AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_hinf_reg_100.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 0.997712 -47 GTCAATTTTGACCGCATTTTTAGCGGTGTT 3 28 1 ACCGCATTTT 0.977165 -29 GCTAAATATAACCGCACTTTTTTATTAAAA 5 30 0 ACCGCACTTT 0.997712 -31 TGAGCTAACGACCCCACTGTATTAAATGG 7 10 0 ACCCCACTGT 0.956949 -291 TCGGTAGAGCAGCGGACTTTTAATCCGTTG 7 41 1 AGCGGACTTT 0.975897 -260 TTCACGACCCACCACTCTCTGATTTAGTTG 7 88 1 ACCACTCTCT 0.897142 -213 TTGGTAGAGTAGCGGACTCTTAATCCGTCA 7 140 1 AGCGGACTCT 0.958159 -161 AACGGAAATTACCGCACTTTAAGAAATAAA 8 133 1 ACCGCACTTT 0.997712 -133 TTCACCGCTCTTCTTAGCATAAA 9 4 1 ACCGCTCTTC 0.969905 -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 ATGTGGGGGCAAATGTAATTTG 2 3 1 GTGGGGGCAA 0.984432 -48 TTCACATCTCGTAGGGGCAAATTACATTTG 2 20 0 GTAGGGGCAA 0.875952 -31 ATGTGAAAAAGTGCGGTCAATTTTGACCGC 3 13 1 GTGCGGTCAA 0.9879 -44 ACCGCTAAAAATGCGGTCAAAATTGACCGC 3 25 0 ATGCGGTCAA 0.854186 -32 TTTTAGCGGTGTTGGGGGATAG 3 45 1 GTTGGGGGAT 0.918802 -12 TAATAAAAAAGTGCGGTTATATTTAGCATA 5 33 1 GTGCGGTTAT 0.973572 -28 ATTTAATACAGTGGGGTCGTTAGCTCAGTC 7 13 1 GTGGGGTCGT 0.992254 -288 ATCAGAGAGTGGTGGGTCGTGAAGGATTCG 7 81 0 GGTGGGTCGT 0.947543 -220 TAGTTGTCCAGTTGGGTTGTTAGCTCAGTT 7 112 1 GTTGGGTTGT 0.939117 -189 TAATAAAAATGGTGGGTTGTGAGAGACTAG 7 180 0 GGTGGGTTGT 0.855492 -121 ATTTCTTAAAGTGCGGTAATTTCCGTTCTT 8 130 0 GTGCGGTAAT 0.935813 -136 ATGCTAAGAAGAGCGGTGAA 9 1 0 GAGCGGTGAA 0.802553 -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 CTCACAACCCACCATTTTTATTATTCATCC 7 187 1 ACCATTTTTA 0.941776 -114 ATTCATCCCTAATATTTTAAATTTCTTTAA 7 209 1 AATATTTTAA 0.875859 -92 TAAATTCTTGACTATTTTTAGCGGTTATTG 7 245 1 ACTATTTTTA 0.950603 -56 AAATTTGGCGAAAATTTTTACTTTAAAATA 8 23 0 AAAATTTTTA 0.981435 -243 AGGGGAAAACAAAATTTTCAGGCAAGAAAA 8 66 0 AAAATTTTCA 0.951235 -200 TAAGAAATAAAAAATTTTTAAAATTTTCTC 8 152 1 AAAATTTTTA 0.981435 -114 CCCGAATTTTAAAATTTTTACTAGGAGTAC 8 243 1 AAAATTTTTA 0.981435 -23 ********** Masking position 4 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 0.951284 -274 GGATTAAAAGTCCGCTGCTCTACCGACTGA 7 37 0 TCCGCTGCTC 0.988937 -264 GGACTTTTAATCCGTTGGTCGAAGGTTCGA 7 54 1 TCCGTTGGTC 0.995176 -247 GGTTGTTAGCTCAGTTGGTAGAGTAGCGGA 7 126 1 TCAGTTGGTA 0.959273 -175 GGATTAAGAGTCCGCTACTCTACCAACTGA 7 136 0 TCCGCTACTC 0.967954 -165 GGACTCTTAATCCGTCAGTCGAGAGTTCTA 7 153 1 TCCGTCAGTC 0.98299 -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 0.962215 -16 TGCTCTACCGACTGAGCTAACGACCCCACT 7 22 0 ACTGAGCTAA 0.970757 -279 TACTCTACCAACTGAGCTAACAACCCAACT 7 121 0 ACTGAGCTAA 0.970757 -180 TAGTCAAGAATTTAAGCTAATTAAAGAAAT 7 229 0 TTTAAGCTAA 0.962206 -72 GAAAAAGGGATTTGTGATAAATTTGGCGAA 8 41 0 TTTGTGATAA 0.860996 -225 ACGCCCTTTGTTTATGCTAAGAAGAGCGGT 9 14 0 TTTATGCTAA 0.962206 -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 GCATTCACTAGAATTGAAAAAAGGAAAGTT 4 37 1 GAATTGAAAA 0.793542 -23 TTGAAAAAAGGAAAGTTAAA 4 50 1 GAAAGTTAAA 0.889811 -10 AAAAGATAAGCAGTATATTT 5 1 1 AAAAGATAAG 0.538339 -60 AAATTAGTCAGATATGTAAGTATTGCGCAA 6 13 1 GATATGTAAG 0.686265 -40 TATTAGGGATGAATAATAAAAATGGTGGGT 7 193 0 GAATAATAAA 0.608306 -108 GCTAATTAAAGAAATTTAAAATATTAGGGA 7 214 0 GAAATTTAAA 0.949445 -87 ATACCCGACTAAAATTTAAGGGTATTCTAC 7 277 0 AAAATTTAAG 0.813105 -24 CGCACTTTAAGAAATAAAAAATTTTTAAAA 8 145 1 GAAATAAAAA 0.743899 -121 TTTCAAGAGAAAATTTTAAAAATTTTTTAT 8 158 0 AAATTTTAAA 0.796532 -108 TATTTATTACGAATTGTAAGATGTGGATAT 8 197 0 GAATTGTAAG 0.93543 -69 GCCCTACCCCGAATTTTAAAATTTTTACTA 8 236 1 GAATTTTAAA 0.940491 -30 ********** Masking position 8 Map Score: 4.75036 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 370 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 7 TTGTAAGTTAATATCATTGCG 1 1 1 TTGTAAGTAA 0.809517 -63 AGAGCAATGGTTTTAAAGGAACGATATAA 1 45 1 TTTTAAAGAA 0.935072 -19 GTGAATGCCATTGTCAGATAATGGCAACTAA 4 14 0 TTGTCAGAAA 0.866384 -46 GCAGTATATTTTTTAATAAAAAAGTGCGGTT 5 20 1 TTTTAATAAA 0.720782 -41 TTCTTTCCTATTTTAAAGTAAAAATTTTCGC 8 15 1 TTTTAAAGAA 0.935072 -251 GAAAACAAAATTTTCAGGCAAGAAAAAGGGA 8 61 0 TTTTCAGGAA 0.826582 -205 CGTTCTTGTTTTTCAAAATAAGTCTCAAATG 8 106 0 TTTCAAAAAA 0.870992 -160 TTCTTTCGCATTTCAAGAGAAAATTTTAAAA 8 167 0 TTTCAAGAAA 0.927859 -99 ******** ** Masking position 6 Map Score: 2.37803 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 211 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 8 TGACCGCATTTTTAGCGGTGTTGGGGGATA 3 36 1 TTTAGCGGTG 0.979282 -21 GCAATTAATTTTTAGGGATTCTTT 6 39 1 TTTAGGGATT 0.951816 -14 AATTTAAAATATTAGGGATGAATAATAAAA 7 202 0 ATTAGGGATG 0.942456 -99 CTTGACTATTTTTAGCGGTTATTGTGGTAG 7 251 1 TTTAGCGGTT 0.968306 -50 CCGACTAAAATTTAAGGGTATTCTACCACA 7 273 0 TTTAAGGGTA 0.900446 -28 AAATTTTAAAATTCGGGGTAGGGCTTTTAG 8 230 0 ATTCGGGGTA 0.919714 -36 ********** Masking position 3 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 9 GTCAAAATTGACCGCACTTTTTCACATGA 3 10 0 ACCGCACTTT 0.993196 -47 GCTAAATATAACCGCACTTTTTTATTAAAA 5 30 0 ACCGCACTTT 0.993196 -31 TCTCTCACAACCCACCATTTTTATTATTCA 7 184 1 CCCACCATTT 0.896383 -117 AACGGAAATTACCGCACTTTAAGAAATAAA 8 133 1 ACCGCACTTT 0.993196 -133 GGCGTGTTTCCACGCCCTTTGTTTATGCTA 9 25 0 CACGCCCTTT 0.991869 -26 GGCGTGGAAACACGCCCTTTTG 9 39 1 CACGCCCTTT 0.991869 -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 AGTGTTATTTATTCACATCTCGTAG 2 36 0 TTATTTATTA 0.918243 -15 ATAACCGCACTTTTTTATTAAAAAATATACT 5 22 0 TTTTTTATTA 0.918243 -39 TTATTTCTTTCCTATTTTAAA 8 1 1 TTATTTCTTC 0.965752 -265 TTGGCGAAAATTTTTACTTTAAAATAGGAAA 8 18 0 TTTTTACTTA 0.837548 -248 TCACAAATCCCTTTTTCTTGCCTGAAAATTT 8 54 1 CTTTTTCTTC 0.941067 -212 TAAAAATTTTTTATTTCTTAAAGTGCGGTAA 8 141 0 TTATTTCTTA 0.966294 -125 ATTTTTAAAATTTTCTCTTGAAATGCGAAAG 8 165 1 TTTTCTCTTA 0.884278 -101 GCTTTTAGACCTATTTATTACGAATTGTAAG 8 207 0 CTATTTATTC 0.861907 -59 ********* * Masking position 4 Map Score: 4.63198 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 219 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 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 Motif number 13 ********** 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