AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i151_Transhydrogenase_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 HI1354 300 glutaminyl-tRNA synthetase (glnS) #2 HI1355 65 conserved hypothetical protein #3 HI1356 61 4-alpha-glucanotransferase (malQ) #4 HI1358 95 glycogen operon protein (glgX) #5 HI1360 107 glycogen synthase (glgA) #6 HI1361 245 glycogen phosphorylase (glgP) #7 HI1362 261 NAD(P) transhydrogenase, subunit alpha (pntA) Motif number 1 TCACGGCGATACCGCTTTTTAATGTGATGT 1 28 0 ACCGCTTTTT 0.985382 -273 CAAAAAACTTACCGCACTTTGTGCATTTAT 1 124 1 ACCGCACTTT 0.998468 -177 GTTTGTTTTGACCGCACTTGGTTGATTAAA 2 12 0 ACCGCACTTG 0.996875 -54 CGTGATTTTGACCGCACTTTTTATTTGTAT 2 41 1 ACCGCACTTT 0.998468 -25 GTTAATTTTGACCGCACTTTTCCTAA 5 7 0 ACCGCACTTT 0.998468 -101 GTCAAAATTAACCGCACTTTCTGAACCTCC 5 25 1 ACCGCACTTT 0.998468 -83 TTAACAATCCACCGCTTGTGAAAGAATATT 6 29 1 ACCGCTTGTG 0.885039 -217 TCAAAATTTGACCGCTCTTTGAGTACGTGA 6 141 0 ACCGCTCTTT 0.997085 -105 TCAAAAATTTACCGCACTTTCCATAAAAAA 7 52 0 ACCGCACTTT 0.998468 -210 ********** Masking position 9 Map Score: 34.6299 Number of sites scoring better than the average of aligned sites = 1309 Number in coding regions = 863 Number in noncoding regions = 446 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 2 AAATGCACAAAGTGCGGTAAGTTTTTTGAAT 1 121 0 AGTGCGGTAG 0.996873 -180 TAATCAACCAAGTGCGGTCAAAACAAACGTG 2 14 1 AGTGCGGTAA 0.999036 -52 ACAAATAAAAAGTGCGGTCAAAATCACGTTT 2 38 0 AGTGCGGTAA 0.999036 -28 TTAGGAAAAGTGCGGTCAAAATTAACCGC 5 9 1 AGTGCGGTAA 0.999036 -99 AGGTTCAGAAAGTGCGGTTAATTTTGACCGC 5 22 0 AGTGCGGTAA 0.999036 -86 ACGTACTCAAAGAGCGGTCAAATTTTGATTG 6 143 1 AGAGCGGTAA 0.995372 -103 TTTTATGGAAAGTGCGGTAAATTTTTGAGAT 7 54 1 AGTGCGGTAA 0.999036 -208 ******** ** Masking position 10 Map Score: 29.292 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 351 Number in noncoding regions = 260 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 3 GAATGCAGGCAAAAACAGCAAAATTTCCTATCA 1 56 1 AAAACACAAA 0.985878 -245 CTTGCCATAAAAAACCGCCACGAAATTATCGTG 1 161 0 AAAACGCCGA 0.942956 -140 ATTTGCCTACAAAATCGATAAAAAT 4 81 1 AAAACGTAAA 0.954979 -15 ATCTTTGCAAAAAACAAGCCCAATCACACCGCT 6 64 0 AAAAAACCAA 0.906771 -182 CACGTACTCAAAGAGCGGTCAAATTTTGATTGA 6 142 1 AAGACGTAAA 0.815623 -104 CACGTTTGCAAAAATCAATCAAAATTTGACCGC 6 156 0 AAAACATAAA 0.967524 -90 TAATAAAATTAAAAGCACCACAAGTTTTTTACT 7 11 1 AAAACACCAA 0.991097 -251 CTTTCCATAAAAAAACACCGCAAGTAAAAAACT 7 33 0 AAAACACCAA 0.991097 -229 ATCCCACATAAAAAACATCTCAAAAATTTACCG 7 68 0 AAAACACCAA 0.991097 -194 AATATCTTGTAAAACCACTTAAAAACGTTACCT 7 120 1 AAAACATAAA 0.967524 -142 **** ** * *** Masking position 4 Map Score: 15.2657 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 175 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 ACAGCAAAATTTCCTATCAAATGGGAGCTG 1 70 1 TTCCTATCAA 0.802446 -231 AAGCTAAACATTCAAAAAACTTACCGCACT 1 112 1 TTCAAAAAAC 0.563049 -189 GTAAAAACTTGCCATAAAAAACCGCCACGA 1 171 0 GCCATAAAAA 0.926796 -130 TCCTGTTCTTGCCATAGAAATACTAGATTT 1 213 0 GCCATAGAAA 0.795688 -88 ACCAAGTGCGGTCAAAACAAACGTGATTTT 2 20 1 GTCAAAACAA 0.712761 -46 TTAGCTATAATCCCTAACAAGAGTTATACA 3 34 1 TCCCTAACAA 0.960127 -28 AATTACATTTGCCCAAAAACATCGGTGGTT 4 54 0 GCCCAAAAAC 0.929962 -42 TTTTTTATTTTCCCTATAAATATAAATAAT 5 84 0 TCCCTATAAA 0.92455 -24 CAAAAAACAAGCCCAATCACACCGCTTGCA 6 60 0 GCCCAATCAC 0.924075 -186 TACCGCACTTTCCATAAAAAAACACCGCAA 7 43 0 TCCATAAAAA 0.904161 -219 TTTTTCGTGATCCCTATCACAATATCTTGT 7 100 1 TCCCTATCAC 0.938937 -162 ********** Masking position 6 Map Score: 7.65726 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 326 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 TTTTGCTGTTTTTGCCTGCATTCACGGCGA 1 49 0 TTTGCCTGCA 0.954358 -252 GCAAATTACATTTGCCCAAAAACATCGGTG 4 57 0 TTTGCCCAAA 0.756095 -39 GCAAATGTAATTTGCCTACAAAATCGATAA 4 72 1 TTTGCCTACA 0.955211 -24 AACTCCTCTCTTTGCTAAAGAGGAGGTTCA 5 46 0 TTTGCTAAAG 0.859085 -62 GAAAGAATATTTTGCAAGCGGTGTGATTGG 6 48 1 TTTGCAAGCG 0.971444 -198 TATGCTTATCTTTGCAAAAAACAAGCCCAA 6 74 0 TTTGCAAAAA 0.852641 -172 TTGATTGATTTTTGCAAACGTGCGTAAATT 6 167 1 TTTGCAAACG 0.971995 -79 CCACAAGTTTTTTACTTGCGGTGTTTTTTT 7 28 1 TTTACTTGCG 0.641253 -234 TAATGATACATTTGCATCCGTTTGACTTTT 7 166 1 TTTGCATCCG 0.926957 -96 ********** Masking position 3 Map Score: 4.95162 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 330 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 GATAGGAAATTTTGCTGTTTTTGCCTGCAT 1 58 0 TTTGCTGTTT 0.646309 -243 CAAATGGGAGCTGGCTGGGTTTGGTAAGCT 1 87 1 CTGGCTGGGT 0.94258 -214 CGAAATTATCGTGGCGATGTATAAATGCAC 1 144 0 GTGGCGATGT 0.876131 -157 CGATAATTTCGTGGCGGTTTTTTATGGCAA 1 163 1 GTGGCGGTTT 0.934241 -138 TATTCTTTCACAAGCGGTGGATTGTTAAGA 6 27 0 CAAGCGGTGG 0.877125 -219 GAATATTTTGCAAGCGGTGTGATTGGGCTT 6 52 1 CAAGCGGTGT 0.968317 -194 ACTACTTTTGTAGGCTGTGTAAACAACATT 6 112 1 TAGGCTGTGT 0.965049 -134 ATAATTAACGTAGGGTGTGTGAATTTTCAA 6 197 0 TAGGGTGTGT 0.800475 -49 AAGTTTTTTACTTGCGGTGTTTTTTTATGG 7 32 1 CTTGCGGTGT 0.974131 -230 ********** Masking position 4 Map Score: 3.5395 Number of sites scoring better than the average of aligned sites = 396 Number in coding regions = 337 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 TAAGCTAAACATTCAAAAAACTTACCGCAC 1 111 1 ATTCAAAAAA 0.782685 -190 GAAATACTAGATTTAAATAAAAGATTGTAA 1 197 0 ATTTAAATAA 0.857363 -104 TCTCTCGTTAAAATAAAAAAATATTCGGCT 1 279 0 AAATAAAAAA 0.884132 -22 AGTTGATACAAATAAAAAGTGCGGT 2 51 0 ATACAAATAA 0.904324 -15 TTCCCTATAAATATAAATAATGCTCGATCA 5 75 0 ATATAAATAA 0.929941 -33 TTTATAGGGAAAATAAAAAACTCA 5 94 1 AAATAAAAAA 0.884132 -14 GAATGCTAAGAAATAATTAACGTAGGGTGT 6 209 0 AAATAATTAA 0.783161 -37 TAATAAAATTAAAAGCACCACA 7 3 1 ATAAAATTAA 0.486545 -259 AAAACACCGCAAGTAAAAAACTTGTGGTGC 7 25 0 AAGTAAAAAA 0.669608 -237 GAAAAATCCCACATAAAAAACATCTCAAAA 7 76 0 ACATAAAAAA 0.774643 -186 ACCTATTTTCATTCAATTAATGATACATTT 7 149 1 ATTCAATTAA 0.630279 -113 ********** Masking position 5 Map Score: 4.87229 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 382 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 8 GTGTGATTGGGCTTGTTTTTTGCAAAGATAA 6 68 1 GCTTGTTTTT 0.889993 -178 TACAAAAGTAGTTCGAATTTTATGCTTATCT 6 93 0 GTTCGATTTT 0.945017 -153 GTCAAATTTTGATTGATTTTTGCAAACGTGC 6 159 1 GATTGATTTT 0.934585 -87 TTGCAAACGTGCGTAAATTTTGAAAATTCAC 6 178 1 GCGTAATTTT 0.859235 -68 AACGTAGGGTGTGTGAATTTTCAAAATTTAC 6 190 0 GTGTGATTTT 0.982688 -56 TGTTTTTTATGTGGGATTTTTCGTGATCCCT 7 84 1 GTGGGATTTT 0.954034 -178 ATTTGCATCCGTTTGACTTTTTGTCATTTTA 7 175 1 GTTTGATTTT 0.979169 -87 ****** **** Masking position 8 Map Score: 4.06716 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 123 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 GGCAAAAACAGCAAAATTTCCTATCAAATG 1 63 1 GCAAAATTTC 0.659936 -238 TAAACATTCAAAAAACTTACCGCACTTTGT 1 116 1 AAAAACTTAC 0.827759 -185 AAAAGATTGTAAAAACTTGCCATAAAAAAC 1 179 0 AAAAACTTGC 0.959751 -122 TGCGGTCAAAACAAACGTGATTTTGACCGC 2 26 1 ACAAACGTGA 0.899379 -40 TTTTATTCGTAAACTTTCTTAACAATCC 6 9 1 GTAAACTTTC 0.796487 -237 ATTGATTTTTGCAAACGTGCGTAAATTTTG 6 170 1 GCAAACGTGC 0.969093 -76 ACCGCAAGTAAAAAACTTGTGGTGCTTTTA 7 20 0 AAAAACTTGT 0.763374 -242 AAAACCACTTAAAAACGTTACCTATTTTCA 7 130 1 AAAAACGTTA 0.780362 -132 AGATTAATGAACAAACCTTCGTCTATTCAT 7 209 0 ACAAACCTTC 0.901816 -53 ********** Masking position 5 Map Score: 1.53509 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 356 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 ********** No masking Map Score: 2.68828e-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: 2.68828e-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 12 ********** No masking Map Score: 2.68828e-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