AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_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 HI0124 234 inorganic pyrophosphatase (ppa) #2 HI0596 300 ornithine carbamoyltransferase (arcB) #3 HI0811 134 argininosuccinate lyase (argH) #4 HI1727 155 argininosuccinate synthetase (argG) Motif number 1 ACCTTATTACTTCCAATTTTTTACTTAACTTCAAGGAACA 1 13 0 TTTTTTTTAT 0.980025 -222 CTCATAACTATTCATAATTTTGACCGCACTTTATCCTAAA 1 103 0 TTATTTTCAT 0.949569 -132 ATGGATCTATTTGCTGATTTTCTCTACAAATGAGACTGCG 1 143 1 TTATTTTTAA 0.921919 -92 GCAACAAGTATAGCAGTTTTCTGCGAACTCGCAGTCTCA 1 173 0 TATTTTCAT 0.913081 -62 GCTATACTTGTTGCGTTTTTTAACTTGATAAAATGAAGGA 1 199 1 TTTTTTTTAA 0.95488 -36 AAATATGTTTTAGTTTATTTTTGATGAAGAGGAATGTGTC 2 29 0 TAATTTTTAA 0.868203 -272 AAATAAACTAAAACATATTTTCGTTTAAATTCATCTACTA 2 49 1 AAATTTTTAT 0.831795 -252 ATCTAACTCTTTATTGTTATTTGTTTGATTTCTAATAGTA 2 84 0 TTTTATTTAT 0.919017 -217 CAATAAAGAGTTAGATTATTTTATTAAATTCTAATAATAC 2 108 1 TTTATTTTAT 0.797595 -193 ATCTTTCATTTTGTCCATTTTATTTGTATTAGTGCTAT 3 9 0 TTATTTTTAT 0.964754 -126 ATGAAAGATTTTGTCCATTTTTGTTTTATTATTAATATAG 3 40 1 TTATTTTTAT 0.964754 -95 TTAATTAATTATTCTATTATTGTGCATATTTATTCATAAA 3 88 0 ATTTATTCAT 0.71654 -47 AATTTTTCCTTTTTGTTTTAATTAATTATTCTA 3 112 0 TTTTTTTTAT 0.980025 -23 AAATTAGGATTTTTTATGCACAAAGCTAAATAAA 4 5 1 TATTTTTCAA 0.890375 -151 CAAAGCTAAATAAAGATTTTTGCTTTTAATGCACAAAACA 4 31 1 TATTTTTTAT 0.964754 -125 GTTATACTCTATAGAATTTTTATTCACAAAAATCGATTAT 4 93 1 ATTTTTTCAA 0.824983 -63 TATTCACAAAAATCGATTATTTATTCAATTCTAATTATTA 4 113 1 AATTATTTAT 0.671907 -43 ** ***** * * * Masking position 10 Map Score: 19.9425 Number of sites scoring better than the average of aligned sites = 847 Number in coding regions = 598 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 2 TACTTATCGTTTTTATGATGTAAAATAGCG 1 54 0 TTTTATGATG 0.741568 -181 TTTGCGTGAGTTTTATTTAGGATAAAGTGC 1 88 1 TTTTATTTAG 0.853858 -147 GTTTCCTTCATTTTATCAAGTTAAAAAACG 1 212 0 TTTTATCAAG 0.918614 -23 TTTTATTAAGTATAGATAGA 2 1 1 TTTTATTAAG 0.922658 -300 TTAGTTTATTTTTGATGAAGAGGAATGTGT 2 30 0 TTTGATGAAG 0.710961 -271 GAAAATATGTTTTAGTTTATTTTTGATGAA 2 41 0 TTTAGTTTAT 0.501162 -260 AGTTAGATTATTTTATTAAATTCTAATAAT 2 116 1 TTTTATTAAA 0.579918 -185 AAATCTTTCATTTTGTCCATTTTATTTGTA 3 21 0 TTTTGTCCAT 0.92444 -114 AAATGAAAGATTTTGTCCATTTTTGTTTTA 3 38 1 TTTTGTCCAT 0.92444 -97 TCCATTTTTGTTTTATTATTAATATAGAAT 3 53 1 TTTTATTATT 0.611149 -82 TAGAATATTGCTTTATGAATAAATATGCAC 3 77 1 CTTTATGAAT 0.894615 -58 ATTATTCTATTATTGTGCATATTTATTCAT 3 91 0 TATTGTGCAT 0.613724 -44 TCCTTTTTGTTTTAATTAATTATTCTATTA 3 109 0 TTTAATTAAT 0.623233 -26 CTTTATTTAGCTTTGTGCATAAAAAATCCT 4 16 0 CTTTGTGCAT 0.909335 -140 AAGCAAAAATCTTTATTTAGCTTTGTGCAT 4 26 0 CTTTATTTAG 0.735849 -130 TTGTCTAGTGTTTTGTGCATTAAAAGCAAA 4 49 0 TTTTGTGCAT 0.954534 -107 CACTTTTCCTCTTTGTCTAGTGTTTTGTGC 4 61 0 CTTTGTCTAG 0.771938 -95 AATAATCGATTTTTGTGAATAAAAATTCTA 4 104 0 TTTTGTGAAT 0.958475 -52 ********** Masking position 6 Map Score: 14.9684 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 787 Number in noncoding regions = 211 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 3 GTGAGTTTTATTTAGGATAAAGTGCGGTCA 1 93 1 TTTAGGATAA 0.769258 -142 TTTTAGTATTATTAGAATTTAATAAAATAA 2 123 0 ATTAGAATTT 0.955968 -178 AATGCCAGTATGTAGAATTTTATTGCGAGA 2 154 0 TGTAGAATTT 0.907237 -147 TTATTATTAATATAGAATATTGCTTTATGA 3 65 1 TATAGAATAT 0.912229 -70 TATGCACAATAATAGAATAATTAATTAAAA 3 100 1 AATAGAATAA 0.818886 -35 AAATTAGGATTTTTTATGCACA 4 3 1 ATTAGGATTT 0.924778 -153 GGTTATACTCTATAGAATTTTTATTCACAA 4 92 1 TATAGAATTT 0.943417 -64 CTTACTAATAATTAGAATTGAATAAATAAT 4 128 0 ATTAGAATTG 0.888123 -28 ********** Masking position 4 Map Score: 4.28924 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 163 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 GCAAACGTTTACTTATCGTTTTTATGATGTAAA 1 60 0 ACTTCGTTTT 0.984612 -175 CCATCTCATAACTATTCATAATTTTGACCGCAC 1 114 0 ACTTCATATT 0.811534 -121 AARCTGCTATACTTGTTGCGTTTTTTAACTTGA 1 194 1 ACTTTGCTTT 0.92071 -41 AAATAATCTAACTCTTTATTGTTATTTGTTTGA 2 96 0 ACTTTATGTT 0.930016 -205 GTAAAATGAAATTTGTTGTCGTTTTTCAACTGG 2 185 0 ATTTTGTGTT 0.905593 -116 CATTCGAGATACTGCTTGTTGTTCGAACAGTTG 2 231 0 ACTTTGTGTT 0.979885 -70 AATAATCTCCTTGTGTTTTGACTATACA 2 283 0 TCTTTGTTTT 0.886809 -18 AATTTTTCCTTTTTGTTTTAATTA 3 121 0 ATTTCCTTTT 0.841685 -14 GTATAACCGCACTTTTCCTCTTTGTCTAGTGTT 4 67 0 ACTTCCTTTT 0.964285 -89 *** **** *** Masking position 6 Map Score: 4.77782 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 115 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 TGGAAGTAATAAGGTGCGCTATTTTACATC 1 38 1 AAGGTGCGCT 0.991158 -197 TATTTAGGATAAAGTGCGGTCAAAATTATG 1 101 1 AAAGTGCGGT 0.995894 -134 ACAAAGAGGAAAAGTGCGGTTATACTCTAT 4 75 1 AAAGTGCGGT 0.995894 -81 ********** Masking position 2 Map Score: 2.61345 Number of sites scoring better than the average of aligned sites = 1131 Number in coding regions = 713 Number in noncoding regions = 418 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 6 GTTAAGTAAAAAATTGGAAGTAATAAGGTG 1 24 1 AAATTGGAAG 0.915317 -211 TTAACTTGATAAAATGAAGGAAACAAA 1 218 1 AAAATGAAGG 0.959689 -17 TAAGAGAGGTAAAATGAAATTTGTTGTCGT 2 196 0 AAAATGAAAT 0.930077 -105 TAAAATGGACAAAATGAAAGATTTTGTCCA 3 27 1 AAAATGAAAG 0.981429 -108 TAATAAAACAAAAATGGACAAAATCTTTCA 3 41 0 AAAATGGACA 0.897538 -94 AATTAAAACAAAAAGGAAAAATT 3 122 1 AAAAGGAAAA 0.895575 -13 ********** Masking position 3 Map Score: 1.85454 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 195 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 TTTATGATGTAAAATAGCGCACCTTATTACT 1 42 0 AAAATACGCA 0.97475 -193 ATCCTAAATAAAACTCACGCAAACGTTTACT 1 80 0 AAACTCCGCA 0.989007 -155 AATAATACTAAAAATCTCGCAATAAAATTCT 2 140 1 AAAATCCGCA 0.993522 -161 AAAAATGGACAAAATCTTTCATTTTGTCCAT 3 31 0 AAAATCTTCA 0.906686 -104 ****** **** Masking position 5 Map Score: 0.353457 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 34 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 TAAAAATCTCGCAATAAAATTCTACATACT 2 148 1 GCAATAAAAT 0.863171 -153 CTACATACTGGCATTACCAGTTGAAAAACG 2 169 1 GCATTACCAG 0.956121 -132 TCGAACAGTTGCATTATAAGAGAGGTAAAA 2 212 0 GCATTATAAG 0.97027 -89 TTAGCTTTGTGCATAAAAAATCCTAATTT 4 10 0 GCATAAAAAA 0.863172 -146 AGTGTTTTGTGCATTAAAAGCAAAAATCTT 4 43 0 GCATTAAAAG 0.988017 -113 ********** Masking position 6 Map Score: 0.396156 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 179 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 ********** No masking Map Score: -1.18417e-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: -1.18417e-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 11 ********** No masking Map Score: -1.18417e-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