AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i316_mixed3_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 HI0030 51 lipoprotein, putative #2 HI0033 53 conserved hypothetical protein #3 HI0034 124 conserved hypothetical protein #4 HI0036 205 ABC transporter, ATP-binding protein #5 HI0037 48 rod shape-determining protein (mreB) #6 HI0038 79 rod shape-determining protein (mreC) Motif number 1 TTTCATTTTTTCTTTCTTAA 1 1 1 TTTCATTTTT 0.742317 -51 AAAATATTAACGCTTTTCATTTATTCT 1 35 0 TAACGCTTTT 0.850062 -17 TTATTTTTTACCGCACTTTACTAAAAT 2 8 0 CCGCACTTTA 0.976059 -46 TAAAAAATAACCGCACTTTTTAGATAAGGA 2 28 1 CCGCACTTTT 0.997906 -26 GCGAAATTAACCGCGCTTTTTATGTCTAAA 3 26 0 CCGCGCTTTT 0.996235 -99 GCGGTTAATTTCGCGCTTATTTTTTGCGTG 3 42 1 TCGCGCTTAT 0.916931 -83 TGATAGAATTCCGCACCTTTATTGCTAAGT 3 96 1 CCGCACCTTT 0.98372 -29 AGGAGTTAAATTTCATTTTTAAGGGGTCAA 4 12 0 TTTCATTTTT 0.742317 -194 GTGACGAACGTATCATTTTTTGAGTTTGGT 4 77 0 TATCATTTTT 0.742317 -129 GATACGTTCGTCACATTTTTTCTTGCGAAA 4 93 1 TCACATTTTT 0.91744 -113 TGAAAAATAACCGCACTTTTTGTAAAAGGG 4 158 0 CCGCACTTTT 0.997906 -48 TTATTTTTCACCGCACTTTTATCTCGGATG 4 178 1 CCGCACTTTT 0.997906 -28 ACTGTAATCGCAACGCTTTTTTTGATACAT 5 26 1 CAACGCTTTT 0.920819 -23 TTATTTTTAACCGCACTTTTTGTTCATATT 6 15 0 CCGCACTTTT 0.997906 -65 TTAAAAATAACCGCACTTTTCCTTTCACTT 6 35 1 CCGCACTTTT 0.997906 -45 GCACTTTTCCTTTCACTTTTTTCATTCAAC 6 47 1 TTTCACTTTT 0.930038 -33 ********** Masking position 8 Map Score: 45.3326 Number of sites scoring better than the average of aligned sites = 1750 Number in coding regions = 1196 Number in noncoding regions = 554 Number of orfs with sites within 600 bp upstream = 350 Fraction of orfs with sites within 600 bp upstream = 0.0562159 Motif number 2 ATTTTAGTAAAGTGCGGTAAAAAATAACCG 2 11 1 AGTGCGGTAA 0.997126 -43 TTATCTAAAAAGTGCGGTTATTTTTTACCG 2 25 0 AGTGCGGTTA 0.999402 -29 AGACATAAAAAGCGCGGTTAATTTCGCGCT 3 29 1 AGCGCGGTTA 0.997752 -96 TCATTTTTTGAGTTTGGTTAAGGTTTTCAA 4 65 0 AGTTTGGTTA 0.954217 -141 TTTTACAAAAAGTGCGGTTATTTTTCACCG 4 161 1 AGTGCGGTTA 0.999402 -45 CCGAGATAAAAGTGCGGTGAAAAATAACCG 4 175 0 AGTGCGGTGA 0.998059 -31 ATGAACAAAAAGTGCGGTTAAAAATAACCG 6 18 1 AGTGCGGTTA 0.999402 -62 TGAAAGGAAAAGTGCGGTTATTTTTAACCG 6 32 0 AGTGCGGTTA 0.999402 -48 ********** Masking position 1 Map Score: 35.3904 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 239 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 3 GCGGTTATTTTTTACCGCACTTTACTAAAA 2 12 0 TTTACCGCAC 0.995718 -42 GCGGTAAAAAATAACCGCACTTTTTAGATA 2 24 1 ATAACCGCAC 0.99857 -30 AAGCGCGAAATTAACCGCGCTTTTTATGTC 3 30 0 TTAACCGCGC 0.99665 -95 TTTGAAAACCTTAACCAAACTCAAAAAATG 4 64 1 TTAACCAAAC 0.933195 -142 GCGGTGAAAAATAACCGCACTTTTTGTAAA 4 162 0 ATAACCGCAC 0.99857 -44 GCGGTTATTTTTCACCGCACTTTTATCTCG 4 174 1 TTCACCGCAC 0.997107 -32 GCGGTTATTTTTAACCGCACTTTTTGTTCA 6 19 0 TTAACCGCAC 0.999108 -61 GCGGTTAAAAATAACCGCACTTTTCCTTTC 6 31 1 ATAACCGCAC 0.99857 -49 ********** Masking position 4 Map Score: 29.8255 Number of sites scoring better than the average of aligned sites = 532 Number in coding regions = 285 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 4 TTTCTTTCTTAAAGAAAGAATAAATGAAAAGCGT 1 19 1 AAAGAATAAA 0.805932 -33 ATTTTAGTAAAGTGCGGTAAAAAATAACCGCAC 2 10 1 AAGGTAAAAA 0.860696 -44 AAATAATTTCAATTTAGACATAAAAAGCGCGGTT 3 14 1 AATACATAAA 0.860892 -111 TCTTGCGCAAAATCCACGCAAAAAATAAGCGCGA 3 52 0 AATGCAAAAA 0.97784 -73 GAGTTTGGTTAAGGTTTTCAAAAAACAACTTGGA 4 52 0 AAGTCAAAAA 0.975275 -154 CACTTTTTGTAAAAGGGTCAAAAATTTTCGGTAT 4 141 0 AAATCAAAAA 0.979415 -65 AAAACGCTAAAAAACACTGTAATC 5 1 1 AAATAAAAAA 0.915843 -48 TAAATGTATCAAAAAAAGCGTTGCG 5 34 0 AAATCAAAAA 0.979415 -15 TCAGAATATGAACAAAAAGTGCGGTTAA 6 5 1 AATACAAAAA 0.951405 -75 *** ******* Masking position 10 Map Score: 7.74864 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 476 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 5 CAAAAAATAAGCGCGAAATTAACCGCGCTT 3 38 0 GCGCGAAATT 0.996002 -87 ATACCCTCTTGCGCAAAATCCACGCAAAAA 3 62 0 GCGCAAAATC 0.973531 -63 AGCAATAAAGGTGCGGAATTCTATCATTGA 3 92 0 GTGCGGAATT 0.989526 -33 ACATTTTTTCTTGCGAAATTGAGCATAGCC 4 105 1 TTGCGAAATT 0.975925 -101 ********** Masking position 7 Map Score: 2.23191 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 40 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 ********** No masking Map Score: 1.74326e-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 7 ********** No masking Map Score: 1.74326e-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 8 ********** No masking Map Score: 1.74326e-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