AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i166_Nitrate_Transport_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 ygaL 300 similar to nitrate ABC transporter (binding protein) #2 ytlA 150 ytlA Motif number 1 ATTGTTGAAAAACCTTGTTGTAACAGCTTT 1 74 1 AACCTTGTTG 0.931479 -227 CTTGTTGTAACAGCTTTTTATGACACTTAA 1 87 1 CAGCTTTTTA 0.936305 -214 ATCACTTACTCTGCTTGTTTCGCAAATAGA 1 145 0 CTGCTTGTTT 0.971539 -156 GATTTTTGATATCCTTGTTTATCACTTACT 1 165 0 ATCCTTGTTT 0.981974 -136 GATATGTCAACTCTTTTTTAAATACGATTT 1 190 0 CTCTTTTTTA 0.887516 -111 AACAGCCGCCTCCTTTTTTCTATATGCTT 2 10 1 CTCCTTTTTT 0.990016 -141 ACATCCGGAGAACCTGGTTAGGCATTCACA 2 56 1 AACCTGGTTA 0.862991 -95 TAGGCATTCACACATTTTTATACCCATCAT 2 74 1 CACATTTTTA 0.843488 -77 TCAAGTTAATATCCTTTTTTGCTTTACATA 2 108 0 ATCCTTTTTT 0.976914 -43 ATAGACAACCTCCTTATTTCGCATCAAGT 2 132 0 CTCCTTATTT 0.960726 -19 ********** Masking position 5 Map Score: 12.8588 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 995 Number in noncoding regions = 376 Number of orfs with sites within 600 bp upstream = 424 Fraction of orfs with sites within 600 bp upstream = 0.0681015 Motif number 2 GTCAATATTATTTTATAATTATT 1 4 1 AATATTATTT 0.959682 -297 ATATTATTTTATAATTATTATAAAATAGTT 1 15 1 ATAATTATTA 0.927347 -286 ATTAATAGAGATAACTATTTTATAATAATT 1 27 0 ATAACTATTT 0.951662 -274 TATTTCTCCAAAAATTATTAAGTGTCATAA 1 104 0 AAAATTATTA 0.959682 -197 TAGAGAAGGAAAAATTATTTCTCCAAAAAT 1 119 0 AAAATTATTT 0.977551 -182 CTCTTTTTTAAATACGATTTTTGATATCCT 1 180 0 AATACGATTT 0.876937 -121 ********** Masking position 4 Map Score: 5.08718 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 143 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 GTTACAACAAGGTTTTTCAACAATTTCGATACT 1 65 0 GGTTTTCAAA 0.97494 -236 AAGGAAAAATTATTTCTCCAAAAATTATTAAGT 1 111 0 TATTTTCCAA 0.806582 -190 TTACTCTGCTTGTTTCGCAAATAGAGAAGGAAA 1 137 0 TGTTTGCAAA 0.966222 -164 TTGATATCCTTGTTTATCACTTACTCTGCTTGT 1 157 0 TGTTTTCACA 0.961684 -144 TGAATTAACATGTTATTCAAACAAAAAAACAAT 1 229 1 TGTTATCAAA 0.972482 -72 CGGAGAACCTGGTTAGGCATTCACACATTTTTA 2 61 1 GGTTAGCATA 0.943572 -90 TCATACGATATGTAAAGCAAAAAAGGATATTAA 2 100 1 TGTAAGCAAA 0.924043 -51 ACAACCTCCTTATTTCGCATCAAGTTAATATCC 2 124 0 TATTTGCATA 0.915556 -27 ***** **** * Masking position 13 Map Score: 4.80774 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 359 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 TTCGATACTATATATCGATTAATAGAGATAAC 1 42 0 TATATCGTTA 0.911222 -259 AAAGAGTTGACATATCGGAATAATTTGAATTA 1 204 1 CATATCGAAA 0.976397 -97 GTAAGGAAAGCATATAGAAAAAAGGAGGCGGC 2 15 0 CATATAGAAA 0.952629 -136 TTTTGCTTTACATATCGTATGATGGGTATAAA 2 90 0 CATATCGATA 0.993419 -61 ACAACCTCCTTATTTCGCATCAAGTTAATATC 2 125 0 TATTTCGATA 0.950832 -26 ******* ** * Masking position 5 Map Score: 2.10268 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 77 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 GGAAAAATTATTTCTCCAAAAATTATTAAG 1 112 0 TTTCTCCAAA 0.983618 -189 GAATAACATGTTAATTCAAATTATTCCGAT 1 217 0 TTAATTCAAA 0.965249 -84 GAATTAACATGTTATTCAAACAAAAAAACA 1 230 1 GTTATTCAAA 0.942246 -71 TATGCTTTCCTTACTCCAAAATTACATCCG 2 33 1 TTACTCCAAA 0.98511 -118 ********** Masking position 5 Map Score: 1.5616 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 199 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 ********** No masking Map Score: -2.17836e-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: -2.17836e-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: -2.17836e-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