AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i220_Ribosomal_Operon_7_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 HI0301 300 hemolysin, putative #2 HI0303 49 conserved hypothetical protein #3 HI0976 119 conserved hypothetical protein #4 HI0978 40 ribosomal protein L11 methyltransferase (prmA) Motif number 1 TTTTTACGAGATCAATTCACAATCAAAAATC 1 46 1 ATCAATTCCA 0.962428 -255 TCAATTCACAATCAAAAATCCATTATTCACA 1 57 1 ATCAAAAACC 0.838392 -244 AAGTGCGGTTAAAAATACACAATTTTTACGG 1 163 0 AAAAATACCA 0.971219 -138 GAAAATCAATAAAAAATAACCGCACATTGGG 1 204 0 AAAAAATACC 0.906111 -97 CATATTTTAGAAAAAATCGCAAAACGCGAAA 1 239 0 AAAAAATCCA 0.971219 -62 ATTGACGGCGAAAAATTATCATATTTTAGAA 1 258 0 AAAAATTACA 0.967618 -43 TAAGACATCAAACACAAATCAAT 1 288 1 AACACAAACA 0.811937 -13 TTTCATTCATATAAATAAACATT 2 37 1 ATAAATAACA 0.936813 -13 AAGTGAGAAAATTAAATATCACCTTCCTCTC 3 45 0 ATTAAATACA 0.754781 -75 ATAGAATTGCAACAATTCACAGGGATACATC 3 98 1 AACAATTCCA 0.9775 -22 AGTGCGGTAAAAATACGCAAAATTTTGAA 4 9 1 AAAAATACCA 0.971219 -32 ******** ** Masking position 4 Map Score: 13.2899 Number of sites scoring better than the average of aligned sites = 484 Number in coding regions = 386 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 ATAAGGATCTTTGCCCTCTTTTTACGAGATCA 1 28 1 TGCCTCTTTT 0.937858 -273 GACAACAAAATATTCTTATTTTGTTTATATGA 1 115 0 TTTCTATTTT 0.949326 -186 TGTGTATTTTTAACCGCACTTTAGGTTTAAAC 1 173 1 TACCCACTTT 0.982379 -128 CAATAAAAAATAACCGCACATTGGGTTTAAAC 1 197 0 TACCCACATT 0.865908 -104 TTTTTATTGATTTTCCTCTTTTCGCGTTTTGC 1 220 1 TTTCTCTTTT 0.95595 -81 CGGCGAAAAATTATCATATTTTAGAAAAAATC 1 252 0 TATCTATTTT 0.957012 -49 CCAGTTAAAATGACCGCACTTTTTCATTCATA 2 16 1 TACCCACTTT 0.982379 -34 CAATATGCTGTCACCTTCTTCTAAATGAGAGG 3 19 1 TACCTCTTCT 0.944441 -101 AAATTAAATATCACCTTCCTCTCATTTAGAAG 3 36 0 TACCTCCTCT 0.964549 -84 TGATATTTAATTTTCTCACTTTCAGCAATTTC 3 55 1 TTTCCACTTT 0.96104 -65 CTTTCAAAATTTTGCGTATTTTTACCGCACT 4 10 0 TTGCTATTTT 0.872612 -31 TTGTTTTTCCTTTCAAAATTTTG 4 28 0 TTTTTCCTTT 0.713651 -13 * *** ****** Masking position 1 Map Score: 13.3005 Number of sites scoring better than the average of aligned sites = 1458 Number in coding regions = 966 Number in noncoding regions = 492 Number of orfs with sites within 600 bp upstream = 333 Fraction of orfs with sites within 600 bp upstream = 0.0534854 Motif number 3 GGATCTTTGCCCTCTTTTTACGAGATCAATTC 1 32 1 CCTCTTTTTG 0.984378 -269 GTATTTTTAACCGCACTTTAGGTTTAAACCCA 1 176 1 CCGCACTTTG 0.996424 -125 TAAAAAATAACCGCACATTGGGTTTAAACCTA 1 194 0 CCGCACATTG 0.99327 -107 TATTGATTTTCCTCTTTTCGCGTTTTGCGATT 1 224 1 CCTCTTTTCG 0.950974 -77 GTTAAAATGACCGCACTTTTTCATTCATATAA 2 19 1 CCGCACTTTC 0.985887 -31 ATATCACCTTCCTCTCATTTAGAAGAAGGTGA 3 29 0 CCTCTCATTG 0.99015 -91 TATTTAATTTTCTCACTTTCAGCAATTTCTAC 3 58 1 TCTCACTTTG 0.975018 -62 ********* * Masking position 8 Map Score: 10.6075 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 398 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 4 TCTCGTAAAAAGAGGGCAAAGATCCTTATC 1 27 0 AGAGGGCAAA 0.980234 -274 ATTTTTACGGAGAGGGGAAAATTCTAGACA 1 143 0 AGAGGGGAAA 0.994306 -158 CAAAACGCGAAAAGAGGAAAATCAATAAAA 1 221 0 AAAGAGGAAA 0.970223 -80 TTCTTCTAAATGAGAGGAAGGTGATATTTA 3 34 1 TGAGAGGAAG 0.976346 -86 AATTGCTGAAAGTGAGAAAATTAAATATCA 3 55 0 AGTGAGAAAA 0.908734 -65 CGCAAAATTTTGAAAGGAAAAACAA 4 26 1 TGAAAGGAAA 0.945839 -15 ********** Masking position 8 Map Score: 5.59338 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 85 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 AGATCCTTATCACATCAAACTTCAAAA 1 8 0 CACATCAAAC 0.981338 -293 ACAAGTTATCCACAACATAGATACTTTTCG 1 85 1 CACAACATAG 0.952246 -216 GAAAATTCTAGACAACAAAATATTCTTATT 1 127 0 GACAACAAAA 0.965614 -174 CCGTCAATAAGACATCAAACACAAATCAAT 1 281 1 GACATCAAAC 0.987112 -20 AGAAGAAGGTGACAGCATATTGATTAATAC 3 11 0 GACAGCATAT 0.942765 -109 ********** Masking position 4 Map Score: 1.97898 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 72 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 ATGGATTTTTGATTGTGAATTGATCTCGTA 1 50 0 GATTGTGAAT 0.977898 -251 GTTGTGGATAACTTGTGAATAATGGATTTT 1 71 0 ACTTGTGAAT 0.987863 -230 TCTCCGTAAAAATTGTGTATTTTTAACCGC 1 160 1 AATTGTGTAT 0.954199 -141 TGATGTATCCCTGTGAATTGTTGCAATT 3 102 0 CCCTGTGAAT 0.975696 -18 ********** Masking position 6 Map Score: 1.21542 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 50 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: -8.78641e-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 8 ********** No masking Map Score: -8.78641e-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 9 ********** No masking Map Score: -8.78641e-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