AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_mixed5_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 HI0317 218 aspartyl-tRNA synthetase (aspS) #2 HI0365 225 conserved hypothetical protein #3 HI0366 101 fimbrial biogenesis and twitching motility protein, putative #4 HI0367 71 conserved hypothetical protein #5 HI0876 300 nucleoside diphosphate kinase (ndk) Motif number 1 GTTGAGATTAAATTACGTTAAGGATAACCAC 1 10 0 AATTCGTAAG 0.976329 -209 GCGGAAAACCAAGAGAGATAAAAAGGTTATTT 1 144 0 AAGAAGTAAA 0.798457 -75 TTTCCGCTATAATTGCGACAGATTTTTGAGCA 1 169 1 AATTCGCAGA 0.940593 -50 ACAGCGGAAAAAGTGCGGTAAAATATCAGCCT 2 31 0 AAGTCGTAAA 0.984747 -195 GATCGCAAAAAAGTGCGGTAAGATTTTCTATC 2 85 1 AAGTCGTAAG 0.975866 -141 AGCGGAATTGAAAAACGATAGAAAATCTTACC 2 101 0 AAAACGTAGA 0.911054 -125 ATCGTTTTTCAATTCCGCTAGATTATGCGGTG 2 114 1 AATTCGTAGA 0.976332 -112 CAATATTAGCAATATCGGCAAAAGATGAATTA 5 73 0 AATACGCAAA 0.909648 -228 ATTTTTTACAAAATACGATAAAAATGCCGTTG 5 138 0 AAATCGTAAA 0.976223 -163 TCACTACCAGATTTACGATAAGTCGCGGAGCA 5 197 0 ATTTCGTAAG 0.839693 -104 TGATAACATTAAATTAGCTAAAGTTTGCACAC 5 258 0 AAATAGTAAA 0.863488 -43 **** ** **** Masking position 10 Map Score: 11.8128 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 369 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 2 GATTTTTTGTTATATTATGCCGCTTGTTGA 1 37 0 TATATTATGC 0.519629 -182 AAATAAAGGCTTTTTTGTGCCATATCATCA 1 67 0 TTTTTTGTGC 0.908973 -152 GATAAAAAGGTTATTTATGCTGACAAATCA 1 130 0 TTATTTATGC 0.902063 -89 GTTTTCCGCTATAATTGCGACAGATTTTTG 1 167 1 ATAATTGCGA 0.889286 -52 TTGTACTCTTTTAATTATGCTCAAAAATCT 1 188 0 TTAATTATGC 0.916285 -31 GTAATTGAAAATATTTGCGATCTAGATCGC 2 61 1 ATATTTGCGA 0.871123 -165 CTTACCGCACTTTTTTGCGATCTAGATCGC 2 77 0 TTTTTTGCGA 0.871123 -149 CGTTCATTTTTTAATTGCGAATTTTTCGTT 2 164 1 TTAATTGCGA 0.952753 -62 TTTCCTCCTTTTAATTGGGCAGGAAGAAAT 3 81 0 TTAATTGGGC 0.952487 -21 ATTTAATCAAATAATTAGGCGGTAAATGGA 4 50 0 ATAATTAGGC 0.745785 -22 AAAGATGAATTAATTTGTGAACGATGAAAA 5 55 0 TAATTTGTGA 0.765834 -246 ********** Masking position 5 Map Score: 8.24541 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 559 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 GGCTTTTTTGTGCCATATCATCAGATTTTT 1 60 0 TGCCATATCA 0.969979 -159 TTATTTATGCTGACAAATCAATCAAAAAAG 1 120 0 TGACAAATCA 0.98688 -99 GATTATGCGGTGACAAATCTGTACAATCGC 2 134 1 TGACAAATCT 0.955871 -92 TATTTCTTCCTGCCCAATTAAAAGGAGGAA 3 80 1 TGCCCAATTA 0.944733 -22 AGCATTGCCAAATCAAGTATTGGAC 4 6 1 TGCCAAATCA 0.992731 -66 TTTTCATCGTTCACAAATTAATTCATCTTT 5 55 1 TCACAAATTA 0.872071 -246 ********** Masking position 7 Map Score: 5.67876 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 119 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 TTTGTTATATTATGCCGCTTGTTGAGATTA 1 32 0 TATGCCGCTT 0.963092 -187 TCTCTCTTGGTTTTCCGCTATAATTGCGAC 1 158 1 TTTTCCGCTA 0.987857 -61 TTACCGCACTTTTTCCGCTGTAATTGAAAA 2 42 1 TTTTCCGCTG 0.979474 -184 ATCGTTTTTCAATTCCGCTAGATTATGCGG 2 114 1 AATTCCGCTA 0.842197 -112 TTTTCCTCCTTTTAATTGGG 3 92 0 TTTTCCTCCT 0.870103 -10 TTAGCCTCCATTTACCGCCTAATTATTTGA 4 44 1 TTTACCGCCT 0.936702 -28 GAAAGGTTCATTTTCTGCTTGTGC 5 5 0 TTTTCTGCTT 0.922051 -296 TAATTCATCTTTTGCCGATATTGCTAATAT 5 73 1 TTTGCCGATA 0.859413 -228 ********** Masking position 3 Map Score: 5.93332 Number of sites scoring better than the average of aligned sites = 476 Number in coding regions = 439 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 ATCTCAACAAGCGGCATAATATAACAAAAA 1 34 1 GCGGCATAAT 0.931082 -185 CTGATATTTTACCGCACTTTTTCCGCTGTA 2 34 1 ACCGCACTTT 0.983222 -192 AGAAAATCTTACCGCACTTTTTTGCGATCT 2 84 0 ACCGCACTTT 0.983222 -142 CAGATTTGTCACCGCATAATCTAGCGGAAT 2 125 0 ACCGCATAAT 0.986051 -101 GCCTCCATTTACCGCCTAATTATTTGATTA 4 47 1 ACCGCCTAAT 0.962753 -25 AAGCACTGCAACGGCATTTTTATCGTATTT 5 130 1 ACGGCATTTT 0.973648 -171 ********** Masking position 10 Map Score: 5.5715 Number of sites scoring better than the average of aligned sites = 1205 Number in coding regions = 764 Number in noncoding regions = 441 Number of orfs with sites within 600 bp upstream = 303 Fraction of orfs with sites within 600 bp upstream = 0.0486669 Motif number 6 GAAAAGTAATAAATATTCAAAATAAAGGCT 1 86 0 AAATATTCAA 0.911925 -133 TAGATCGCAAATATTTTCAATTACAGCGGA 2 55 0 ATATTTTCAA 0.930949 -171 TCACAACGAAAAATTCGCAATTAAAAAATG 2 168 0 AAATTCGCAA 0.792672 -58 TAGGTATGTGAATTAATCAAGTTCACATAC 3 16 1 AATTAATCAA 0.801233 -86 AATGGAGGCTAAATTTTAAAGTCCAATACT 4 26 0 AAATTTTAAA 0.773352 -46 AAATTTAATCAAATAATTAGGC 4 60 0 ATTTAATCAA 0.733572 -12 TGAACGATGAAAATCTTCAAATGGTAAACG 5 38 0 AAATCTTCAA 0.858625 -263 AACCGAACCAATATTAGCAATATCGGCAAA 5 83 0 ATATTAGCAA 0.87718 -218 ATTTTGTAAAAAATTATAAACAAAATTGGT 5 156 1 AAATTATAAA 0.807833 -145 AGCTAATTTAATGTTATCAAGATCATTGAA 5 271 1 ATGTTATCAA 0.815212 -30 ********** Masking position 4 Map Score: 3.05698 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 681 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 7 GGTTATCCTTAACGTAATTTAATCTCAACA 1 13 1 AACGTAATTT 0.879313 -206 GTGCCATATCATCAGATTTTTTGTTATATT 1 51 0 ATCAGATTTT 0.878351 -168 TATTCAAAATAAAGGCTTTTTTGTGCCATA 1 73 0 AAAGGCTTTT 0.798514 -146 CTATAATTGCGACAGATTTTTGAGCATAAT 1 175 1 GACAGATTTT 0.836691 -44 AAAAGAGTACAAAGGATTTTGAA 1 206 1 AAAGGATTTT 0.901728 -13 CAAGCACTGCAACGGCATTTTTATCGTATT 5 129 1 AACGGCATTT 0.946494 -172 CGGCATTTTTATCGTATTTTGTAAAAAATT 5 141 1 ATCGTATTTT 0.879562 -160 ********** Masking position 8 Map Score: 1.66839 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 406 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 TAAATATTCAAAATAAAGGCTTTTTTGTGC 1 77 0 AAATAAAGGC 0.924279 -142 AAATCTGTCGCAATTATAGCGGAAAACCAA 1 164 0 CAATTATAGC 0.856152 -55 AAGTGCGGTAAAATATCAGCCTATTTTTTA 2 23 0 AAATATCAGC 0.93765 -203 CAAATATTTTCAATTACAGCGGAAAAAGTG 2 48 0 CAATTACAGC 0.959427 -178 GTTTTCATACAAATTAAAGCATATTAAGTA 3 52 1 AAATTAAAGC 0.95233 -50 TTGGACTTTAAAATTTAGCCTCCATTTACC 4 30 1 AAATTTAGCC 0.790115 -42 AAATTTAATCAAATAATTAG 4 62 0 AAATTTAATC 0.721547 -10 CCAATATTAGCAATATCGGCAAAAGATGAA 5 76 0 CAATATCGGC 0.935267 -225 ********** Masking position 3 Map Score: 2.78659 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 348 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 AACTTGATTAATTCACATACCTAGAATA 3 8 0 ATTCCATACC 0.975193 -94 AATTAATCAAGTTCACATACCCCTATGTTTT 3 26 1 GTTCCATACC 0.993625 -76 ATACCCCTATGTTTTCATACAAATTAAAGCA 3 42 1 GTTTCATACA 0.962132 -60 ATTAGCTAAAGTTTGCACACCAATTCCTGTT 5 247 0 GTTTCACACC 0.983384 -54 **** ****** Masking position 7 Map Score: 0.229785 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 13 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 10 ********** No masking Map Score: -5.44113e-14 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 11 ********** No masking Map Score: -5.44113e-14 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: -5.44113e-14 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