AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00730_hinf_reg_300.orf -o00730_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -x5 -e 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 = 1 Input sequences: #1 HI0415 300 hydroxyethylthiazole kinase #2 HI1303 147 riboflavin synthase, beta chain (ribH) #3 HI1334 126 cell division protein (ftsJ) #4 HI1335 90 cell division protein (ftsH) #5 HI1336 111 dihydropteroate synthase (folP-1) #6 HI1337 37 mrsA protein (mrsA) #7 HI1338 58 conserved hypothetical protein Motif number 1 CGGTCAAATTTTTCCCTCATTTTGCAAATAATG 1 30 0 TTTCCATTTT 0.982416 -271 GAGGGAAAAATTTGACCGCTTGTTTTTTCTTGA 1 45 1 TTTACCTTGT 0.722205 -256 CGAAAGAAGTTTACGCTTCTTTTCAAGAAAAAA 1 67 0 TTAGCCTTTT 0.906855 -234 AGGAAACTAATATGCCACATATTCAACCTTTCT 1 166 1 TATCCATATT 0.646684 -135 ATCCTGTTTATTTTCCCAATTTTCTACATTTTA 1 212 1 TTTCCATTTT 0.982416 -89 TAGCGGGCATTTTTGTTTATTTTATATTCAACA 1 272 1 TTTGTATTTT 0.88588 -29 TAAGGTAAACTATCGGCAATTTTAT 2 3 0 TATGGATTTT 0.88701 -145 TTTACCTTAATGAAGGAAATTTTCCATAAAAAT 2 27 1 TGAGGATTTT 0.702417 -121 GGACTCATTTTTAAGGCGATTTTATTGTTCATA 2 77 0 TTAGGATTTT 0.945643 -71 TTAATAAGGCTTTACCCTATTTTATTTAGGACT 2 105 0 TTTCCATTTT 0.982416 -43 TAATATTGAATATACGCGATTTT 2 135 1 TATCGATTTT 0.88701 -13 TCTCAATGTTTTTTACTGATTTCAATTAGCTTC 3 43 1 TTTACATTTC 0.796556 -84 TCGGCTTGAATTTGACAGATTGTACCCAAATAT 3 74 1 TTTACATTGT 0.884358 -53 TTTGTAGTCGTTTCGCCTATATTTGGGTACAAT 3 92 0 TTTGCATATT 0.887804 -35 TTGCTTTGATAGCTTTTCATTGCTAAT 4 5 1 TTTATCTTTT 0.62247 -86 CGGTTAATTTTTAGAGTGATTTTGGTGGGCGAT 5 83 0 TTAAGATTTT 0.915749 -29 ACTCTAAAAATTAACCGCATTTT 5 99 1 TTACCATTTT 0.96626 -13 CGATAAAAAATTAAAGGAATTTTATT 6 22 1 TTAAGATTTT 0.915749 -16 *** ** ***** Masking position 10 Map Score: 20.3369 Number of sites scoring better than the average of aligned sites = 1348 Number in coding regions = 1046 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 2 TAATGAGAAGAATTTGACCGCTTA 1 4 0 AATTGACCGC 0.991089 -297 ATGAGGGAAAAATTTGACCGCTTGTTTTTTC 1 43 1 AATTGACCGC 0.991089 -258 TTACACCTGCTAATTGCTCACAGTGAATAGC 1 245 1 TAATGCTCAC 0.711719 -56 AAAATAAACAAAAATGCCCGCTATTCACTGT 1 264 0 AAAAGCCCGC 0.977666 -37 ATTTTATTGTTCATAACCCGCACCAACACTA 2 61 0 TCATACCCGC 0.919391 -87 GGTTATGAACAATAAAATCGCCTTAAAAATG 2 74 1 AATAAATCGC 0.69092 -74 AACATTGAGAAAATCAACCGCTCTTTTTTAT 3 22 0 AAATAACCGC 0.990018 -105 TATTTCGCTATAATCGCCCACCAAAATCACT 5 71 1 TAATGCCCAC 0.941263 -41 ATCACTCTAAAAATTAACCGCATTTT 5 96 1 AAATAACCGC 0.990018 -16 TTTTTGACCGCACTTAGTAAA 7 1 1 TTTTGACCGC 0.902226 -58 AACTTTATAAAAATAAACCGCACTTTACTAA 7 24 0 AAATAACCGC 0.990018 -35 **** ****** Masking position 9 Map Score: 16.2093 Number of sites scoring better than the average of aligned sites = 981 Number in coding regions = 693 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 3 TTAGCACTGACGTAGGAAACTAATATGCCA 1 153 1 CGTAGGAAAC 0.923149 -148 AATGTAGAAAATTGGGAAAATAAACAGGAT 1 212 0 ATTGGGAAAA 0.847693 -89 GCTCTTTTTTATTAGGAATCCTT 3 4 0 ATTAGGAATC 0.911056 -123 ACTACACATCATTAGCAATGAAAAGCTATC 4 18 0 ATTAGCAATG 0.800671 -73 AATTTTTTAACTTAGGAAAGGTAGGTTAGA 4 60 1 CTTAGGAAAG 0.991276 -31 CAAAGCCTTTCTTCGGAAAGGCTTTATTTT 5 16 1 CTTCGGAAAG 0.969456 -96 GAACAAAATCATTAGGAAAAAATAAAGCCT 5 34 0 ATTAGGAAAA 0.954449 -78 TTTGACCGCACTTAGTAAAGTGCGGTTTAT 7 13 1 CTTAGTAAAG 0.930988 -46 TTATAAAGTTTTTAGGAAAGCAAA 7 45 1 TTTAGGAAAG 0.958775 -14 ********** Masking position 7 Map Score: 8.93759 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 57 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 CGCTTCTTTTCAAGAAAAAACAAGCGGTCAAA 1 55 0 CAGAAAAAAA 0.948444 -246 AGGAAATTTTCCATAAAAATATAGTGTTGGTG 2 40 1 CATAAAAATT 0.887111 -108 AATAAAATCGCCTTAAAAATGAGTCCTAAATA 2 84 1 CTTAAAAATA 0.850202 -64 AAGGATTCCTAATAAAAAAGAGCGGTTGATT 3 10 1 TATAAAAAAA 0.903124 -117 TAATTGAAATCAGTAAAAAACATTGAGAAAAT 3 39 0 CGTAAAAAAA 0.948444 -88 GGCGAAACGACTACAAAAAATAGAAGATT 3 108 1 CACAAAAAAA 0.948444 -19 ACAAAATCATTAGGAAAAAATAAAGCCTTTCC 5 30 0 TGGAAAAAAA 0.690155 -82 CTATAATCGCCCACCAAAATCACTCTAAAAAT 5 78 1 CACCAAAATA 0.744596 -34 ACCAAAATCACTCTAAAAATTAACCGCATTTT 5 90 1 CCTAAAAATA 0.893753 -22 GGTTTTATAACGATAAAAAATTAAAGGAATTT 6 12 1 CATAAAAAAT 0.903271 -26 CCTAAAAACTTTATAAAAATAAACCGCACTTT 7 29 0 TATAAAAATA 0.886939 -30 * ******** * Masking position 6 Map Score: 6.92917 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 355 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 5 TAAGCGGTCAAATTCTTCTCATTATTT 1 8 1 TCAAATTCTT 0.936548 -293 AAACAAGCGGTCAAATTTTTCCCTCATTTT 1 40 0 TCAAATTTTT 0.882089 -261 ATAAAATAGGGTAAAGCCTTATTAATATTG 2 113 1 GTAAAGCCTT 0.853358 -35 GTTGATTTTCTCAATGTTTTTTACTGATTT 3 35 1 TCAATGTTTT 0.878721 -92 ATCGTTCAAAGTCTAACCTACCTTT 4 76 0 TCAAAGTCTA 0.876563 -15 CTCATCAAAGCCTTTCTTCGGAAA 5 5 1 TCAAAGCCTT 0.973793 -107 TTAGGAAAAAATAAAGCCTTTCCGAAGAAA 5 23 0 ATAAAGCCTT 0.873794 -89 TAAAATTCCTTTAATTTTTTATCGTTATAA 6 16 0 TTAATTTTTT 0.547209 -22 GTTTATTTTTATAAAGTTTTTAGGAAAGCA 7 37 1 ATAAAGTTTT 0.810214 -22 ********** Masking position 4 Map Score: 4.15505 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 420 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 ********** No masking Map Score: 9.53751e-15 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: 9.53751e-15 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: 9.53751e-15 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