AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i220_Ribosomal_Operon_7_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 HI0301 300 hemolysin, putative #2 HI0303 49 conserved hypothetical protein #3 HI0974.1 300 conserved hypothetical protein #4 HI0976 119 conserved hypothetical protein #5 HI0978 40 ribosomal protein L11 methyltransferase (prmA) Motif number 1 TTTTGAAGTTTGATGTGATAA 1 1 1 TTTTGAAGTT 0.889107 -300 GGATTTTTGATTGTGAATTGATCTCGTAAAA 1 47 0 TTGTGAATTA 0.892562 -254 TGTGGATAACTTGTGAATAATGGATTTTTGA 1 68 0 TTGTGAATAT 0.918745 -233 AATAAGAATATTTTGTTGTCTAGAATTTTCC 1 127 1 TTTTGTTGTT 0.751286 -174 TCCGTAAAAATTGTGTATTTTTAACCGCACT 1 162 1 TTGTGTATTT 0.981168 -139 TTTTCGCGTTTTGCGATTTTTTCTAAAATAT 1 238 1 TTGCGATTTT 0.92802 -63 ATTGATTTGTGTTTGATGTCTTATTGA 1 284 0 TTGTGTTTGT 0.944211 -17 CAGCAAAACCTTTTGAATTATTCAAAAAAGT 3 184 1 TTTTGAATTT 0.958565 -117 CATACGTCCCTTGTGTTTGCTAATCTTACAA 3 214 0 TTGTGTTTGT 0.944211 -87 AAAGTATATTTTTTGAATGGTATAAGGGGCG 3 252 0 TTTTGAATGT 0.935441 -49 TGATGTATCCCTGTGAATTGTTGCAATTCTA 4 99 0 CTGTGAATTT 0.924886 -21 TTTCAAAATTTTGCGTATTTTTACCGCACT 5 10 0 TTGCGTATTT 0.947526 -31 ********* * Masking position 2 Map Score: 14.065 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 302 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 2 ATAAGGATCTTTGCCCTCTTTTTACGAGATCA 1 28 1 TGCCTCTTTT 0.94415 -273 GACAACAAAATATTCTTATTTTGTTTATATGA 1 115 0 TTTCTATTTT 0.929467 -186 TGTGTATTTTTAACCGCACTTTAGGTTTAAAC 1 173 1 TACCCACTTT 0.965992 -128 CAATAAAAAATAACCGCACATTGGGTTTAAAC 1 197 0 TACCCACATT 0.722249 -104 TTTTTATTGATTTTCCTCTTTTCGCGTTTTGC 1 220 1 TTTCTCTTTT 0.948987 -81 CGGCGAAAAATTATCATATTTTAGAAAAAATC 1 252 0 TATCTATTTT 0.938523 -49 CCAGTTAAAATGACCGCACTTTTTCATTCATA 2 16 1 TACCCACTTT 0.965992 -34 ACTGATGCATATTCCTTATTTTTTTGACGAAT 3 26 0 ATCCTATTTT 0.659394 -275 GGATGATTACTTGTTACCTTTTGATACGACCA 3 113 0 TGTTCCTTTT 0.481516 -188 AGGTAACAAGTAATCATCCTTTTTATGAATAT 3 126 1 TATCTCCTTT 0.968176 -175 CAATATGCTGTCACCTTCTTCTAAATGAGAGG 4 19 1 TACCTCTTCT 0.902766 -101 AAATTAAATATCACCTTCCTCTCATTTAGAAG 4 36 0 TACCTCCTCT 0.929112 -84 TGATATTTAATTTTCTCACTTTCAGCAATTTC 4 55 1 TTTCCACTTT 0.938571 -65 CTTTCAAAATTTTGCGTATTTTTACCGCACT 5 10 0 TTGCTATTTT 0.777782 -31 TTGTTTTTCCTTTCAAAATTTTG 5 28 0 TTTTTCCTTT 0.738141 -13 * *** ****** Masking position 12 Map Score: 12.1631 Number of sites scoring better than the average of aligned sites = 1714 Number in coding regions = 1172 Number in noncoding regions = 542 Number of orfs with sites within 600 bp upstream = 379 Fraction of orfs with sites within 600 bp upstream = 0.0608738 Motif number 3 ATGACGAAAAGTATCTATGTTGTGGATAAC 1 89 0 GTATCTATGT 0.913822 -212 TTCTTATTTTGTTTATATGACGAAAAGTAT 1 105 0 GTTTATATGA 0.887967 -196 AATGTTTATTTATATGAATGAAAAAGT 2 33 0 ATTTATATGA 0.889952 -17 AAATATGAAAGTTTCTATGCCAGATAGTAA 3 60 0 GTTTCTATGC 0.978569 -241 GGTTTTGCTGATTTCTACGTAAATTCGATT 3 164 0 ATTTCTACGT 0.966733 -137 GGGACGTATGAAATATACGCCCCTTATACC 3 235 1 AAATATACGC 0.704905 -66 ACTTTCAGCAATTTCTACGCTAAAACATAG 4 72 1 ATTTCTACGC 0.978584 -48 GAATTGTTGCAATTCTATGTTTTAGCGTAG 4 86 0 AATTCTATGT 0.915631 -34 ********** Masking position 7 Map Score: 4.99201 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 157 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 TTTAAACCTAAAGTGCGGTTAAAAATACACA 1 173 0 AGTGCGGTTA 0.996506 -128 TTTAAACCCAATGTGCGGTTATTTTTTATTG 1 198 1 AGTGCGGTTA 0.996506 -103 ATGAATGAAAAAGTGCGGTCATTTTAACTGG 2 16 0 AGTGCGGTCA 0.997738 -34 GTATTAATCAATATGCTGTCACCTTCTTCTA 4 11 1 AATGCTGTCA 0.965456 -109 * ********* Masking position 4 Map Score: 4.41401 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 409 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 5 GATCTCGTAAAAAGAGGGCAAAGATCCTTA 1 29 0 AAAGAGGGCA 0.863374 -272 ATTTTTACGGAGAGGGGAAAATTCTAGACA 1 143 0 AGAGGGGAAA 0.838029 -158 CAAAACGCGAAAAGAGGAAAATCAATAAAA 1 221 0 AAAGAGGAAA 0.945056 -80 ATTTTTTCTAAAATATGATAATTTTTCGCC 1 253 1 AAATATGATA 0.872358 -48 GTAATTCCCCAAATATGAAAGTTTCTATGC 3 70 0 AAATATGAAA 0.872358 -231 GGTCGTATCAAAAGGTAACAAGTAATCATC 3 114 1 AAAGGTAACA 0.805393 -187 TCCTTTTTATGAATATGATAAAAATCGAAT 3 142 1 GAATATGATA 0.849336 -159 TCATTTAGAAGAAGGTGACAGCATATTGAT 4 17 0 GAAGGTGACA 0.972083 -103 TAAATGAGAGGAAGGTGATATTTAATTTTC 4 40 1 GAAGGTGATA 0.956793 -80 ********** Masking position 3 Map Score: 3.78254 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 272 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 ATTTTTGATTGTGAATTGATCTCGTAAAAA 1 46 0 GTGAATTGAT 0.88486 -255 GTGAATAATGGATTTTTGATTGTGAATTGA 1 57 0 GATTTTTGAT 0.406461 -244 CGTAAAAATTGTGTATTTTTAACCGCACTT 1 164 1 GTGTATTTTT 0.963222 -137 CCAATGTGCGGTTATTTTTTATTGATTTTC 1 205 1 GTTATTTTTT 0.846221 -96 TTCGCGTTTTGCGATTTTTTCTAAAATATG 1 240 1 GCGATTTTTT 0.907305 -61 TCTAAAATATGATAATTTTTCGCCGTCAAT 1 259 1 GATAATTTTT 0.789735 -42 AATGTTTATTTATATGAATGAAA 2 37 0 GTTTATTTAT 0.864403 -13 ATGCATATTCCTTATTTTTTTGACGAATAC 3 24 0 CTTATTTTTT 0.349464 -277 GGTATAAGGGGCGTATATTTCATACGTCCC 3 235 0 GCGTATATTT 0.722728 -66 ATAAGTGAAAGTATATTTTTTGAATGGTAT 3 260 0 GTATATTTTT 0.856924 -41 GAAGGTGACAGCATATTGATTAATAC 4 7 0 GCATATTGAT 0.6557 -113 ATGTATCCCTGTGAATTGTTGCAATTCTAT 4 98 0 GTGAATTGTT 0.943184 -22 TCAAAATTTTGCGTATTTTTACCGCACT 5 9 0 GCGTATTTTT 0.960775 -32 ********** Masking position 6 Map Score: 7.43943 Number of sites scoring better than the average of aligned sites = 1351 Number in coding regions = 1063 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 7 TTGTTGTCTAGAATTTTCCCCTCTCCGTAA 1 139 1 GAATTTTCCC 0.972676 -162 AAAAATTGTGTATTTTTAACCGCACTTTAG 1 167 1 TATTTTTAAC 0.729497 -134 ATTTTTTATTGATTTTCCTCTTTTCGCGTT 1 218 1 GATTTTCCTC 0.939797 -83 CATATTTGGGGAATTACACCGAAATTATCT 3 83 1 GAATTACACC 0.822904 -218 ACGTAAATTCGATTTTTATCATATTCATAA 3 148 0 GATTTTTATC 0.945279 -153 AGGTGATATTTAATTTTCTCACTTTCAGCA 4 52 1 TAATTTTCTC 0.870756 -68 TGATGTATCCCTGTGAATTGT 4 109 0 GATGTATCCC 0.847112 -11 AAATTTTGCGTATTTTTACCGCACT 5 6 0 TATTTTTACC 0.933658 -35 ********** Masking position 2 Map Score: 2.96355 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 504 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 8 ********** No masking Map Score: -1.56076e-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 9 ********** No masking Map Score: -1.56076e-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 10 ********** No masking Map Score: -1.56076e-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