AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i079_Phospholipid_Biosynthesis_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 purT 230 phosphoribosylglycinamide formyltransferase 2 #2 mpr 143 extracellular metalloprotease #3 ybfK 165 similar to carboxylesterase #4 pssA 195 phosphatidylserine synthase Motif number 1 TTTGGGGGATTTCTTGTATGATGTTGCTGTTTA 1 59 1 TTCTTGAGAG 0.844276 -172 ATCTTTTAAATTCTTAAACGAAAGCAGACAAAT 1 114 0 TTCTTAAGAA 0.97124 -117 GATAAAATTATTATTGAGGGTTAAAATCTTTTA 1 139 0 TTATTGGGTA 0.837422 -92 AAATAAATTTTTATTAAAAAAGATAAAATTATT 1 160 0 TTATTAAAAA 0.937806 -71 AGGTTTCTGATTCTTATGATAAAACTTTTACGG 2 58 0 TTCTTAGTAA 0.813725 -86 AGAAACCTGATTATAATGTAAAAGTCTTCCATC 2 83 1 TTATAAGAAA 0.669256 -61 CCTTTTTTATTTATTGCAGGAAACCAAACTATA 3 37 1 TTATTGAGAA 0.974612 -129 TACTGGAAATTTATTATGTGAGATAATAAGAAA 3 70 1 TTATTAGGAA 0.979404 -96 TAGGTATTTTTTCTTACGAGACAAAAGGGGCGT 3 103 1 TTCTTAGGAA 0.975074 -63 TCAAATTCTATTATTATACAACATTTGTTACCT 4 47 0 TTATTAAAAA 0.937817 -149 GTTATCATGCTTATTGGAGAAAAATTTTTCCTG 4 107 1 TTATTGAAAA 0.933782 -89 ACCATCTATATTATTTGACGATAGTGATCGAAT 4 147 0 TTATTTAGAA 0.880331 -49 ****** * ** * Masking position 4 Map Score: 13.3143 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 201 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 AGACCACCACACCGACAGGAGGCATCCC 1 8 0 ACGACAGGAG 0.927199 -223 GTTTAGGAATAGAGAAAGCAGACCGTTATTT 1 87 1 AAGAAAGCAG 0.990956 -144 TAAATTCTTAAACGAAAGCAGACAAATAACG 1 110 0 ACGAAAGCAG 0.987344 -121 ATGGTTTGGAACAGATAGGAGGGGCAAAG 1 212 1 AAGATAGGAG 0.95512 -19 AAGTTTTATCATAAGAATCAGAAACCTGATT 2 64 1 AAAGAATCAG 0.74416 -80 AACCACCCGTATCGATGGAAGACTTTTACAT 2 98 0 ACGATGGAAG 0.827239 -46 GGTTGACACTAAAGGAGGGAGATGACAAA 2 125 1 AAGGAGGGAG 0.971543 -19 TGCAATAAATAAAAAAGGCAGTTCCCTTAAA 3 24 0 AAAAAGGCAG 0.970839 -142 ACCCGGAGGAAAAAGAAGAAG 3 155 1 AAAGAAGAAG 0.900815 -11 GAATGCTCCCAAAAAAAGCAGCATTCAAATT 4 73 0 AAAAAAGCAG 0.979062 -123 * ********* Masking position 10 Map Score: 11.0009 Number of sites scoring better than the average of aligned sites = 1273 Number in coding regions = 1053 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 234 Fraction of orfs with sites within 600 bp upstream = 0.0375843 Motif number 3 ATGTTGCTGTTTAGGAATAGAGAAAGCAGACCG 1 79 1 TAGGAAAAGA 0.922957 -152 AAATTTTTATTAAAAAAGATAAAATTATTATTG 1 156 0 TAAAAAAAAA 0.750687 -75 AACTGAAATATTTGAAAAATAAATTTTTATTAA 1 176 0 TTGAAAAAAA 0.938347 -55 GTTATAATGGTTTGGAACAGATAGGAGGGGCAA 1 206 1 TTGGAAAATA 0.850251 -25 AAACTTTTACGGAGAAAGAAAAAAACAGGCCTT 2 37 0 GAGAAAAAAA 0.959895 -107 AGTTTTATCATAAGAATCAGAAACCTGATTATA 2 65 1 TAGAATAAAA 0.829222 -79 TTTATTTATTGCAGGAAACCAAACTATATACTG 3 42 1 GAGGAACAAA 0.858128 -124 TGTGAGATAATAAGAAATAGGTATTTTTTCTTA 3 86 1 TAGAAAAGTA 0.908545 -80 AATCAAACCCGGAGGAAAAAGAAGAAG 3 149 1 GAGGAAAGAA 0.967782 -17 TAAGGAACATGAAAAGATTGGCA 4 1 1 TAGGAAAGAA 0.979575 -195 TTTGTTACCTTTTGAAAAATGAATGCCAATCTT 4 24 0 TTGAAAAGAA 0.934361 -172 * ***** * *** Masking position 6 Map Score: 8.68038 Number of sites scoring better than the average of aligned sites = 1157 Number in coding regions = 947 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 4 TTTAAGAATTTAAAAGATTTTAACCCTCAA 1 129 1 TAAAAGATTT 0.94552 -102 TAACCCTCAATAATAATTTTATCTTTTTTA 1 149 1 TAATAATTTT 0.889557 -82 TCTTTTTTAATAAAAATTTATTTTTCAAAT 1 170 1 TAAAAATTTA 0.80512 -61 CATTATAACTGAAATATTTGAAAAATAAAT 1 185 0 GAAATATTTG 0.648725 -46 TCTTTCTCCGTAAAAGTTTTATCATAAGAA 2 51 1 TAAAAGTTTT 0.970201 -93 GATTATAATGTAAAAGTCTTCCATCGATAC 2 91 1 TAAAAGTCTT 0.885774 -53 TTATCTCACATAATAAATTTCCAGTATATA 3 66 0 TAATAAATTT 0.810069 -100 TAAGGAACATGAAAAGATTGGCATTCATTT 4 11 1 GAAAAGATTG 0.890473 -185 GCTTATTGGAGAAAAATTTTTCCTGTAACG 4 115 1 GAAAAATTTT 0.954545 -81 ********** Masking position 3 Map Score: 4.65364 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 277 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 5 ********** No masking Map Score: 1.20325e-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: 1.20325e-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: 1.20325e-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