AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i175_biotin_biosynthesis1_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 HI1019 300 thiamin ABC transporter, periplasmic-binding protein (tbpA) #2 HI1022 112 biotin synthetase (bioB) #3 HI1556 59 2-hydroxyacid dehydrogenase #4 HI1560 22 H. influenzae predicted coding region HI1560 #5 HI1561 106 peptide chain release factor 1 (prfA) #6 HI1562 252 H. influenzae predicted coding region HI1562 #7 HI1563 32 conserved hypothetical protein #8 HI1564 32 H. influenzae predicted coding region HI1564 #9 HI1564.1 284 H. influenzae predicted coding region HI1564.1 Motif number 1 TTTTGTATAGATTTCTTTAATTTACAATGAGTTA 1 12 1 ATTCTATTTA 0.934678 -289 TTACAATGAGTTATCTTCATTTTTATAGACTAGT 1 33 1 TTACTTTTTT 0.843295 -268 ATGTAGAAAGTTTATTTCTTTTTAAAAAGCCGTT 1 108 1 TTTTTTTTTA 0.826001 -193 TTTCGTCATTATTGCTGCCTTTTAATCATAAATA 1 266 1 ATTCTTTTTA 0.961668 -35 TAATTGCTCCTTTTTTATATACAAAG 3 44 0 ATTCTTTTTT 0.977771 -16 CTCAGACGCTTTATTTGTGATTTACCCA 5 5 0 TTATTATTTA 0.442089 -102 AGTGATCAAAATTGCTCACTTTTTTCAGTCTTAA 6 19 1 ATTCTTTTTT 0.977771 -234 TCCTAATTAAATAGTTCAATTTTTAATCATTTCA 6 67 1 ATATTTTTTT 0.853519 -186 GTCGCCTTGTTTTAGTGTGTTTTTGATTTGCCAA 6 182 1 TTTGTTTTTT 0.848502 -71 TTCTTCTTTAATTGCTTCAATTTTTTCTTGAAGA 6 226 0 ATTCTATTTT 0.961668 -27 TTAATCTAAAATTGGTCATATTTAGTCCTATAAA 9 50 1 ATTGTATTTA 0.813374 -235 TTTGAGAATTATTATTATTTTTTTTATAGGACTA 9 72 0 ATTTTTTTTT 0.952176 -213 AATAGTTTTTATTTCTTGATTTTTATCAAAAATC 9 149 0 ATTCTTTTTT 0.977771 -136 AATAAAAACTATTCTTATTATTTTCTGTATTTAA 9 170 1 ATTTTATTTT 0.919066 -115 *** ** ***** Masking position 6 Map Score: 15.6084 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 354 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 2 ACCACGCTTTTTATACTTTCTTAATTGATGAA 2 62 0 TTATACTCTT 0.954198 -51 CGTGGTGTTTTTAACCGCACTTTCAAAGGAAA 2 88 1 TTAACCCCTT 0.988208 -25 GCGGTCAAAATTAACCGCACTTTTGATGAAAT 3 11 0 TTAACCCCTT 0.988208 -49 GCGGTTAATTTTGACCGCACTTTGTATATAAA 3 25 1 TTGACCCCTT 0.987973 -35 ATACTGGGTGTTGTACTCTCTTTACAGAGAGT 6 109 1 TTGTACCCTT 0.981217 -144 TTATGCTTTGTTGTACTCTCTGTAAAGAGAGT 6 123 0 TTGTACCCTG 0.932775 -130 CAATTTTAGATTAAACGTGCTTGCCTATTCCG 9 32 0 TTAAACTCTT 0.970948 -253 TTTTCTGTATTTAAACCTGCTTGTTTCCTATA 9 190 1 TTAAACTCTT 0.970948 -95 ****** * *** Masking position 2 Map Score: 10.4177 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 292 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 3 GGTTAAAAACACCACGCTTTTTATACTTTC 2 74 0 ACCACGCTTT 0.982186 -39 GGTGTTTTTAACCGCACTTTCAAAGGAAAA 2 91 1 ACCGCACTTT 0.997239 -22 GTCAAAATTAACCGCACTTTTGATGAAAT 3 10 0 ACCGCACTTT 0.997239 -50 GTTAATTTTGACCGCACTTTGTATATAAAA 3 28 1 ACCGCACTTT 0.997239 -32 ********** Masking position 8 Map Score: 8.0367 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 4 ACATTTTCTGAAAAAATAAAGGGGCTGACG 1 82 0 AAAAAATAAA 0.867134 -219 TATATGGTAGAAACAATCAATTCAACGTTA 2 26 0 AAACAATCAA 0.895666 -87 TGGGTAAATCACAAATAAAGCGTCTGAGA 5 10 1 CACAAATAAA 0.873609 -97 TGTAAGTCACCGAAAATAAAATCGGCGTAT 5 86 0 CGAAAATAAA 0.873609 -21 GCCTGATCTTCAAGAAAAAATTGAAGCAAT 6 220 1 CAAGAAAAAA 0.739235 -33 TATTTTCTCACAACAATAAAGATTGATTTT 9 125 1 CAACAATAAA 0.964712 -160 TGATTTTTATCAAAAATCAATCTTTATTGT 9 137 0 CAAAAATCAA 0.981431 -148 TGATTTTTGATAAAAATCAAGAAATAAAAA 9 148 1 TAAAAATCAA 0.855118 -137 AACTACTAATCAACAATCAACGGCTCGCAT 9 222 0 CAACAATCAA 0.977576 -63 TTTAGCCCACCAAAAAACAATCGAGAGATA 9 263 1 CAAAAAACAA 0.936274 -22 ********** Masking position 5 Map Score: 10.3565 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 160 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 TACAATGAGTTATCTTCATTTTTATAGACTA 1 34 1 TATCTCATTT 0.54815 -267 AGAAATAAACTTTCTACATTTTCTGAAAAAA 1 96 0 TTTCACATTT 0.54815 -205 CTTATCTCCTTTTCGTCATTATTGCTGCCTT 1 256 1 TTTCTCATTA 0.946913 -45 ATTGCTGCCTTTTAATCATAAATAAGGATGT 1 276 1 TTTATCATAA 0.93756 -25 TATTACATCCTTATTTATGATTA 1 288 0 TTACTCCTTA 0.611233 -13 AATTAGTTTCATTCATAACGTTGAATTG 2 8 1 TTCATCATAA 0.893565 -105 ATTTCATCAAAAGTGCGGTTAA 3 2 1 TTTCTCAAAA 0.850791 -58 GCTCACTTTTTTCAGTCTTAAGCCCTCCAAT 6 32 1 TTCATCTTAA 0.698844 -221 AGCCCTCCAATTCCCTCCTAATTAAATAGTT 6 52 1 TTCCTCCTAA 0.907199 -201 TAGTTCAATTTTTAATCATTTCACACCCAGT 6 78 1 TTTATCATTT 0.859782 -175 GGCAAGCACGTTTAATCTAAAATTGGTCATA 9 39 1 TTTATCTAAA 0.459626 -246 ATTGGTCATATTTAGTCCTATAAAAAAAATA 9 60 1 TTTATCCTAT 0.857338 -225 AGAAAATACCTTTCTTCATATAATATGTTTG 9 102 0 TTTCTCATAT 0.946922 -183 **** ****** Masking position 1 Map Score: 5.40532 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 530 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 6 GACTAGTGCACTTGCTAATCTACGTCAGCC 1 60 1 CTTGCTAATC 0.973125 -241 TTAAAAAGCCGTTGGCAATCTTAGTAAATT 1 129 1 GTTGGCAATC 0.896818 -172 TCGGCGTATTCTAGCCGATTTTAGGGAAAA 5 65 0 CTAGCCGATT 0.834745 -42 GCTAATCCTAGTTGCCAATTATGCTTTGTT 6 143 0 GTTGCCAATT 0.936788 -110 CGACAATATGCTTGCTAATCCTAGTTGCCA 6 156 0 CTTGCTAATC 0.973125 -97 TCAATTTTTTCTTGAAGATCAGGCTGTTTT 6 214 0 CTTGAAGATC 0.869228 -39 AGTAGTTACTTGAAAATCTTCAAATTTA 8 15 0 CTTGAAAATC 0.90807 -18 ATTAAACGTGCTTGCCTATTCCGTTATGCT 9 25 0 CTTGCCTATT 0.911769 -260 ********** Masking position 8 Map Score: 3.35485 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 286 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 AAAAATAAAGGGGCTGACGTAGATTAGCAAG 1 70 0 GGGCTGACGA 0.987053 -231 GGGAATTGGAGGGCTTAAGACTGAAAAAAGT 6 36 0 GGGCTTAAGC 0.992357 -217 CGTTATGCTTGGGCTAACGGCAA 9 3 0 GGGCTAACGC 0.997158 -282 GTTTTTTGGTGGGCTAAAGCCCACCCTACAA 9 250 0 GGGCTAAAGC 0.994085 -35 ********* * Masking position 5 Map Score: 2.60404 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 5 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 AAGGTTATATTCCTAGTTTCCTACGTCAGT 1 229 0 TCCTAGTTTC 0.923689 -72 CTCCTTTTCGTCATTATTGCTGCCTTTTAA 1 261 1 TCATTATTGC 0.885455 -40 TATTACATCCTTATTTATGATTAAAAG 1 284 0 TCCTTATTTA 0.799291 -17 TTTTATACTTTCTTAATTGATGAATTAGTG 2 56 0 TCTTAATTGA 0.897865 -57 CAAAGTGCGGTCAAAATTAACCGCACTTTT 3 19 0 TCAAAATTAA 0.57308 -41 CGTCTGAGATTCTTAATTTCCTTTTCGCTG 5 31 1 TCTTAATTTC 0.893247 -76 CAGAAAGTGATCAAAATTGCTCACTTTTTT 6 14 1 TCAAAATTGC 0.885119 -239 TCCAATTCCCTCCTAATTAAATAGTTCAAT 6 57 1 TCCTAATTAA 0.897917 -196 TGCTTGCTAATCCTAGTTGCCAATTATGCT 6 148 0 TCCTAGTTGC 0.961538 -105 ********** Masking position 7 Map Score: 2.70106 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 184 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 CTTTATTTTTTCAGAAAATGTAGAAAGTTT 1 91 1 TCAGAAAATG 0.924642 -210 ATTCATCAATTAAGAAAGTATAAAAAGCGT 2 61 1 TAAGAAAGTA 0.903621 -52 TTGTAAGTCACCGAAAATAAAATCGGCGT 5 88 0 ACCGAAAATA 0.882269 -19 TGGCAGAAAGTGATCAAAATTG 6 3 1 GCAGAAAGTG 0.919459 -250 TACTCTCTGTAAAGAGAGTACAACACCCAG 6 112 0 AAAGAGAGTA 0.873628 -141 TACTCTCTTTACAGAGAGTACAACAAAGCA 6 122 1 ACAGAGAGTA 0.962038 -131 TTTATTGTTGTGAGAAAATACCTTTCTTCA 9 115 0 TGAGAAAATA 0.832446 -170 AGGTTTAAATACAGAAAATAATAAGAATAG 9 178 0 ACAGAAAATA 0.96577 -107 ********** Masking position 5 Map Score: 2.54494 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 222 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 ATTTTGTATAGATTTCTTTAAT 1 3 1 TTTGTATAGA 0.957165 -298 GTTATCTTCATTTTTATAGACTAGTGCACT 1 42 1 TTTTTATAGA 0.973978 -259 AATTGCTCCTTTTTTATATACAAAGTGCGG 3 39 0 TTTTTATATA 0.906786 -21 ATTATTATTTTTTTTATAGGACTAAATATG 9 66 0 TTTTTATAGG 0.958166 -219 ********** Masking position 5 Map Score: 0.539373 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 10 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 ********** No masking Map Score: 3.38462e-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 12 ********** No masking Map Score: 3.38462e-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 13 ********** No masking Map Score: 3.38462e-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