AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_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 HI0071 63 heat shock protein (grpE) #2 HI0374 50 H. influenzae predicted coding region HI0374 #3 HI0376 56 conserved hypothetical protein #4 HI0377 59 iscU protein (iscU) #5 HI0378 60 nifS protein (nifS) #6 HI0379 52 conserved hypothetical protein #7 HI0380 300 conserved hypothetical protein #8 HI1237 265 heat shock protein 70 (dnaK) #9 HI1238 50 heat shock protein (dnaJ) Motif number 1 GTCAAAATTGACCGCACTTTTTCACATGA 3 10 0 ACCGCACTTT 0.997463 -47 GTCAATTTTGACCGCATTTTTAGCGGTGTT 3 28 1 ACCGCATTTT 0.974735 -29 GCTAAATATAACCGCACTTTTTTATTAAAA 5 30 0 ACCGCACTTT 0.997463 -31 TGAGCTAACGACCCCACTGTATTAAATGG 7 10 0 ACCCCACTGT 0.952474 -291 TCGGTAGAGCAGCGGACTTTTAATCCGTTG 7 41 1 AGCGGACTTT 0.973337 -260 TTCACGACCCACCACTCTCTGATTTAGTTG 7 88 1 ACCACTCTCT 0.887182 -213 TTGGTAGAGTAGCGGACTCTTAATCCGTCA 7 140 1 AGCGGACTCT 0.953814 -161 AACGGAAATTACCGCACTTTAAGAAATAAA 8 133 1 ACCGCACTTT 0.997463 -133 TTCACCGCTCTTCTTAGCATAAA 9 4 1 ACCGCTCTTC 0.966729 -47 ********** Masking position 8 Map Score: 18.1385 Number of sites scoring better than the average of aligned sites = 1786 Number in coding regions = 1227 Number in noncoding regions = 559 Number of orfs with sites within 600 bp upstream = 346 Fraction of orfs with sites within 600 bp upstream = 0.0555734 Motif number 2 CAAATTACATTTGCCCCCACAT 2 3 0 TTGCCCCCAC 0.983883 -48 CAAATGTAATTTGCCCCTACGAGATGTGAA 2 20 1 TTGCCCCTAC 0.872076 -31 GCGGTCAAAATTGACCGCACTTTTTCACAT 3 13 0 TTGACCGCAC 0.987472 -44 GCGGTCAATTTTGACCGCATTTTTAGCGGT 3 25 1 TTGACCGCAT 0.849746 -32 CTATCCCCCAACACCGCTAAAA 3 45 0 ATCCCCCAAC 0.916136 -12 TATGCTAAATATAACCGCACTTTTTTATTA 5 33 0 ATAACCGCAC 0.97265 -28 GACTGAGCTAACGACCCCACTGTATTAAAT 7 13 0 ACGACCCCAC 0.991979 -288 CGAATCCTTCACGACCCACCACTCTCTGAT 7 81 1 ACGACCCACC 0.945765 -220 AACTGAGCTAACAACCCAACTGGACAACTA 7 112 0 ACAACCCAAC 0.937072 -189 CTAGTCTCTCACAACCCACCATTTTTATTA 7 180 1 ACAACCCACC 0.851085 -121 AAGAACGGAAATTACCGCACTTTAAGAAAT 8 130 1 ATTACCGCAC 0.933665 -136 TTCACCGCTCTTCTTAGCAT 9 1 1 TTCACCGCTC 0.796914 -50 ********** Masking position 5 Map Score: 14.0277 Number of sites scoring better than the average of aligned sites = 1210 Number in coding regions = 827 Number in noncoding regions = 383 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 3 GGATGAATAATAAAAATGGTGGGTTGTGAG 7 187 0 TAAAAATGGT 0.935611 -114 TTAAAGAAATTTAAAATATTAGGGATGAAT 7 209 0 TTAAAATATT 0.863725 -92 CAATAACCGCTAAAAATAGTCAAGAATTTA 7 245 0 TAAAAATAGT 0.945319 -56 TATTTTAAAGTAAAAATTTTCGCCAAATTT 8 23 1 TAAAAATTTT 0.979413 -243 TTTTCTTGCCTGAAAATTTTGTTTTCCCCT 8 66 1 TGAAAATTTT 0.946017 -200 GAGAAAATTTTAAAAATTTTTTATTTCTTA 8 152 0 TAAAAATTTT 0.979413 -114 GTACTCCTAGTAAAAATTTTAAAATTCGGG 8 243 0 TAAAAATTTT 0.979413 -23 ********** Masking position 5 Map Score: 8.58377 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 114 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 4 GGTCGTTAGCTCAGTCGGTAGAGCAGCGGA 7 27 1 TCAGTCGGTA 0.947781 -274 GGATTAAAAGTCCGCTGCTCTACCGACTGA 7 37 0 TCCGCTGCTC 0.988107 -264 GGACTTTTAATCCGTTGGTCGAAGGTTCGA 7 54 1 TCCGTTGGTC 0.994812 -247 GGTTGTTAGCTCAGTTGGTAGAGTAGCGGA 7 126 1 TCAGTTGGTA 0.956318 -175 GGATTAAGAGTCCGCTACTCTACCAACTGA 7 136 0 TCCGCTACTC 0.965606 -165 GGACTCTTAATCCGTCAGTCGAGAGTTCTA 7 153 1 TCCGTCAGTC 0.981723 -148 ********** Masking position 9 Map Score: 5.91135 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 16 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 TCCTAAATTATGCTAAATATAACCGC 5 45 0 ATTATGCTAA 0.963354 -16 TGCTCTACCGACTGAGCTAACGACCCCACT 7 22 0 ACTGAGCTAA 0.971647 -279 TACTCTACCAACTGAGCTAACAACCCAACT 7 121 0 ACTGAGCTAA 0.971647 -180 TAGTCAAGAATTTAAGCTAATTAAAGAAAT 7 229 0 TTTAAGCTAA 0.963345 -72 GAAAAAGGGATTTGTGATAAATTTGGCGAA 8 41 0 TTTGTGATAA 0.864757 -225 ACGCCCTTTGTTTATGCTAAGAAGAGCGGT 9 14 0 TTTATGCTAA 0.963345 -37 ********** Masking position 3 Map Score: 4.50169 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 69 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 AGTGTTATTTATTCACATCTCGTAGGGGCA 2 31 0 TTTTCACTCT 0.963549 -20 TAACTTTCCTTTTTTCAATTCTAGTGAATGCC 4 36 0 TTTTCAATCT 0.906466 -24 ACCATTTTTATTATTCATCCCTAATATTTTAA 7 197 1 TTTTCATCCT 0.985042 -104 TTATTTCTTTCCTATTTTAAAGT 8 2 1 TATTCTTCCT 0.913041 -264 CACAAATCCCTTTTTCTTGCCTGAAAATTTTG 8 55 1 TTTTCTTCCT 0.980611 -211 CCTGAAAATTTTGTTTTCCCCTTGAAGTTCAT 8 74 1 TTTTTTCCCT 0.919601 -192 ATTTTAAAAATTTTTTATTTCTTAAAGTGCGG 8 144 0 TTTTTATTCT 0.896887 -122 ** ***** *** Masking position 5 Map Score: 3.39845 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 103 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 TATCCCCCAACACCGCTAAAAATGCGGTCA 3 36 0 CACCGCTAAA 0.97907 -21 AAAGAATCCCTAAAAATTAATTGC 6 39 0 AATCCCTAAA 0.951337 -14 TTTTATTATTCATCCCTAATATTTTAAATT 7 202 1 CATCCCTAAT 0.941891 -99 CTACCACAATAACCGCTAAAAATAGTCAAG 7 251 0 AACCGCTAAA 0.967986 -50 TGTGGTAGAATACCCTTAAATTTTAGTCGG 7 273 1 TACCCTTAAA 0.899512 -28 CTAAAAGCCCTACCCCGAATTTTAAAATTT 8 230 1 TACCCCGAAT 0.918945 -36 ********** Masking position 8 Map Score: 1.93306 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 79 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 GCAATGATATTAACTTACAA 1 1 0 TAACTTACAA 0.928799 -63 TAGTTGCCATTATCTGACAATGGCATTCAC 4 15 1 TATCTGACAA 0.98516 -45 AATACTTACATATCTGACTAATTTAG 6 7 0 TATCTGACTA 0.95278 -46 AGAGTTCTAGTCTCTCACAACCCACCATTT 7 174 1 TCTCTCACAA 0.94203 -127 AGAATATCCACATCTTACAATTCGTAATAA 8 194 1 CATCTTACAA 0.950821 -72 ********** Masking position 5 Map Score: 1.23111 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 19 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 GTCAAAATTGACCGCACTTTTTCACATGA 3 10 0 ACCGCACTTT 0.993367 -47 GCTAAATATAACCGCACTTTTTTATTAAAA 5 30 0 ACCGCACTTT 0.993367 -31 TCTCTCACAACCCACCATTTTTATTATTCA 7 184 1 CCCACCATTT 0.898753 -117 AACGGAAATTACCGCACTTTAAGAAATAAA 8 133 1 ACCGCACTTT 0.993367 -133 GGCGTGTTTCCACGCCCTTTGTTTATGCTA 9 25 0 CACGCCCTTT 0.992074 -26 GGCGTGGAAACACGCCCTTTTG 9 39 1 CACGCCCTTT 0.992074 -12 ********** Masking position 8 Map Score: 11.7247 Number of sites scoring better than the average of aligned sites = 1189 Number in coding regions = 753 Number in noncoding regions = 436 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 10 ********** No masking Map Score: 2.29806e-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 11 ********** No masking Map Score: 2.29806e-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 12 ********** No masking Map Score: 2.29806e-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