AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_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 HI0229 298 polynucleotide phosphorylase (pnp) #2 HI0963 34 riboflavin kinase / FMN adenylyltransferase (ribF) #3 HI0964 300 virulence factor (mviN) #4 HI1282 300 conserved hypothetical protein #5 HI1288 300 ribosome binding factor A (rbfA) #6 HI1328 135 ribosomal protein S15 (rpS15) Motif number 1 TCATTACATTATATTTCATATAAAAGAACCTAAT 1 17 1 ATATTTCTTA 0.695779 -282 TGGGCGTTTAAAAATTTCTTTTGATAGCCGCACG 1 184 0 AAAATTTTTA 0.976957 -115 TGTTTTCCTTAAAATTTATATTAAAAACAATGCC 1 273 0 AAAATTTTTA 0.976954 -26 TCCTAAAATTTCTGTTGATTGATAGACA 3 5 1 AAAATTTTTA 0.976957 -296 TTGTCAATGGAAAATTTGTGTTGATTTCGGTGAG 3 75 1 AAAATTTTTA 0.976957 -226 GCGTAAAAACAAAATTTCTATACAATTAGGCAAA 3 211 1 AAAATTTTTA 0.976957 -90 TCTCTACCCTAAAATTTTTGCCTAATTGTATAGA 3 227 0 AAAATTTTCA 0.93053 -74 GTTTACTCAAAATATTCTTCTCTACCCTAAAATT 3 245 0 AATATTCTTA 0.787764 -56 CCCAGTTACTAAATTTCTTATAGAAAAAAACCCC 4 91 0 AAATTTCTTA 0.918018 -210 TTCTTGTAAATTTTGTTCTAATGTAGCCAAT 4 280 0 AAATTTTTCA 0.811332 -21 ACTTCCGATAAAAATCACTTTACAGAGGGCATAA 5 150 0 AAAATCATTA 0.678617 -151 ATGACACCTGATAATTTGTTTGAATATTCAAACT 5 181 0 ATAATTTTTA 0.896475 -120 TTAGCACGCAAAAATCCCTTTCAACTTAATACTG 5 227 0 AAAATCCTTA 0.9168 -74 ******* * * * Masking position 1 Map Score: 15.342 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 127 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 2 TATTTCATATAAAAGAACCTAATTTCAGAG 1 28 1 AAAAGAACCT 0.968301 -271 TGCGGCTATCAAAAGAAATTTTTAAACGCC 1 186 1 AAAAGAAATT 0.946469 -113 TGCGACTAGCAAAAGAAATCTTTCGAAAAA 1 230 0 AAAAGAAATC 0.950385 -69 TCTATCAATCAACAGAAATTTTAGGA 3 7 0 AACAGAAATT 0.786655 -294 TGACAAAAGTATAAAAAATCGGCATATTGA 3 51 0 ATAAAAAATC 0.70992 -250 ATATTCCGTGAAAAAAAACTGATAAAATCC 3 180 0 AAAAAAAACT 0.888337 -121 TAAGTTCAGTAAAAGAACCCCAGTTTTGGG 4 64 1 AAAAGAACCC 0.97067 -237 TTTCTTATAGAAAAAAACCCCAAAACTGGG 4 82 0 AAAAAAACCC 0.90327 -219 GTTTTTTTCTATAAGAAATTTAGTAACTGG 4 94 1 ATAAGAAATT 0.888961 -207 GGTTAGGTTCATAAGAACCTAAGCCCAGTT 4 118 0 ATAAGAACCT 0.932578 -183 ********** Masking position 6 Map Score: 10.0515 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 187 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 GTATTTTCCTCCTAAAAATTGATTGTTCTCTC 1 55 0 CCTAAATTGA 0.84769 -244 GAAAATACTGTCGAAACAATGATAATTAAGTT 1 79 1 TCGAAAATGA 0.962279 -220 AGCCAAACATCCTGTATAATGCACGGGCTTTA 1 139 1 CCTTAAATGC 0.844584 -160 AAGAAATCTTTCGAAAAAATGACCGCACTTTG 1 216 0 TCGAAAATGA 0.961489 -83 AATGTTTTCCTTAAAATTTATATTAAAAAC 1 279 0 CCTAAATTTA 0.4809 -20 CTTCTCGCTATAATGCCGAAATTCTC 2 5 1 TCGTAAATGC 0.949556 -30 TCCTAAAATTTCTGTTGATTGATAGACAAAAT 3 11 1 TCTTTATTGA 0.596428 -290 GTATAAAAAATCGGCATATTGATGCCCTTTAT 3 41 0 TCGCAATTGA 0.876946 -260 AAAGTAAGTATCGTTATTTTTACAAGCTCTTT 3 118 1 TCGTATTTTA 0.496573 -183 AAACAAAATTTCTATACAATTAGGCAAAAATT 3 217 1 TCTTAAATTA 0.779669 -84 AATTATGCCCTCTGTAAAGTGATTTTTATCGG 5 148 1 TCTTAAGTGA 0.832194 -153 GTGATTTTTATCGGAAGTTTGAATATTCAAAC 5 166 1 TCGAATTTGA 0.77193 -135 ATACTGTTTTTCGATAAAATGACACCTGATAA 5 201 0 TCGTAAATGA 0.972273 -100 TCAATGATTTCCAGTAGAATGAGGCGCTTTTA 5 263 1 CCATAAATGA 0.727339 -38 AACTTATTCATCGTTAGAATGCGATTTCCTTG 6 52 1 TCGTAAATGC 0.950048 -84 *** ** ***** Masking position 10 Map Score: 9.86577 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 336 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 4 TTAAACGCCCAAAGTGCGGTCATTTTTTCG 1 207 1 AAAGTGCGGT 0.995917 -92 AAAAACCCCAAAACTGGGGTTCTTTTACTG 4 70 0 AAACTGGGGT 0.971454 -231 AGGTTATGATATAGTGCGGTGAATTACACC 4 234 1 ATAGTGCGGT 0.989763 -67 TAATGAAAAGTGCGGTAACTTTAATC 6 7 1 AAAGTGCGGT 0.995917 -129 ********** Masking position 5 Map Score: 4.5683 Number of sites scoring better than the average of aligned sites = 1129 Number in coding regions = 705 Number in noncoding regions = 424 Number of orfs with sites within 600 bp upstream = 293 Fraction of orfs with sites within 600 bp upstream = 0.0470607 Motif number 5 CATTACATTATATTTCATATAAAAGAACCTAAT 1 18 1 TTTTCATAAA 0.825072 -281 AACAATCAATTTTTAGGAGGAAAATACTGTCGA 1 60 1 TTTAGGAAAA 0.887871 -239 GCAAAAGAAATCTTTCGAAAAAATGACCGCACT 1 219 0 TTTTCGAAAA 0.971287 -80 TAAGGCATTGTTTTTAATATAAATTTTAAGGAA 1 270 1 TTTTAATAAA 0.51709 -29 TTTTACGCTATATTCCGTGAAAAAAAACTGATA 3 186 0 TTTCCGTAAA 0.94308 -115 TAGAGAAGAATATTTTGAGTAAACGACTTTTAA 3 255 1 TTTTTGAAAA 0.81491 -46 AACCCGAAGGTCGTTGGTTCAAATCCAGCCCCC 4 20 1 TGTTGGTAAA 0.750209 -281 ATGCCCAAAGTTTTTCGTCTAAWTCATTTAAAA 5 45 1 TTTTCGTAAW 0.971385 -256 GAATATTCAAACTTCCGATAAAAATCACTTTAC 5 161 0 ATTCCGAAAA 0.65777 -140 CTTAATACTGTTTTTCGATAAAATGACACCTGA 5 204 0 TTTTCGAAAA 0.969618 -97 CGAAAAACAGTATTAAGTTGAAAGGGATTTTTG 5 220 1 TTTAAGTAAA 0.778528 -81 CAACACTACCTTTTAGGAGTAAAAA 6 121 1 TTTAGGAAAA 0.887871 -15 * ****** *** Masking position 11 Map Score: 7.01591 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 281 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 6 GCCATCATTACATTATATTTCATATAAAAGAACCT 1 13 1 CTTATATAAT 0.842914 -286 TATAAAAGAACCTAATTTCAGAGAGAACAATCAAT 1 35 1 CTAATTTAAG 0.964958 -264 AATGCACGGGCTTTATTTTCTACATTAGCGTGCGG 1 156 1 CTTATTTAAT 0.974443 -143 AAAAACAATGCCTTATTTCCCAGATTGCGACTAGC 1 250 0 CTTATTTAAT 0.974447 -49 GGAAATAAGGCATTGTTTTTAATATAAATTTTAAG 1 265 1 CTTGTTTAAT 0.888305 -34 TATTGATGCCCTTTATTTTGTCTATCAATCAACAG 3 22 0 CTTATTTCAT 0.964478 -279 AAGTAAGTATCGTTATTTTTACAAGCTCTTTCAAT 3 119 1 CTTATTTCAG 0.977426 -182 AGCCCAGTTACTAAATTTCTTATAGAAAAAAACCC 4 92 0 CAAATTTAAG 0.79485 -209 TTACAGAGGGCATAATTTATGCAAGCGAGACGAGA 5 130 0 CTAATTTCAG 0.951471 -171 AGTTATTCCTTATTTATAAAAGCGCCTCATTC 5 279 0 CTTATTTAAG 0.983768 -22 * ****** * ** Masking position 8 Map Score: 10.103 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 81 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 TTATATTAAAAACAATGCCTTATTTCCCAG 1 262 0 AACAATGCCT 0.980526 -37 TTGTAAAAATAACGATACTTACTTTCGGTT 3 113 0 AACGATACTT 0.890186 -188 AGAACTAACAACAATGCTAGATTTTAAAA 3 282 0 AACAATGCTA 0.896459 -19 CCTTATCCTAAACAATACTTATCCCTCTAT 4 197 0 AACAATACTT 0.963553 -104 TAAWTCATTTAAAAATGCTTGTTGTAATGT 5 64 1 AAAAATGCTT 0.919098 -237 TTTAGCACGCAAAAATCCCTTTCAACTTAA 5 232 0 AAAAATCCCT 0.836714 -69 ATGTATTAACAACACTACCTTTTAGGAGTA 6 112 1 AACACTACCT 0.90788 -24 ********** Masking position 2 Map Score: 2.81907 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 97 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 TTCTTTTGATAGCCGCACGCTAATGTAGAAAA 1 171 0 ACCGCACCTA 0.96897 -128 GGTTGTGTCTCACCGAAATCAACACAAATTTT 3 85 0 CCCGAAACAA 0.983542 -216 GGTGAGACACAACCGAAAGTAAGTATCGTTAT 3 103 1 ACCGAAATAA 0.716076 -198 CAAATCCAGCCCCCGCAACCAATAATAAGTTC 4 39 1 CCCGCAACAA 0.991963 -262 GGGTGTAATTCACCGCACTATATCATAACCTT 4 233 0 CCCGCACATA 0.946549 -68 TGCTGATAAACTCCGCAAACAACTTGATGCCG 5 12 0 CCCGCAACAA 0.991963 -289 ATACATCATTCGCCGATCTCTAACTCAGCGAT 6 86 0 CCCGATCCTA 0.920041 -50 * ****** *** Masking position 12 Map Score: 4.13874 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 53 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GGAGGAAAATACTGTCGAAACAATGATAAT 1 75 1 ACTGTCGAAA 0.86981 -224 TTTAAAAATTTCTTTTGATAGCCGCACGCT 1 182 0 TCTTTTGATA 0.905854 -117 GCAAAAGAAATCTTTCGAAAAAATGACCGC 1 222 0 TCTTTCGAAA 0.939173 -77 TTTTACAAGCTCTTTCAATATGGGCTCACA 3 135 1 TCTTTCAATA 0.845112 -166 TTTTGGGGTTTTTTTCTATAAGAAATTTAG 4 87 1 TTTTTCTATA 0.641361 -214 ACTTTGGGCATCTGCTGATAAACTCCGCAA 5 26 0 TCTGCTGATA 0.795056 -275 GACGACCAAGATTGTCGATAAAAATCACAC 5 92 0 ATTGTCGATA 0.873884 -209 GAATATTCAAACTTCCGATAAAAATCACTT 5 164 0 ACTTCCGATA 0.926085 -137 CTTAATACTGTTTTTCGATAAAATGACACC 5 207 0 TTTTTCGATA 0.941224 -94 ********** Masking position 3 Map Score: 3.79463 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 197 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 TTAATTATCATTGTTTCGACAGTATTTTCC 1 78 0 TTGTTTCGAC 0.956641 -221 AGTGCGGTCATTTTTTCGAAAGATTTCTTT 1 219 1 TTTTTTCGAA 0.83736 -80 CTCAAAATATTCTTCTCTACCCTAAAATTT 3 244 0 TCTTCTCTAC 0.794838 -57 GATGCCCAAAGTTTTTCGTCTAAWTCATTT 5 44 1 GTTTTTCGTC 0.788443 -257 AATGTGTGATTTTTATCGACAATCTTGGTC 5 89 1 TTTTATCGAC 0.940152 -212 ACAATCTTGGTCGTCTCGTCTCGTCTCGTC 5 107 1 TCGTCTCGTC 0.95495 -194 TCGTCTCGTCTCGTCTCGTCTCGCTTGCAT 5 117 1 TCGTCTCGTC 0.95495 -184 TCAGGTGTCATTTTATCGAAAAACAGTATT 5 204 1 TTTTATCGAA 0.782278 -97 ********** Masking position 6 Map Score: 2.16908 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 115 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 ********** No masking Map Score: 2.14117e-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: 2.14117e-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: 2.14117e-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