AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -icpxR9_aquae_opreg_100.orf -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 phoB 284 transcriptional regulator (PhoB-like) #2 xanB 33 mannose-6-phosphate isomerase/mannose-1-phosphate guanyl transferase #3 aq_592 96 hypothetical protein #4 motA 42 flagellar motor protein MotA #5 htrA 28 periplasmic serine protease Motif number 1 ATTAATAAGTCTTGAAATCTTATACTAATA 1 32 1 CTTGAAATCT 0.944001 -253 TACTAATATACTTAAATTTTCTATTAACAT 1 54 1 CTTAAATTTT 0.920659 -231 TTAACATTAATTTAAAACATTTCCTTAACC 1 77 1 TTTAAAACAT 0.934376 -208 TTAACCGAAACTTAAAATTTGGGGTTTAAA 1 101 1 CTTAAAATTT 0.988019 -184 AAATTTGGGGTTTAAAACCTTAAGTAAGGA 1 115 1 TTTAAAACCT 0.969771 -170 ATCCGCTTTCTTTAAAATATCGTTCTTCAG 1 255 0 TTTAAAATAT 0.970686 -30 ATTTTAGCAGTTTAAAATTATCCCCT 2 7 0 TTTAAAATTA 0.914607 -27 ACTTAGAATTTTAGCAGTTTA 2 23 0 CTTAGAATTT 0.94505 -11 CACCAAATCCTTTAAAATCTTTCTC 3 82 1 TTTAAAATCT 0.986774 -15 GGATTTCCTTTTTAAAATTTAAATT 4 6 0 TTTAAAATTT 0.987033 -37 ********** Masking position 6 Map Score: 17.5217 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 119 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 TAATATATTACTATGTTCGAGCTTT 1 4 0 CATGTTGAGC 0.928552 -281 CCTTAAGTAAGGAGGTGTGAGATGAAGGTCTT 1 132 1 GAGGTGGAGA 0.987552 -153 GGTGTGAGATGAAGGTCTTAGCAGTCAGGAAT 1 145 1 GAGGTCTAGC 0.995243 -140 AGGGTAATTAGTAGGTTTTTGAAAAAGAGGAA 1 192 1 GAGGTTTTGA 0.94653 -93 TGAAAAAGAGGAAGGTTGTAGCGGTTGTGAAC 1 211 1 GAGGTTTAGC 0.996053 -74 GCGTAGCTCAGCTGGTCAGAGCGGGGATCTCA 3 14 1 GTGGTCGAGC 0.988963 -83 GTCCCAGGTCGGAGGTTCGAGTCCTCCCGCCG 3 49 1 GAGGTTGAGT 0.990086 -48 * ***** **** Masking position 6 Map Score: 8.328 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 95 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 TCTCTTTCTGCCTCTTATTCCTGACTGCTA 1 163 0 CCTCTTATTC 0.979428 -122 TACTAATTACCCTCTCTTTCTGCCTCTTAT 1 175 0 CCTCTCTTTC 0.994121 -110 CTACAACCTTCCTCTTTTTCAAAAACCTAC 1 202 0 CCTCTTTTTC 0.993656 -83 ATTACAACATCCGCTTTCTTTAAAATATCG 1 263 0 CCGCTTTCTT 0.950016 -22 TATGAGATCCCCGCTCTGACCAGCTGAGCT 3 18 0 CCGCTCTGAC 0.970188 -79 ********** Masking position 5 Map Score: 4.23576 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 129 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 TCATCTCACACCTCCTTACTTAAGGTTTTA 1 127 0 CCTCCTTACT 0.976562 -158 TCTGCCTCTTATTCCTGACTGCTAAGACCT 1 157 0 ATTCCTGACT 0.830401 -128 ATTACCCTCTCTTTCTGCCTCTTATTCCTG 1 170 0 CTTTCTGCCT 0.969446 -115 ACCGCTACAACCTTCCTCTTTTTCAAAAAC 1 206 0 CCTTCCTCTT 0.874376 -79 AGGACTCGAACCTCCGACCTGGGACTTATG 3 44 0 CCTCCGACCT 0.976124 -53 AGGTTCGAGTCCTCCCGCCGCCACCAAATC 3 61 1 CCTCCCGCCG 0.990916 -36 ********** Masking position 3 Map Score: 0.92732 Number of sites scoring better than the average of aligned sites = 822 Number in coding regions = 731 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 CCAAATTTTAAGTTTCGGTTAAGGAAATGT 1 93 0 AGTTTCGGTT 0.957559 -192 GAAACTTAAAATTTGGGGTTTAAAACCTTA 1 107 1 ATTTGGGGTT 0.930429 -178 AGAGGAAGGTTGTAGCGGTTGTGAACAATC 1 217 1 TGTAGCGGTT 0.99051 -68 ACTTAGAATTTTAGCAGTTTAAAATTATC 2 15 0 TTTAGCAGTT 0.948784 -19 TCTAAATAAATTTATCGGATTTCCTTTTTA 4 22 0 TTTATCGGAT 0.928791 -21 ********** Masking position 3 Map Score: 0.349212 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 198 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 ********** No masking Map Score: -6.37056e-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: -6.37056e-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: -6.37056e-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