AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i348_weak9_hinf_reg_300.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0813 77 carbon storage regulator (csrA) #2 HI0814 187 alanyl-tRNA synthetase (alaS) #3 HI0815 101 universal stress protein A (uspA) #4 HI0817 170 conserved hypothetical protein #5 HI0819 37 galactokinase (galK) #6 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) Motif number 1 TTTGCATTTATTAGATATCCTATCAATCAAGGAACG 1 37 0 TTATTATCAA 0.872253 -41 TTTAAGTTATTTCAGATTATTCAAAAAACAATTTCT 2 17 0 TTTTTCAAAA 0.753433 -171 TTGCATATTTTTGAAATTTATAAAAAGGCTTTTTGC 2 109 0 TTTTTAAAAA 0.970718 -79 AGAATCCTTGTTACCCATAATAAAAATAAAAACTAA 2 157 0 TTATTAAAAA 0.977212 -31 AGTACACAGTTTTTTATTGCTCAAAATGTTAGCATT 3 34 1 TTTTTCAAAA 0.922126 -68 GCCATTATTTATAATAAAAATGTCATTACA 4 5 1 TTATTAAAAA 0.930636 -166 CTGAGTAAATTTGAAATTAGTGTAAACCTTTGTAAA 4 135 0 TTTTTGTAAA 0.78445 -36 AATATAAGATTTATAGATTATAACAAGGAAAAAGTT 6 11 0 TTATTAACAA 0.964866 -197 TTATCGTAAATTATTTATGATCAAAATATAAGATTT 6 35 0 TTATTCAAAA 0.977996 -173 TAAATAAACCGTGATCTTTGTCACAAAATAAGAAAA 6 125 0 GTTTTCACAA 0.869648 -83 AATGTAATCGTTTACATTGATAAAAAACAGGAGTCA 6 180 1 TTTTTAAAAA 0.893378 -28 ** ** ****** Masking position 15 Map Score: 13.8947 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 204 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 2 AAAATTTAAGTTATTTCAGATTATTCAAAAA 2 26 0 TTATTTCAAT 0.917302 -162 ATAAAAAGGCTTTTTGCCAAAACTCCAAAAT 2 95 0 TTTTTGCCAA 0.785905 -93 AGTCGCCCTATTTTTGCATATTTTTGAAATT 2 127 0 TTTTTGCAAT 0.847929 -61 CTTAGTTTTTATTTTTATTATGGGTAACAAG 2 156 1 ATTTTTATAT 0.630987 -32 ACACAGTTTTTTATTGCTCAAAATGTTAGCA 3 37 1 TTATTGCTAA 0.885321 -65 GCCATTATTTATAATAAAAATGTCA 4 5 1 TTATTTATAT 0.95801 -166 GATGGCTTTTTTATTTACAAAGGTTTACACT 4 122 1 TTATTTACAA 0.855535 -49 AGGTTTACACTAATTTCAAATTTACTCAGGA 4 142 1 TAATTTCAAT 0.675504 -29 AATATAAGATTTATAGATTATAACAAGGAAA 6 16 0 TTATAGATAT 0.599282 -192 TTATCGTAAATTATTTATGATCAAAATATAA 6 40 0 TTATTTATAT 0.958179 -168 ATAAGCAAAATTTTTTATGATTTAGTTCATA 6 95 0 TTTTTTATAT 0.945647 -113 AAATTTTGCTTATTTTCTTATTTTGTGACAA 6 113 1 TATTTTCTAT 0.798732 -95 AGATCACGGTTTATTTACAATAATTTAGTAT 6 144 1 TTATTTACAT 0.934693 -64 TTGACTCCTGTTTTTTATCAATGTAAACGAT 6 186 0 TTTTTTATAA 0.879063 -22 ******** ** Masking position 10 Map Score: 11.2657 Number of sites scoring better than the average of aligned sites = 779 Number in coding regions = 581 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 3 ATTATTCAAAAAACAATTTCTTGTTAA 2 6 0 AACAATTCTT 0.845033 -182 TAAAAAGAATCCTTGTTACCCATA 2 174 0 AAAGAATCTT 0.914539 -14 AATCGACTCCTTAACTGATTGG 3 90 0 AACGACTCTT 0.982804 -12 TTAATTGGTCAAGCGATGGCTTTTTTATTTAC 4 108 1 AACGATGCTT 0.821628 -63 AATAGATTTCCTGAGTAAATTT 4 159 0 AAAGATTCCT 0.94043 -12 GATAAATTGAAAGCGGTTACTTTCATAAGTAT 6 66 1 AACGGTTCTT 0.967037 -142 TTATCAATGTAAACGATTACATTAATTTATAC 6 171 0 AACGATTCAT 0.975115 -37 ** ***** *** Masking position 2 Map Score: 4.61043 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 75 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 TTACCCATAATAAAAATAAAAACTAAGTCG 2 153 0 TAAAAATAAA 0.863216 -35 ACATTTTTATTATAAATAATGGC 4 4 0 TATAAATAAT 0.958924 -167 TGTAAACCTTTGTAAATAAAAAAGCCATCG 4 121 0 TGTAAATAAA 0.953271 -50 ATATTTTGATCATAAATAATTTACGATAAA 6 42 1 CATAAATAAT 0.940163 -166 TGAACTAAATCATAAAAAATTTTGCTTATT 6 97 1 CATAAAAAAT 0.765368 -111 ACTAAATTATTGTAAATAAACCGTGATCTT 6 143 0 TGTAAATAAA 0.953271 -65 AATAATTTAGTATAAATTAATGTAATCGTT 6 162 1 TATAAATTAA 0.863216 -46 ********** Masking position 5 Map Score: 4.70993 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 123 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 CTATCAATCAAGGAACGGTTGGCATTCCAC 1 24 0 AGGAACGGTT 0.969051 -54 GCTATTTGAGAAGTGCGGTTAAAATTTAAG 2 47 0 AAGTGCGGTT 0.991677 -141 TAGCGTCGTGAAGTGCGGTTTTATTTTGGA 2 73 1 AAGTGCGGTT 0.991677 -115 CTTAACTGATTGGTTCGGTTTTTAACTGGC 3 73 0 TGGTTCGGTT 0.969054 -29 ********** Masking position 9 Map Score: 2.4312 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 293 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 6 GTGCGGTTAAAATTTAAGTTATTTCAGATTA 2 34 0 AATTTAATTA 0.887083 -154 TTGACCAATTAAATTAGATTAAGAGGCTGGT 4 89 0 AAATTAGTTA 0.956371 -82 AGTAAATTTGAAATTAGTGTAAACCTTTGTA 4 137 0 AAATTAGGTA 0.959563 -34 AACCGCTTTCAATTTATCGTAAATTATTTAT 6 53 0 AATTTATGTA 0.894562 -155 AATCATAAAAAATTTTGCTTATTTTCTTATT 6 104 1 AATTTTGTTA 0.910051 -104 TATTTACAATAATTTAGTATAAATTAATGTA 6 155 1 AATTTAGATA 0.941966 -53 ******* *** Masking position 5 Map Score: 1.28896 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 37 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 CTTTTATCTCCTTAGTTTGCATTTATT 1 61 0 CTCCTTAGTT 0.965899 -17 TTTTAACTGGCTCCAATGCTAACATTTTGA 3 54 0 CTCCAATGCT 0.905042 -48 AATCGACTCCTTAACTGATTGGTTCG 3 86 0 CTCCTTAACT 0.973828 -16 CACCACCAGCCTCTTAATCTAATTTAATTG 4 85 1 CTCTTAATCT 0.920153 -86 GTCAGTCTCCCTCTTTAGCTTTAGCAAAGA 5 15 1 CTCTTTAGCT 0.984911 -23 ********** Masking position 2 Map Score: 0.805307 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 21 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 TAATAAAAATAAAAACTAAGTCGCCCTATT 2 146 0 AAAAACTAAG 0.905999 -42 TTGAGCAATAAAAAACTGTGTACTAGATCA 3 28 0 AAAAACTGTG 0.98155 -74 GGAGCCAGTTAAAAACCGAACCAATCAGTT 3 70 1 AAAAACCGAA 0.895777 -32 TTCTAGCGTTAAAAGCTGTGACGCACCACC 4 62 1 AAAAGCTGTG 0.977624 -109 TTGTAAATAAAAAAGCCATCGCTTGACCAA 4 112 0 AAAAGCCATC 0.86941 -59 ATTATTGTAAATAAACCGTGATCTTTGTCA 6 138 0 ATAAACCGTG 0.953801 -70 ********** Masking position 4 Map Score: 1.70305 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 171 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 ********** No masking Map Score: -1.79524e-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: -1.79524e-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 11 ********** No masking Map Score: -1.79524e-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