AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_Glycogen_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 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) Motif number 1 TCCCTCCACTACATCACATTAAAAAGCGGT 1 18 1 ACATCACATT 0.69912 -283 TCACGGCGATACCGCTTTTTAATGTGATGT 1 28 0 ACCGCTTTTT 0.963761 -273 CAAAAAACTTACCGCACTTTGTGCATTTAT 1 124 1 ACCGCACTTT 0.996067 -177 GTTTGTTTTGACCGCACTTGGTTGATTAAA 2 12 0 ACCGCACTTG 0.986781 -54 AGTGCGGTCAAAATCACGTTTGTTTTGACC 2 29 0 AAATCACGTT 0.687098 -37 CGTGATTTTGACCGCACTTTTTATTTGTAT 2 41 1 ACCGCACTTT 0.996067 -25 AGCCAGTTGTCATCACTTTCAGCTTAGCT 3 10 1 TCATCACTTT 0.828557 -52 ACAACTGTATAACTCTTGTTAGGGATTATA 3 39 0 AACTCTTGTT 0.556311 -23 GTTAATTTTGACCGCACTTTTCCTAA 5 7 0 ACCGCACTTT 0.996067 -101 GTCAAAATTAACCGCACTTTCTGAACCTCC 5 25 1 ACCGCACTTT 0.996067 -83 CTCGATCAACTCCTCTCTTTGCTAAAGAGG 5 53 0 TCCTCTCTTT 0.938287 -55 TTAACAATCCACCGCTTGTGAAAGAATATT 6 29 1 ACCGCTTGTG 0.850044 -217 TCAAAATTTGACCGCTCTTTGAGTACGTGA 6 141 0 ACCGCTCTTT 0.99317 -105 TTTCAAAATTTACGCACGTTTGCAAAAATC 6 173 0 TACGCACGTT 0.908914 -73 ********** Masking position 9 Map Score: 30.088 Number of sites scoring better than the average of aligned sites = 2069 Number in coding regions = 1457 Number in noncoding regions = 612 Number of orfs with sites within 600 bp upstream = 371 Fraction of orfs with sites within 600 bp upstream = 0.0595888 Motif number 2 TTCAAAAAACTTACCGCACTTTGTGCATTT 1 122 1 TTACCGCACT 0.996142 -179 ACGTTTGTTTTGACCGCACTTGGTTGATTA 2 14 0 TGACCGCACT 0.999222 -52 AACGTGATTTTGACCGCACTTTTTATTTGT 2 39 1 TGACCGCACT 0.999222 -27 CGGTTAATTTTGACCGCACTTTTCCTAA 5 9 0 TGACCGCACT 0.999222 -99 CGGTCAAAATTAACCGCACTTTCTGAACCT 5 23 1 TAACCGCACT 0.996142 -85 AATCAAAATTTGACCGCTCTTTGAGTACGT 6 143 0 TGACCGCTCT 0.996249 -103 ********** Masking position 3 Map Score: 23.7854 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 257 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 CCAGCTCCCATTTGATAGGAAATTTTGCTGTTTT 1 67 0 TTTAGGAAAT 0.950346 -234 TCGTGGCGGTTTTTTATGGCAAGTTTTTACAATC 1 171 1 TTTTGGCAAT 0.993764 -130 AAATCTAGTATTTCTATGGCAAGAACAGGAGATG 1 213 1 TTTTGGCAAA 0.961674 -88 AATAGATAAATTGTAGGGGCGAATTACATTCGCC 4 15 1 TTGAGGCGAT 0.869611 -81 ACATCGGTGGTTTATCAGGCGAATGTAATTCGCC 4 32 0 TTTTGGCGAT 0.987256 -64 AACCACCGATGTTTTTGGGCAAATGTAATTTGCC 4 54 1 GTTTGGCAAT 0.97386 -42 TTTTTATCGATTTTGTAGGCAAATTACATTTGCC 4 71 0 TTTGGGCAAT 0.979898 -25 ATTATTTATATTTATAGGGAAAATAAAAAACTCA 5 84 1 TTTTGGAAAT 0.981206 -24 TTTTATTCGTAAACTTTCTTAACAA 6 2 1 TTTTGTAAAT 0.836735 -244 *** * ***** * Masking position 12 Map Score: 10.052 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 148 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 CGCCGTGAATGCAGGCAAAAACAGCAAAAT 1 50 1 GCAGGCAAAA 0.962373 -251 TGAATGTTTAGCTTACCAAACCCAGCCAGC 1 96 0 GCTTACCAAA 0.870934 -205 TCAACCAAGTGCGGTCAAAACAAACGTGAT 2 17 1 GCGGTCAAAA 0.980081 -49 AATAAAAAGTGCGGTCAAAATCACGTTTGT 2 36 0 GCGGTCAAAA 0.980081 -30 AATTACATTCGCCTGATAAACCACCGATGT 4 36 1 GCCTGATAAA 0.563669 -60 AATGTAATTTGCCTACAAAATCGATAAAAA 4 75 1 GCCTACAAAA 0.978455 -21 TAGGAAAAGTGCGGTCAAAATTAACCGCAC 5 12 1 GCGGTCAAAA 0.980081 -96 CAATCACACCGCTTGCAAAATATTCTTTCA 6 47 0 GCTTGCAAAA 0.983426 -199 TGTTTACACAGCCTACAAAAGTAGTTCGAA 6 107 0 GCCTACAAAA 0.978455 -139 ATTTACGCACGTTTGCAAAAATCAATCAAA 6 166 0 GTTTGCAAAA 0.836574 -80 ********** Masking position 8 Map Score: 15.1791 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 268 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 5 ATACGCCTCCCTCCACTACATCACATTAAA 1 11 1 CTCCACTACA 0.980523 -290 ATTTATACATCGCCACGATAATTTCGTGGC 1 148 1 CGCCACGATA 0.99126 -153 CATAAAAAACCGCCACGAAATTATCGTGGC 1 159 0 CGCCACGAAA 0.991258 -142 GAATGTAATTCGCCCCTACAATTTATCTAT 4 16 0 CGCCCCTACA 0.991548 -80 ********** Masking position 8 Map Score: 2.76778 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 16 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 ATCACATTAAAAAGCGGTATCGCCGTGAAT 1 30 1 AAAGCGGTAT 0.967349 -271 TAATCCCTAACAAGAGTTATACAGTTGTGA 3 41 1 CAAGAGTTAT 0.822075 -21 TCTCTTTGCTAAAGAGGAGGTTCAGAAAGT 5 40 0 AAAGAGGAGG 0.961504 -68 TCTTTAGCAAAGAGAGGAGTTGATCGAGCA 5 55 1 AGAGAGGAGT 0.916778 -53 TATTCTTTCACAAGCGGTGGATTGTTAAGA 6 27 0 CAAGCGGTGG 0.991056 -219 GAATATTTTGCAAGCGGTGTGATTGGGCTT 6 52 1 CAAGCGGTGT 0.99264 -194 ********** Masking position 3 Map Score: 2.70523 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 147 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TTCGTGGCGGTTTTTTATGGCAAGTTTTTACA 1 170 1 TTTTTATGCA 0.910959 -131 TAAATCTAGTATTTCTATGGCAAGAACAGGAG 1 212 1 ATTTTATGCA 0.982784 -89 TTTCCCTTAGATTTGTATAGAATAGCCGAATA 1 256 1 ATTTTATGAA 0.971633 -45 AACAAACGTGATTTTGACCGCACTTTTTATTT 2 35 1 ATTTGACGCA 0.97413 -31 ATTTTTATCGATTTTGTAGGCA 4 84 0 ATTTTATGAT 0.929437 -12 AGTGCGGTTAATTTTGACCGCACTTTTCCTAA 5 11 0 ATTTGACGCA 0.97413 -97 CATTATTTATATTTATAGGGAAAATAAAAAAC 5 83 1 ATTTTAGGAA 0.92931 -25 GAGCGGTCAAATTTTGATTGATTTTTGCAAAC 6 154 1 ATTTGATGAT 0.928135 -92 **** *** *** Masking position 7 Map Score: 7.42809 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 135 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 8 GTGCGGTAAGTTTTTTGAATGTTTAGCTTA 1 111 0 TTTTTTGAAT 0.844616 -190 TTACAATCTTTTATTTAAATCTAGTATTTC 1 197 1 TTATTTAAAT 0.913127 -104 AGCCGAATATTTTTTTATTTTAACGAGAGA 1 279 1 TTTTTTATTT 0.93447 -22 ACCGCACTTTTTATTTGTATCAACT 2 51 1 TTATTTGTAT 0.942093 -15 TGATCGAGCATTATTTATATTTATAGGGAA 5 75 1 TTATTTATAT 0.960209 -33 TGAGTTTTTTATTTTCCCTATAAA 5 94 0 TTTTTTATTT 0.93447 -14 ACACCCTACGTTAATTATTTCTTAGCATTC 6 209 1 TTAATTATTT 0.794026 -37 ********** Masking position 5 Map Score: 4.44327 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 221 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 9 ********** No masking Map Score: -4.87842e-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 10 ********** No masking Map Score: -4.87842e-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 11 ********** No masking Map Score: -4.87842e-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