AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_ecoli_hinf_reg_100.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 malP 300 maltodextrin phosphorylase #2 glgB 272 1,4-alpha-glucan branching enzyme #3 HI1354 300 glutaminyl-tRNA synthetase (glnS) #4 HI1355 65 conserved hypothetical protein #5 HI1356 61 4-alpha-glucanotransferase (malQ) #6 HI1358 95 glycogen operon protein (glgX) #7 HI1360 107 glycogen synthase (glgA) #8 HI1361 245 glycogen phosphorylase (glgP) Motif number 1 GCGTATTTTCAAAAAGCGGAAGGTAACTCT 1 57 0 AAAAAGCGGA 0.940418 -244 AGCCTTACCTGAAGTGAGGACGACGCAGAG 2 152 1 GAAGTGAGGA 0.899763 -121 ACATCACATTAAAAAGCGGTATCGCCGTGA 3 28 1 AAAAAGCGGT 0.96399 -273 ATAAATGCACAAAGTGCGGTAAGTTTTTTG 3 124 0 AAAGTGCGGT 0.996618 -177 TTTAATCAACCAAGTGCGGTCAAAACAAAC 4 12 1 CAAGTGCGGT 0.98399 -54 ATACAAATAAAAAGTGCGGTCAAAATCACG 4 41 0 AAAGTGCGGT 0.996618 -25 AGCTAAGCTGAAAGTGATGACAACTGGCT 5 10 0 AAAGTGATGA 0.772285 -52 TTAGGAAAAGTGCGGTCAAAATTAAC 7 7 1 AAAGTGCGGT 0.996618 -101 GGAGGTTCAGAAAGTGCGGTTAATTTTGAC 7 25 0 AAAGTGCGGT 0.996618 -83 CCTCTTTAGCAAAGAGAGGAGTTGATCGAG 7 53 1 AAAGAGAGGA 0.96209 -55 TCACGTACTCAAAGAGCGGTCAAATTTTGA 8 141 1 AAAGAGCGGT 0.994278 -105 ********** Masking position 3 Map Score: 28.6731 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 90 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 ATTCAAAAAACTTACCGCACTTTGTGCATT 3 121 1 CTTACCGCAC 0.977795 -180 CACGTTTGTTTTGACCGCACTTGGTTGATT 4 15 0 TTGACCGCAC 0.99841 -51 AAACGTGATTTTGACCGCACTTTTTATTTG 4 38 1 TTGACCGCAC 0.99841 -28 GCGGTTAATTTTGACCGCACTTTTCCTAA 7 10 0 TTGACCGCAC 0.99841 -98 GCGGTCAAAATTAACCGCACTTTCTGAACC 7 22 1 TTAACCGCAC 0.991765 -86 CAATCAAAATTTGACCGCTCTTTGAGTACG 8 144 0 TTGACCGCTC 0.993592 -102 ********** Masking position 4 Map Score: 17.8187 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 10 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 3 CTTCCGCTTTTTGAAAATACGCAACGGCCA 1 65 1 TTGAAAATAC 0.731521 -236 TGTATCTAAGTGCAAAAAATGGCCGTTGCG 1 84 0 TGCAAAAAAT 0.688274 -217 CGCCGTTCAGGTCAAAAAAATGTCACAACC 2 200 1 GTCAAAAAAA 0.899119 -73 ACAACCAGAAGTCAAAAATCCAATTGGATG 2 224 1 GTCAAAAATC 0.856718 -49 CGTGAATGCAGGCAAAAACAGCAAAATTTC 3 53 1 GGCAAAAACA 0.832411 -248 AAGCTAAACATTCAAAAAACTTACCGCACT 3 112 1 TTCAAAAAAC 0.874577 -189 ACAAATCTAAGGGAAAATAAAGGTTCATCT 3 242 0 GGGAAAATAA 0.848486 -59 ACCAAGTGCGGTCAAAACAAACGTGATTTT 4 20 1 GTCAAAACAA 0.703023 -46 AAAAAGTGCGGTCAAAATCACGTTTGTTTT 4 33 0 GTCAAAATCA 0.778341 -33 CGATTTTGTAGGCAAATTACATTTGCCCAA 6 68 0 GGCAAATTAC 0.691088 -28 GAAAAGTGCGGTCAAAATTAACCGCACTTT 7 15 1 GTCAAAATTA 0.808998 -93 TATATTTATAGGGAAAATAAAAAACTCA 7 90 1 GGGAAAATAA 0.848486 -18 TCACACCGCTTGCAAAATATTCTTTCACAA 8 44 0 TGCAAAATAT 0.715099 -202 TGCTTATCTTTGCAAAAAACAAGCCCAATC 8 72 0 TGCAAAAAAC 0.918118 -174 TACGCACGTTTGCAAAAATCAATCAAAATT 8 163 0 TGCAAAAATC 0.824172 -83 TGCGTAAATTTTGAAAATTCACACACCCTA 8 187 1 TTGAAAATTC 0.532498 -59 ********** Masking position 5 Map Score: 12.0549 Number of sites scoring better than the average of aligned sites = 1845 Number in coding regions = 1564 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 326 Fraction of orfs with sites within 600 bp upstream = 0.0523611 Motif number 4 AGCTTTAAGTGGTTGAGATCACATTTCCTTGCT 1 166 1 GGTTGGTACA 0.905564 -135 GGAGTTGCGGGGATGAGCAAGGAAATGTGATCT 1 181 0 GGATGGAGGA 0.98024 -120 ATCCCCCGCAGGATGAGGAAGGTCAACATCGAG 1 224 1 GGATGGAGGT 0.98024 -77 CTTCAGGTAAGGCTGTGAATACTCATGTATTCA 2 133 0 GGCTGGAACT 0.983902 -140 GACGCAGAGAGGATGCACAGAGTGCTGCGCCGT 2 173 1 GGATGAAAGT 0.849665 -100 AAATCCAATTGGATGGGGTGACACAATAAAACA 2 239 1 GGATGGTACA 0.969277 -34 AATGGGAGCTGGCTGGGTTTGGTAAGCTAAACA 3 89 1 GGCTGGTGGT 0.97392 -212 TACTTTTGTAGGCTGTGTAAACAACATTCACGT 8 114 1 GGCTGGAACA 0.983901 -132 ***** * * *** Masking position 4 Map Score: 5.40421 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 261 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 AGATTTTCTGCGCTGTATTGCATTGATTTG 1 113 1 CGCTGTATTG 0.926313 -188 GATGCTAATCCTGTGGTTTGCACTAGCTTT 1 142 1 CTGTGGTTTG 0.948573 -159 CCTCATCCTGCGGGGGATTAGGCAGGGAGG 1 212 0 CGGGGGATTA 0.942097 -89 ACAACGTTATCGCTAGTTTGCCAGGCTCGA 1 252 0 CGCTAGTTTG 0.902751 -49 AATTTCGTGGCGGTTTTTTATGGCAAGTTT 3 167 1 CGGTTTTTTA 0.743963 -134 CCAAAAACATCGGTGGTTTATCAGGCGAAT 6 42 0 CGGTGGTTTA 0.985684 -54 CTTTCACAAGCGGTGGATTGTTAAGAAAGT 8 23 0 CGGTGGATTG 0.990926 -223 ********** Masking position 8 Map Score: 3.33263 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 650 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 TGATTTGATGCTAATCCTGTGGTTTGCACT 1 136 1 CTAATCCTGT 0.838938 -165 CTCATCCCCGCAACTCCTCCCTGCCTAATC 1 197 1 CAACTCCTCC 0.968994 -104 GTTGACCTTCCTCATCCTGCGGGGGATTAG 1 221 0 CTCATCCTGC 0.840702 -80 ACATCTGCGCTTACTCCTGTATTACGCACT 2 51 0 TTACTCCTGT 0.869412 -222 ATACGCCTCCCTCCACTACA 3 1 1 ATACGCCTCC 0.694426 -300 AATAAAGGTTCATCTCCTGTTCTTGCCATA 3 227 0 CATCTCCTGT 0.922511 -74 CACAACTGTATAACTCTTGTTAGGGATTAT 5 40 0 TAACTCTTGT 0.736637 -22 GCACTTTCTGAACCTCCTCTTTAGCAAAGA 7 38 1 AACCTCCTCT 0.876986 -70 AATGCTCGATCAACTCCTCTCTTTGCTAAA 7 57 0 CAACTCCTCT 0.970945 -51 CTTAACAATCCACCGCTTGTGAAAGAATAT 8 28 1 CACCGCTTGT 0.906003 -218 AGCCCAATCACACCGCTTGCAAAATATTCT 8 51 0 CACCGCTTGC 0.90014 -195 ********** Masking position 8 Map Score: 5.12573 Number of sites scoring better than the average of aligned sites = 2159 Number in coding regions = 1984 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 7 AACCACAGGATTAGCATCAAATCAATGCAAT 1 129 0 TTGCATCAAA 0.852771 -172 TTGTAAAAACTTGCCATAAAAAACCGCCACG 3 172 0 TTCCATAAAA 0.794455 -129 AAATACTAGATTTAAATAAAAGATTGTAAAA 3 195 0 TTAAATAAAA 0.906457 -106 GGCTATTCTATACAAATCTAAGGGAAAATAA 3 252 0 TAAAATCTAA 0.538353 -49 TTTCTCTCGTTAAAATAAAAAAATATTCGG 3 281 0 TTAAATAAAA 0.906875 -20 AGTTGATACAAATAAAAAGTGCGGTCA 4 49 0 TAAAATAAAA 0.907035 -17 TTATTTTCCCTATAAATATAAATAATGCTCG 7 79 0 TAAAATATAA 0.730603 -29 TAAGAAAGTTTACGAATAAAA 8 1 0 TAGAATAAAA 0.926254 -245 TATGCTTATCTTTGCAAAAAACAAGCCCAAT 8 73 0 TTGCAAAAAA 0.65693 -173 TTTGCAAAGATAAGCATAAAATTCGAACTAC 8 86 1 TAGCATAAAA 0.931548 -160 ** ******** Masking position 6 Map Score: 2.89562 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 67 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 8 TCAATGCAATACAGCGCAGAAAATCTGTAT 1 109 0 ACAGCGCAGA 0.947424 -192 AATACAGGAGTAAGCGCAGATGTTTCATGA 2 58 1 TAAGCGCAGA 0.911886 -215 TGAAGTGAGGACGACGCAGAGAGGATGCAC 2 161 1 ACGACGCAGA 0.979894 -112 TTTGACCTGAACGGCGCAGCACTCTGTGCA 2 186 0 ACGGCGCAGC 0.980671 -87 ********** Masking position 8 Map Score: 0.760718 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 338 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TTTAATGTGATGTAGTGGAGGGAGGCGTAT 3 11 0 TGTAGTGGAG 0.965462 -290 GCCACGAAATTATCGTGGCGATGTATAAAT 3 148 0 TATCGTGGCG 0.984371 -153 GCCACGATAATTTCGTGGCGGTTTTTTATG 3 159 1 TTTCGTGGCG 0.984369 -142 ATAGATAAATTGTAGGGGCGAATTACATTC 6 16 1 TGTAGGGGCG 0.984882 -80 ********** Masking position 3 Map Score: 0.684216 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 90 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 TTATGAAACTGTTTCACTCCTTTACTTAAT 1 23 1 GTTTCACTCC 0.933401 -278 ACATTTCCTTGCTCATCCCCGCAACTCCTC 1 186 1 GCTCATCCCC 0.905738 -115 TCTAAGAAAAGTGGAACTCCT 1 290 1 GTGGAACTCC 0.93431 -11 CCAATGCTCTATTTAACTCCCGGTAAATCA 2 85 0 ATTTAACTCC 0.734314 -188 GCAGCACTCTGTGCATCCTCTCTGCGTCGT 2 171 0 GTGCATCCTC 0.77283 -102 CTGTTTTATTGTGTCACCCCATCCAATTGG 2 243 0 GTGTCACCCC 0.930867 -30 GAAAATAAAGGTTCATCTCCTGTTCTTGCC 3 230 0 GTTCATCTCC 0.969571 -71 AATAATGCTCGATCAACTCCTCTCTTTGCT 7 60 0 GATCAACTCC 0.913885 -48 ********** Masking position 7 Map Score: 1.03249 Number of sites scoring better than the average of aligned sites = 685 Number in coding regions = 603 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 11 TCAAATCAATGCAATACAGCGCAGAAAATC 1 114 0 GCAATACAGC 0.950932 -187 TGGCAAACTAGCGATAACGTTGTGTTGAAA 1 259 1 GCGATAACGT 0.899982 -42 AATCTGGGGCGCGATGCCGCCCCTGTTAGT 2 24 1 GCGATGCCGC 0.908531 -249 TGCATTCACGGCGATACCGCTTTTTAATGT 3 33 0 GCGATACCGC 0.625875 -268 ********** Masking position 5 Map Score: 1.31152 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 348 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 TTATCGCTAGTTTGCCAGGCTCGATGTTGA 1 246 0 TTTGCCAGGC 0.960849 -55 CCAGCTCCCATTTGATAGGAAATTTTGCTG 3 71 0 TTTGATAGGA 0.755493 -230 GCTGGCTGGGTTTGGTAAGCTAAACATTCA 3 96 1 TTTGGTAAGC 0.972389 -205 TTTTTATCGATTTTGTAGGCAAATTACATT 6 75 0 TTTTGTAGGC 0.985136 -21 TGAAAGAATATTTTGCAAGCGGTGTGATTG 8 47 1 TTTTGCAAGC 0.948697 -199 TTCGAACTACTTTTGTAGGCTGTGTAAACA 8 107 1 TTTTGTAGGC 0.985136 -139 ********** Masking position 7 Map Score: 3.61255 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 143 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 13 ********** No masking Map Score: 8.05345e-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 14 ********** No masking Map Score: 8.05345e-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 15 ********** No masking Map Score: 8.05345e-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