AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_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) Motif number 1 ACCGCTTTTTAATGTGATGTAGTGGAGGGA 1 18 0 AATGTGATGT 0.712476 -283 ACATCACATTAAAAAGCGGTATCGCCGTGA 1 28 1 AAAAAGCGGT 0.965942 -273 ATAAATGCACAAAGTGCGGTAAGTTTTTTG 1 124 0 AAAGTGCGGT 0.996304 -177 TTTAATCAACCAAGTGCGGTCAAAACAAAC 2 12 1 CAAGTGCGGT 0.987594 -54 GGTCAAAACAAACGTGATTTTGACCGCACT 2 29 1 AACGTGATTT 0.700731 -37 ATACAAATAAAAAGTGCGGTCAAAATCACG 2 41 0 AAAGTGCGGT 0.996304 -25 AGCTAAGCTGAAAGTGATGACAACTGGCT 3 10 0 AAAGTGATGA 0.837502 -52 TATAATCCCTAACAAGAGTTATACAGTTGT 3 39 1 AACAAGAGTT 0.572126 -23 TTAGGAAAAGTGCGGTCAAAATTAAC 5 7 1 AAAGTGCGGT 0.996304 -101 GGAGGTTCAGAAAGTGCGGTTAATTTTGAC 5 25 0 AAAGTGCGGT 0.996304 -83 CCTCTTTAGCAAAGAGAGGAGTTGATCGAG 5 53 1 AAAGAGAGGA 0.941908 -55 AATATTCTTTCACAAGCGGTGGATTGTTAA 6 29 0 CACAAGCGGT 0.85806 -217 TCACGTACTCAAAGAGCGGTCAAATTTTGA 6 141 1 AAAGAGCGGT 0.993585 -105 GATTTTTGCAAACGTGCGTAAATTTTGAAA 6 173 1 AACGTGCGTA 0.914058 -73 ********** Masking position 2 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 AAATGCACAAAGTGCGGTAAGTTTTTTGAA 1 122 0 AGTGCGGTAA 0.996764 -179 TAATCAACCAAGTGCGGTCAAAACAAACGT 2 14 1 AGTGCGGTCA 0.999334 -52 ACAAATAAAAAGTGCGGTCAAAATCACGTT 2 39 0 AGTGCGGTCA 0.999334 -27 TTAGGAAAAGTGCGGTCAAAATTAACCG 5 9 1 AGTGCGGTCA 0.999334 -99 AGGTTCAGAAAGTGCGGTTAATTTTGACCG 5 23 0 AGTGCGGTTA 0.996764 -85 ACGTACTCAAAGAGCGGTCAAATTTTGATT 6 143 1 AGAGCGGTCA 0.996587 -103 ********** Masking position 8 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 AAAACAGCAAAATTTCCTATCAAATGGGAGCTGG 1 67 1 ATTTCCTAAA 0.959742 -234 GATTGTAAAAACTTGCCATAAAAAACCGCCACGA 1 171 0 ATTGCCAAAA 0.994985 -130 CATCTCCTGTTCTTGCCATAGAAATACTAGATTT 1 213 0 TTTGCCAAAA 0.968961 -88 GGCGAATGTAATTCGCCCCTACAATTTATCTATT 4 15 0 ATCGCCTCAA 0.892558 -81 GGCGAATTACATTCGCCTGATAAACCACCGATGT 4 32 1 ATCGCCAAAA 0.989707 -64 GGCAAATTACATTTGCCCAAAAACATCGGTGGTT 4 54 0 ATTGCCAAAC 0.978901 -42 GGCAAATGTAATTTGCCTACAAAATCGATAAAAA 4 71 1 ATTGCCCAAA 0.983737 -25 TGAGTTTTTTATTTTCCCTATAAATATAAATAAT 5 84 0 ATTTCCAAAA 0.984844 -24 TTGTTAAGAAAGTTTACGAATAAAA 6 2 0 ATTTACAAAA 0.864564 -244 * ***** * *** Masking position 3 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 ATTTTGCTGTTTTTGCCTGCATTCACGGCG 1 50 0 TTTTGCCTGC 0.964544 -251 GCTGGCTGGGTTTGGTAAGCTAAACATTCA 1 96 1 TTTGGTAAGC 0.877708 -205 ATCACGTTTGTTTTGACCGCACTTGGTTGA 2 17 0 TTTTGACCGC 0.98125 -49 ACAAACGTGATTTTGACCGCACTTTTTATT 2 36 1 TTTTGACCGC 0.98125 -30 ACATCGGTGGTTTATCAGGCGAATGTAATT 4 36 0 TTTATCAGGC 0.578772 -60 TTTTTATCGATTTTGTAGGCAAATTACATT 4 75 0 TTTTGTAGGC 0.979717 -21 GTGCGGTTAATTTTGACCGCACTTTTCCTA 5 12 0 TTTTGACCGC 0.98125 -96 TGAAAGAATATTTTGCAAGCGGTGTGATTG 6 47 1 TTTTGCAAGC 0.984391 -199 TTCGAACTACTTTTGTAGGCTGTGTAAACA 6 107 1 TTTTGTAGGC 0.979717 -139 TTTGATTGATTTTTGCAAACGTGCGTAAAT 6 166 1 TTTTGCAAAC 0.844551 -80 ********** Masking position 3 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 AAGCGGTATCGCCGTGAATGCAGGCAAAAACAGCA 1 41 1 GCCTGATGGC 0.878413 -260 AATTATCGTGGCGATGTATAAATGCACAAAGTGCG 1 136 0 GCGTGTTTGC 0.939617 -165 TAATTTCGTGGCGGTTTTTTATGGCAAGTTTTTAC 1 166 1 GCGTTTTGGC 0.952689 -135 TAAGCTGAAAGTGATGACAACTGGCT 3 2 0 GTGTGAAGGC 0.959431 -60 TGATAAACCACCGATGTTTTTGGGCAAATGTAATT 4 49 1 CCGTGTTGGC 0.991785 -47 TTCAGAAAGTGCGGTTAATTTTGACCGCACTTTTC 5 15 0 GCGTTATGAC 0.944425 -93 TATTTTGCAAGCGGTGTGATTGGGCTTGTTTTTTG 6 55 1 GCGTGTAGGC 0.993879 -191 *** *** * *** Masking position 5 Map Score: 5.61289 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 87 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 TTTAATGTGATGTAGTGGAGGGAGGCGTAT 1 11 0 TGTAGTGGAG 0.984415 -290 GCCACGAAATTATCGTGGCGATGTATAAAT 1 148 0 TATCGTGGCG 0.993022 -153 GCCACGATAATTTCGTGGCGGTTTTTTATG 1 159 1 TTTCGTGGCG 0.993018 -142 ATAGATAAATTGTAGGGGCGAATTACATTC 4 16 1 TGTAGGGGCG 0.993252 -80 ********** Masking position 3 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 7 GTGCGGTAAGTTTTTTGAATGTTTAGCTTA 1 111 0 TTTTTTGAAT 0.838168 -190 TTACAATCTTTTATTTAAATCTAGTATTTC 1 197 1 TTATTTAAAT 0.909222 -104 AGCCGAATATTTTTTTATTTTAACGAGAGA 1 279 1 TTTTTTATTT 0.931448 -22 ACCGCACTTTTTATTTGTATCAACT 2 51 1 TTATTTGTAT 0.9394 -15 TGATCGAGCATTATTTATATTTATAGGGAA 5 75 1 TTATTTATAT 0.958328 -33 TGAGTTTTTTATTTTCCCTATAAA 5 94 0 TTTTTTATTT 0.931448 -14 ACACCCTACGTTAATTATTTCTTAGCATTC 6 209 1 TTAATTATTT 0.786011 -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 8 TCGTGGCGGTTTTTTATGGCAAGTTTTTACA 1 171 1 TTTTATGGCA 0.978316 -130 AAATCTAGTATTTCTATGGCAAGAACAGGAG 1 213 1 TTTTATGGCA 0.978313 -88 TTCCCTTAGATTTGTATAGAATAGCCGAATA 1 257 1 TTTTATAGAA 0.828944 -44 AACCACCGATGTTTTTGGGCAAATGTAATTT 4 54 1 GTTTTGGGCA 0.941 -42 TTTTATCGATTTTGTAGGCAAATTACATTTG 4 73 0 TTTTAGGCAA 0.950092 -23 ATTATTTATATTTATAGGGAAAATAAAAAAC 5 84 1 TTTTAGGGAA 0.978314 -24 GATTGGGCTTGTTTTTTGCAAAGATAAGCAT 6 72 1 GTTTTTGCAA 0.821905 -174 *** ******* Masking position 11 Map Score: 3.89193 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 162 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 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