATTTCTGTTATTGTATCAAATCCATA 3 194 0 CTGTTATTAT 0.890683 -40 ******* *** Masking position 6 Map Score: 2.89157 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 179 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 ATGTAAACGGCGTGTTGGAAAACTATTAAT 1 27 0 CGTGTTGGAA 0.972241 -72 GAAAACACCCCTTGTCAAAAGGGGTTGGAT 2 204 0 CTTGTCAAAA 0.929577 -93 TTGTTGTGAACATGTCGAAAGACCTAATTT 3 50 1 CATGTCGAAA 0.981289 -184 AGACACTCAGCGTATCAGAACACATTTCGT 3 84 0 CGTATCAGAA 0.972976 -150 TTTTTTCTGCCATATCGGAATGGTCCGGGC 3 138 0 CATATCGGAA 0.981289 -96 ********** Masking position 5 Map Score: 2.38156 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 212 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 GAAAGACACATAAAAGATTA 1 1 1 GAAAGACACA 0.955634 -98 TTTTTATTATGAAAGACAGGTAGTGCTTAT 1 61 1 GAAAGACAGG 0.979537 -38 GATAATTTAAGAAAGCGCTATCATGATAAG 2 140 1 GAAAGCGCTA 0.884515 -157 TGGAGATGAGGAGAGCCAGGAATCCAACCC 2 183 1 GAGAGCCAGG 0.984227 -114 GAAAAACAAAAAGAGCCAGAAAACACCCCT 2 222 0 AAGAGCCAGA 0.920914 -75 TGAACATGTCGAAAGACCTAATTTTCTGAC 3 56 1 GAAAGACCTA 0.955047 -178 ********** Masking position 4 Map Score: 1.62525 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 491 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 ********** No masking Map Score: 1.5372e-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 9 ********** No masking Map Score: 1.5372e-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 10 ********** No masking Map Score: 1.5372e-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