AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i229_sel_operon_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 HI0701 108 conserved hypothetical protein #2 HI0706 23 lipoprotein #3 HI0707 132 DNA mismatch repair protein (mutS) #4 HI0708 205 L-seryl-tRNA selenium transferase (selA) Motif number 1 TCCACTAAAATAACCGCACTTTTGTTCTTGTT 1 24 0 TACCGCCTTT 0.997506 -85 AGTTAAGGGCTCTTTTTTATCGAAA 1 94 0 TAGGGCCTTT 0.97718 -15 TTGAGATTTTTTACCGCACTTTTTACAGGAAG 3 12 0 TACCGCCTTT 0.997696 -121 CAACAAATTTTTACCGCACTTTTATCTGGCTT 3 41 1 TACCGCCTTT 0.997696 -92 ATAGGTTTTGTGGCGGCTATTTTAGGTGCCGA 3 82 0 TGCGGCATTT 0.940224 -51 TTGGGTGGGTTCAACTCCCATTCCCCTCCGCC 4 52 0 TAACTCCATT 0.785858 -154 TACGCTAAAGTGACCGCAATTTCAACCACGGA 4 143 0 TACCGCATTT 0.995495 -63 TGCGGTCACTTTAGCGTAAATTAATTGGCAAT 4 157 1 TAGCGTAATT 0.853014 -49 AATTGGCAATTCAACGTTATTTTAAACGGATT 4 179 1 TAACGTATTT 0.922315 -27 * ***** **** Masking position 11 Map Score: 16.2904 Number of sites scoring better than the average of aligned sites = 1704 Number in coding regions = 1160 Number in noncoding regions = 544 Number of orfs with sites within 600 bp upstream = 350 Fraction of orfs with sites within 600 bp upstream = 0.0562159 Motif number 2 CAAGAACAAAAGTGCGGTTATTTTAGTGGA 1 26 1 AGTGCGGTTA 0.990289 -83 TCCTGTAAAAAGTGCGGTAAAAAATCTCAA 3 14 1 AGTGCGGTAA 0.996133 -119 GCCAGATAAAAGTGCGGTAAAAATTTGTTG 3 41 0 AGTGCGGTAA 0.996133 -92 GGCTATTTTAGGTGCCGAAAGGGGAAAAAG 3 70 0 GGTGCCGAAA 0.938225 -63 AGCGTTCTTGGGTGGGTTCAACTCCCATTC 4 61 0 GGTGGGTTCA 0.937195 -145 TCAACCACGGAGGGGCGTCATCTCCGGTGA 4 124 0 AGGGGCGTCA 0.956894 -82 CGTGGTTGAAATTGCGGTCACTTTAGCGTA 4 145 1 ATTGCGGTCA 0.981323 -61 ********** Masking position 10 Map Score: 10.41 Number of sites scoring better than the average of aligned sites = 1258 Number in coding regions = 827 Number in noncoding regions = 431 Number of orfs with sites within 600 bp upstream = 297 Fraction of orfs with sites within 600 bp upstream = 0.0477032 Motif number 3 AATAAAATCCTTCAACAAGAACAAAA 1 5 1 AAATCCTAAC 0.972357 -104 TTTAGTGGATAAATCACGAAAAGTCGCATAGA 1 47 1 AAATCAGAAA 0.864064 -62 TCGATAAAAAAGAGCCCTTAACT 1 96 1 AGAGCCTAAC 0.84103 -13 GAAAGGGGAAAAAGCCAGATAAAAGTGCGGTA 3 52 0 AAAGCCGTAA 0.976719 -81 TCCCCTCCGCCAATCCATATAAACCTTTGAAT 4 31 0 CAATCCTTAA 0.934973 -175 GCAGGATTTCAAATCCTGTTGAGGACGCCAGC 4 88 0 AAATCCGTGA 0.951657 -118 ACAGGATTTGAAATCCTGCCACCTCACCGGAG 4 101 1 AAATCCGCAC 0.970345 -105 TTTTGAATCCGTTTAAAATAACGTTG 4 190 0 GAATCCTTAA 0.934967 -16 ****** * *** Masking position 3 Map Score: 2.22017 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 335 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 AATAAAATCCTTCAACAAGAACAAAAGTG 1 10 1 CTTCAACAAG 0.942381 -99 CGGTAAAAAATCTCAACAAATTTTTACCGC 3 28 1 TCTCAACAAA 0.951808 -105 CCTAAAATAGCCGCCACAAAACCTATCTTT 3 88 1 CCGCCACAAA 0.974789 -45 CTCCCATTCCCCTCCGCCAATCCATATAAA 4 40 0 CCTCCGCCAA 0.955266 -166 ACGCTGGCGTCCTCAACAGGATTTGAAATC 4 86 1 CCTCAACAGG 0.988312 -120 AATCCTGCCACCTCACCGGAGATGACGCCC 4 112 1 CCTCACCGGA 0.955521 -94 ********** Masking position 4 Map Score: 1.18629 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 135 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 ********** No masking Map Score: -2.17836e-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 6 ********** No masking Map Score: -2.17836e-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 7 ********** No masking Map Score: -2.17836e-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