AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inagC_ecoli_bsub_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 nagD 47 N-acetylglucosamine metabolism #2 nagA 59 N-acetylglucosamine-6-phosphate deacetylase #3 nagB_nagE 332 nagB: glucosamine-6-phosphate deaminase, nagE: PTS system, N-acetylglucosamine-specific enzyme IIABC #4 manX 300 PTS enzyme IIAB, mannose-specific #5 manY 62 PTS enzyme IIC, mannose-specific #6 glmS 161 L-glutamine:D-fructose-6-phosphate aminotransferase #7 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #8 metS 300 methionyl-tRNA synthetase #9 yabD 78 similar to hypothetical proteins #10 yabE 155 similar to hypothetical proteins #11 yabF 144 similar to hypothetical proteins #12 yabG 161 yabG #13 veg 210 veg #14 sspF 159 small acid-soluble spore protein (alpha/beta-type SASP) #15 yabH 147 similar to hypothetical proteins #16 purR 55 transcriptional regulator #17 spoVG 193 spoVG #18 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #19 glmS 300 L-glutamine-D-fructose-6-phosphate amidotransferase #20 ybfT 218 similar to glucosamine-6-phosphate isomerase #21 yflF 171 similar to phosphotransferase system enzyme II #22 ykvY 300 similar to Xaa-Pro dipeptidase #23 ykvZ 281 similar to transcriptional regulator (LacI family) #24 glcT 62 transcriptional antiterminator (BglG family) #25 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #26 xylR 300 transcriptional regulator #27 yqgQ 109 yqgQ #28 yqgP 89 similar to hypothetical proteins #29 yqgO 66 yqgO #30 yqgN 300 similar to 5-formyltetrahydrofolate cyclo-ligase #31 levD 189 phosphotransferase system (PTS) fructose-specific enzyme IIA component #32 levR 300 transcriptional regulator (NifA/NtrC family) #33 yutF 28 similar to N-acetyl-glucosamine catabolism #34 yutE 23 yutE #35 yutD 81 yutD #36 nagA 181 N-acetylglucosamine-6-phosphate deacetylase Motif number 1 ATTTGCAGCAAAATAAAAATACGGCTTGAAACGA 3 41 0 AAAAAAAACG 0.914038 -292 TAAGGGCTACAACCAAAAACCCCTGCGTTTCGCG 4 195 0 AAAAAAACCT 0.914038 -106 TATTTCGATCAATGAATAAACAGGAAAACAGGGG 7 65 0 AAAATAACAG 0.835679 -236 TGTCTATTATAACGAAAAAAACAGAGGGCGCAAA 11 35 0 AAAAAAAACG 0.914038 -110 GTGGTGCGCAAAACAAAAAGCCCTT 12 2 0 AAAAAAACCT 0.914038 -160 TCATTATGTAAAATAAAAAACCCGCATAGCTCTC 13 30 0 AAAAAAACCG 0.981446 -181 AAAAAGGGCAAAACAAAAAGCAGTAAACAAAAGG 14 22 0 AAAAAAACAT 0.804147 -138 TTATATCCAAAATAAAAAAACCAGGGAACAGCAC 15 29 0 AAAAAAACCG 0.981446 -119 AAAATAACCAAAAAGCAAGGACTGCTGAA 18 6 1 AAAAAAACAG 0.953326 -187 ATTATAGGTAAAGCAATAATCCCGTCTTCTTTTC 19 28 0 AAAATAACCG 0.92943 -273 TTATGGTCTCAATGAAAAAGAACGGATTGCATAC 20 28 0 AAAAAAAAAG 0.804147 -191 TCAGTGATTGAGGGAAAAAAACGGGAAGTTCATT 25 63 1 AGAAAAAACG 0.807668 -176 CTGACCTTACAGCTAAAAATCATGACAACGAATT 25 188 0 AGAAAAACAG 0.889705 -51 AGAAAACGCTGACAAAAAAGCCAGCTTCCTTTCC 27 22 0 GAAAAAACCG 0.834892 -88 GCCTACTGAAAGCAAAAAATCCCGTTTTTCACGG 28 15 0 AGAAAAACCG 0.954317 -75 CAGCTGTTATAATGAAAAAAAACTATTGGAGCGG 28 61 1 AAAAAAAAAT 0.452164 -29 TTTGAGGTGTAAGAAAAAAGCCAGAGCTTTGAAA 30 238 1 AAAAAAACCG 0.981446 -63 CCCTCGGAATAGAAAAAAAGCCAGAACCTTTTTC 30 268 0 AGAAAAACCG 0.954317 -33 CTTAAAACGAAAAAAATAAACCTGTATTAAAATG 31 50 0 AAAATAACCG 0.92943 -140 TCCCCTTCAAAAGTAATAATCAGTAAACAGTTTA 32 90 0 AAAATAACAT 0.505513 -211 TCAATTGCTAAAGAATAAATCATGCGATTTGGCT 35 38 0 AAATAAACAG 0.568487 -44 ** ***** ** * Masking position 8 Map Score: 27.2186 Number of sites scoring better than the average of aligned sites = 705 Number in coding regions = 463 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 2 GGTGTTAACGATAATAAAGGAGGTAGCAA 4 282 1 AAATAAAGGG 0.518101 -19 AATTTTCTGCAGACAAAAGGCGTGACGATGGT 7 143 1 AACAAAAGGG 0.931043 -158 GTGACGATGGTCGAAAATGGCGCTTTCGTCAG 7 164 1 TGAAAATGGG 0.465601 -137 TGATAAACAAAAGGTGTTTCACGTGT 9 5 1 AACAAAAGGG 0.931043 -74 TCTTGTCGAAACACAAAAGGTGTTCGACGAAT 9 41 0 AACAAAAGGG 0.931043 -38 TTGTGTTTCGACAAGAAAGGAGTTTTTCACTT 9 57 1 AAAGAAAGGG 0.74571 -22 TTGGACTCAGCGAAAAAAGGCGCTTTCTCAAG 12 93 1 CAAAAAAGGG 0.944013 -69 ATTTTATTTGACAAAAATGGGCTCGTGTTGTA 13 164 1 AAAAAATGGC 0.55806 -47 AAAAAGCAGTAAACAAAAGGTTCACTGCCCG 14 10 0 AACAAAAGGT 0.774652 -150 TTATTGGAAACCAAAAAAGGGCAAAACAAAAA 14 37 0 CAAAAAAGGC 0.852093 -123 GCTATCACTTCTAAAAAAGGAGTTGTTTCGT 14 139 1 CAAAAAAGGG 0.944013 -21 GCTTTTATATAGGGAAAAGGTGGTGAACTACT 17 172 1 AGGAAAAGGG 0.775785 -22 AAAGGACCGCCGGCAAAAGGCTTATGTCAGCC 18 42 0 CGCAAAAGGT 0.601054 -151 AAAATCAGAATTAAAAAAGGACCGCCGGCAAA 18 57 0 TAAAAAAGGC 0.756025 -136 ACTAAGCGCCCGGAAAAAGGCTTAGTTGACGA 19 74 1 CGAAAAAGGT 0.680992 -227 CCTCCTAAGATTGTAAAAGGAGACGAAGAAAG 19 270 0 TGTAAAAGGG 0.510566 -31 GGTATATTTGAAAAAAAAGGGTATGAGGGGGA 21 145 1 AAAAAAAGGT 0.829663 -27 ATCTTCATCCCGATAAAAGGAGCGGAAATTCC 22 63 1 CATAAAAGGG 0.795923 -238 TAGAAATAAAAAAGGACTTTGTTCTCG 23 6 1 AAAAAAAGGC 0.867311 -276 TTTAATGCAGATAAAAAAGGACGATGTCGAGA 23 33 0 AAAAAAAGGC 0.867311 -249 TGAATGCATTGAAAAAAGGTTTGACGTGCAT 24 10 1 TAAAAAAGGT 0.697804 -53 TTTAAAGATTAAACAAATGGAGTGGATGAAGT 26 179 1 AACAAATGGG 0.722865 -122 TAGTTAAGTTCAAGAAATGGTGAGGAAA 27 92 1 CAGAAATGGG 0.542281 -18 AGCCAGAGCTTTGAAAAAGGTTCTGGCTTTTT 30 256 1 TGAAAAAGGT 0.534503 -45 GATGTACAAAACAGGAAAGGAGCAATAGAT 31 170 1 AAGGAAAGGG 0.516112 -20 AAAACAGATTTTATAAAAGGGGGGAAAACACC 36 87 1 TATAAAAGGG 0.677193 -95 * ******** * Masking position 6 Map Score: 19.7891 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 341 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 3 CTGCTTGTGGGAGGGAGATTATGTTATCTC 6 44 0 GAGGGAGATT 0.745551 -118 AACAGGAAAACAGGGGGGTTTTATATCAGC 7 51 0 CAGGGGGGTT 0.881772 -250 ATTTAAGCGTCAGGTGGATGTTTTTGCTCT 7 99 0 CAGGTGGATG 0.87978 -202 TAAATGTAGTGAGGTGGATGCA 13 199 1 GAGGTGGATG 0.87978 -12 GGATGTGACCCGGGGGACGTGCTGTTCCC 15 10 1 CCGGGGGACG 0.878161 -138 CTTCTGATTTCAAGGAGACTTCATGAAGTG 18 122 0 CAAGGAGACT 0.679222 -71 TTCTTCAAACCAAGGGGGTGACTCCTTGAA 19 170 1 CAAGGGGGTG 0.92846 -131 AAAACATGTAGGAGGGGACGATTGAAAGTC 19 226 1 GGAGGGGACG 0.902358 -75 AGTCAAATTTCAAGGGGACTTTCAATCGTC 19 242 0 CAAGGGGACT 0.940668 -59 TAAGATTGTAAAAGGAGACGAAGAAAGTCA 19 267 0 AAAGGAGACG 0.477593 -34 AAAAGGGTATGAGGGGGATGGGT 21 159 1 GAGGGGGATG 0.982077 -13 CGTTCAATCGCAGGGGGGTTGTTCCGTTTG 22 143 0 CAGGGGGGTT 0.881772 -158 CATTCCAGATCAAGGGGATTTAGAAAGAAG 23 255 1 CAAGGGGATT 0.938595 -27 TTAAACAAATGGAGTGGATGAAGTGGATAT 26 187 1 GGAGTGGATG 0.54337 -114 TTTCTATTCCGAGGGGGATGAGAG 30 287 1 GAGGGGGATG 0.982077 -14 TATTACTTTTGAAGGGGACTGGCCCTCCAG 32 106 1 GAAGGGGACT 0.940668 -195 ATATACACAAAGGGGATGCTGTC 34 9 1 AAAGGGGATG 0.868413 -15 TTTAGCAATTGATGGGGACGGGGCAATGAA 35 60 1 GATGGGGACG 0.847833 -22 ********** Masking position 4 Map Score: 16.4862 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 369 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 4 CTTATTCCCCCTACGAGAACCC 3 1 1 CTTTTCCCCT 0.965296 -332 TGAACATATCCATATTCAGCCCATTATGTATT 15 62 0 CATTTCACCC 0.944262 -86 TGAATATGGATATGTTCATCCTGTACTTCAAA 15 76 1 TATTTCACCT 0.868761 -72 GCCGTAAGAATTTCTTCAAACCAAGGGGGTGA 19 159 1 TTTTTCAACC 0.667947 -142 ATTTTTCTTCCTCCTAAGATTGTAA 19 286 0 TTTTTCCCCT 0.926419 -15 AAAAGCCCACCATCTTCATCCCGATAAAAGGA 22 52 1 CATTTCACCC 0.944262 -249 TTCTTGTTCCTCCCTGCCATTTGC 22 287 0 CTTTTCCCCC 0.969899 -14 GCTTCCTTTCCATATTCCACCT 27 1 0 CATTTCCCCT 0.959029 -109 AAATCATTTACTTATTCAGACTTATATATAAT 30 27 0 CTTTTCAACT 0.793233 -274 GATATGTTCCTCCTGTTCCGGGCT 36 3 1 TATTTCCCCT 0.913757 -179 CCAGCTGAGGTGTTTTCCCCCCTTTTATAAAA 36 95 0 TGTTTCCCCC 0.817775 -87 TTATTTTACTCTTTTTCAGACTAGTGATCTAG 36 128 0 CTTTTCAACT 0.793233 -54 *** **** *** Masking position 6 Map Score: 7.3243 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 200 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 CAACGATATAAATCGGAATCAAAAACT 6 145 1 AAGAATAAAA 0.86331 -17 CTGTAATTTGAGAACGAATTTAAACCGCTTCACC 7 266 0 AGGAATTAAA 0.743201 -35 GTATATAATCAAATGAAATAAAAAACTTTGGTTC 8 57 0 AAAAATAAAA 0.901782 -244 AAAAATCTTTAATGAAAATAAAAAAAGTCTGTTC 8 106 0 AAAAATAAAA 0.901782 -195 GAAAAAGAATAATTAAAATTAAAAATCTTTAATG 8 126 0 AAAAATAAAA 0.901782 -175 TCATAGATAAAGGATAAATATAAATAATATTCAT 8 203 1 AGAAATTAAA 0.807959 -98 GAAACCTCCTAATCAGAATGTCAAAAAGCTCCCG 8 274 0 AAGAATTCAA 0.561713 -27 ATTTCCTCCAAGACAAAATAAAAACTTTTGTATA 11 120 0 AGAAATAAAA 0.882918 -25 ATGTATCATTATGTAAAATAAAAAACCCGCATAG 13 35 0 ATAAATAAAA 0.672898 -176 CATTTTTGTCAAATAAAATTTAAATTATATCAAC 13 149 0 AAAAATTAAA 0.836667 -62 ATGTATTTATATCCAAAATAAAAAAACCAGGGAA 15 35 0 ATAAATAAAA 0.672898 -113 TTTCGGGCATAAGGTAAATAAAAAAGTGATCCCG 17 35 0 AAAAATAAAA 0.901782 -159 AAGTTTGAAAAATCAGAATTAAAAAAGGACCGCC 18 63 0 AAGAATAAAA 0.86331 -130 GAGACGAAGAAAGTCAAATTTCAAGGGGACTTTC 19 249 0 AAAAATTCAA 0.650729 -52 GTTGTGTAAAAGGGCAAATGTAAACGGTTAAACT 25 136 1 AGAAATTAAA 0.807959 -103 CTTTGTCAAAAAAGTAAATCAAAAGTTATTATTA 26 229 1 AAAAATAAAA 0.901782 -72 AGAATAAATAAGGTAGAATAACAAACCCTATTGG 29 30 1 AGGAATACAA 0.653585 -37 ** **** **** Masking position 7 Map Score: 11.2741 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 77 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 GTCTTTTGTGAGTTTTGTCACCAAATATCG 3 162 1 AGTTTTGTCA 0.899123 -171 CACATAAAATAATTTTTTCGATATCTAAAA 4 160 1 AATTTTTTCG 0.834229 -141 CCTGTATGCCCGTTTTTTCGGGCGCCCCGA 6 107 0 CGTTTTTTCG 0.666454 -55 AAAAAACTACATTTTTTTCATCGTGAAATG 7 233 0 ATTTTTTTCA 0.791352 -68 AAAAAAATGTAGTTTTTTCAAGGTGAAGCG 7 245 1 AGTTTTTTCA 0.930757 -56 GTTCGTGTCGAATTTTGTCGTATATAATCA 8 80 0 AATTTTGTCG 0.76942 -221 GCTGAGTCCAAGTTTTTTCTTATCATTGAA 12 74 0 AGTTTTTTCT 0.679386 -88 GGAATCATAGAATTTTGTCAAAATAATTTT 13 99 1 AATTTTGTCA 0.766064 -112 ACACGAGCCCATTTTTGTCAAATAAAATTT 13 162 0 ATTTTTGTCA 0.715496 -49 CTAAAAAAGGAGTTGTTTCGT 14 149 1 AGTTGTTTCG 0.666454 -11 TTTGCTGATGAATTTTTTCAGACGAAAAGC 22 117 0 AATTTTTTCA 0.83161 -184 TAACCTCGTCAGTATTTTCAATATTTTTTT 26 83 1 AGTATTTTCA 0.56952 -218 AAACAGTTTTTTCATATGAACCTG 31 5 1 AGTTTTTTCA 0.930757 -185 ATACAGGTTTATTTTTTTCGTTTTAAGTGT 31 57 1 ATTTTTTTCG 0.794442 -133 ********** Masking position 6 Map Score: 8.3543 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 160 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 GGCTTTTTGTTTTGCGCACCACATGGACTG 12 14 1 TTTGCGCACC 0.945258 -148 GACTTTCAATCGTCCCCTCCTACATGTTTT 19 226 0 CGTCCCCTCC 0.786972 -75 CATAATACCATTTGCCCTCCCAATATGAAA 20 57 1 TTTGCCCTCC 0.96857 -162 GTTTTGGGAATTTCCGCTCCTTTTATCGGG 22 71 0 TTTCCGCTCC 0.96857 -230 TTCTCGTTCTTTTGCGCACCCAATTTTGCT 25 95 1 TTTGCGCACC 0.945258 -144 TTTCCTCACCATTTCTTGAA 27 100 0 TTTCCTCACC 0.683416 -10 ATTATAACAGCTGGCGCTCCGAAACGCCTA 28 44 0 CTGGCGCTCC 0.929995 -46 GTTTACCGCTCCAATAGTTTTT 28 78 0 TTACCGCTCC 0.846686 -12 ACGCGCATTATTTTCCCTCCAAACTAAAAT 30 55 0 TTTTCCCTCC 0.826613 -246 TTGAAGGGGACTGGCCCTCCAGAACTGAGC 32 114 1 CTGGCCCTCC 0.914714 -187 ********** Masking position 5 Map Score: 4.72873 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 149 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 TATTTTACCTTTCGAAATTTCTGCTAATCGAAAGT 4 107 1 TCAATTTGCT 0.481392 -194 ACCCCTGCGTTTCGCGATTTATTTTAGATATCGAA 4 176 0 TCCATTTTTT 0.88809 -125 CACCTCAACGTGCCAGATGTATTTTTGAATCGTCG 4 251 0 TCAATTTTTT 0.920233 -50 TCTATAAAAGTTCTACATGCTTTCTTCTCCTCATA 10 59 1 TCAATCTTCT 0.838187 -97 CAGAGGGTTTTGCGCCCTCTGTTTTTTTCGTTATA 11 27 1 TCCCTTTTTT 0.620941 -118 CCTGCTCGTTTTTAAAATATTTTTTGAAAAAATAG 17 103 0 TTAATTTTTT 0.72572 -91 GTGTATCAATTCCACGATTTTTTCTGAAATCCTGC 17 133 0 TCCATTTTCT 0.857582 -61 GAAAAATATATCCTAAATATCTTCTGATTTCAAGG 18 137 0 TCAATTTTCT 0.897475 -56 TTATTGGCCTCCAATATCCCTTTTATCCATAGAA 18 169 0 TCAATCTTTT 0.872231 -24 AATCGTCCCCTCCTACATGTTTTTTGGAAGATCAT 19 214 0 TCAATTTTTT 0.920233 -87 CCCCATTCTGTATGCAATCCGTTCTTTTTCATTGA 20 19 1 TTCATCTTCT 0.449715 -200 CTGTCATTCCCGCTTTCTTTTTAAATAATCT 21 7 1 TCCCTTTTTT 0.620941 -165 ACGCCTTCATTTTCTAATGCATTTTATTTCCTGCT 22 197 0 TTTATCTTTT 0.227089 -104 GATATGGACGTACCAGATATCTTTTTGTGTTTTTA 23 205 0 TCAATTTTTT 0.920233 -77 CGTCAGTATTTTCAATATTTTTTTTAGTTTTTTAT 26 89 1 TCAATTTTTT 0.920233 -212 GTTTACCGCTCCAATAGTTTTTTTTCATTATAAC 28 66 0 TCAAGTTTTT 0.550221 -24 TTTGTTATTCTACCTTATTTATTCTCGAATAAGGG 29 20 0 TCTATTTTCT 0.621593 -47 TGTCATGATCTATAAGATTCATTTTTTGTCATTGA 32 22 1 TTAATCTTTT 0.610245 -279 TCCCCCCTTTTATAAAATCTGTTTTAGGTTCAAGC 36 77 0 TTAATTTTTT 0.72572 -105 * * * ** * **** Masking position 12 Map Score: 8.04496 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 104 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 AGGTGGATGTTTTTGCTCTTATTTCGATCA 7 88 0 TTTTGCTCTT 0.968106 -213 CTGCTTTTTGTTTTGCCCTTTTTTGGTTTC 14 33 1 TTTTGCCCTT 0.953327 -127 CGAAAAGCAGTTATGCTCTTAACGGTTTTG 22 95 0 TTATGCTCTT 0.863046 -206 GCGCACCCAATTTTGCTCATGCCTTTTTGT 25 108 1 TTTTGCTCAT 0.863046 -131 AACCGTTTACATTTGCCCTTTTACACAACA 25 135 0 ATTTGCCCTT 0.809178 -104 TTCAGATAATTTTGCTCTTGAAATAGGTG 26 282 0 TTTTGCTCTT 0.968106 -19 AATACCTTTATTTTACTCTTTTTCAGACTA 36 137 0 TTTTACTCTT 0.797457 -45 ********** Masking position 4 Map Score: 3.49424 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 33 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 GCAAGGAGCCAGGGCAGGGATAACAA 2 4 0 AGGGCGATAA 0.968435 -56 TCACATAGATCCTGCTGATATAAAACCCCCCTG 7 38 1 CCTGCGATAA 0.71871 -263 GGCGCTTTCGTCAGCGGGGATAATCCGTTATTG 7 182 1 TCAGCGATAA 0.81858 -119 CCAAAGGACGAGAGCGGCGATAAGTGCAAATCA 8 240 0 AGAGCGATAA 0.973819 -61 TGATTCTGGGAGAGCCGGGATCACTTTTTTATT 17 20 1 AGAGCGATCA 0.885805 -174 GACTGCTGAAAGGGCTGACATAAGCCTTTTGCC 18 30 1 AGGGCGATAA 0.968435 -163 TGTGCAGATCACAGCCGTAAGAATTTCTTCAAA 19 146 1 ACAGCGAGAA 0.840021 -155 CAGTTTGATAAGGGCGGTGCTAAATTCGTAATG 20 133 1 AGGGCGCTAA 0.864836 -86 AGCCTATGATAGAGCTGTAATAATAAAAGCCCA 22 28 1 AGAGCGATAA 0.973819 -273 TTTCGGAGCGCCAGCTGTTATAATGAAAAAAAA 28 50 1 CCAGCGATAA 0.924852 -40 ***** * **** Masking position 13 Map Score: 2.45356 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 77 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TGCCCGTTTTTTCGGGCGCCCCGAGCCTTG 6 101 0 TTCGGGCGCC 0.930814 -61 AAAAAAGTGATCCCGGCTCTCCCAGAATCA 17 20 0 TCCCGGCTCT 0.966273 -174 ATAAGCCTTTTGCCGGCGGTCCTTTTTTAA 18 49 1 TGCCGGCGGT 0.943781 -144 GGGCGCTTAGTTCGGGCGCTATAATTATAG 19 55 0 TTCGGGCGCT 0.952365 -246 TAAGCCTTTTTCCGGGCGCTTAGTTCGGGC 19 68 0 TCCGGGCGCT 0.986458 -233 TCGCGGATCCTCCCGGCTGAGTGTGCAGAT 19 125 1 TCCCGGCTGA 0.876023 -176 ATACCAATTTTCCCGGGGGTATTTCTTTTT 21 94 0 TCCCGGGGGT 0.923788 -78 TTCCTCCTGTTCCGGGCTGCCCCGAGCTTG 36 17 1 TCCGGGCTGC 0.95068 -165 ********** Masking position 1 Map Score: 1.97529 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 447 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TATTCACCTCAATAAGTAAAAT 3 321 0 TTCACCTCAA 0.877857 -12 TTTATTATCGTTAACACCTCAACGTGCCAGAT 4 268 0 TACACCTCAA 0.677772 -33 GGAGATTATGTTATCTCCTCATCCCATGTGAC 6 29 0 TACTCCTCAT 0.849746 -133 CTACATGCTTTCTTCTCCTCATAGGATAGGTT 10 71 1 TTCTCCTCAT 0.950797 -85 AAGCTCAGTGTCCTCTTCATTATCCTGAAA 10 136 0 TTCTCTTCAT 0.777945 -20 TGCATCCACCTCACTACATTTATT 13 197 0 CTCACCTCAC 0.836699 -14 ATAGAAAATTCTTGCACTTCATGAAGTCTCCT 18 108 1 CTCACTTCAT 0.831439 -85 TTCATTCTCCCCATTCTGTATGCA 20 3 1 CTCTCCCCAT 0.774056 -216 ACCCATCCCCCTCATACCCTTTTTT 21 157 0 CTCCCCTCAT 0.87844 -15 CATTTTATTTCCTGCTCCTCTTCCTGTATACT 22 181 0 CTCTCCTCTT 0.815057 -120 AAGAATTGACCTCCTCTTTTTACTAGTC 25 221 0 TACTCCTCTT 0.514857 -18 TGATCAGCGATATCCACTTCATCCACTCCATT 26 194 0 TTCACTTCAT 0.802317 -107 TGGCTTTTTTCTTACACCTCAAACAGCAAAGC 30 229 0 CTCACCTCAA 0.897276 -72 TGTTGAATCATTTGCACCTCATATTAGTATGA 32 149 0 TTCACCTCAT 0.95724 -152 * * ******** Masking position 7 Map Score: 6.68721 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 133 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 13 CCCCGCTGACGAAAGCGCCATTTTCGACCAT 7 170 0 GAAAGGCCAT 0.96635 -131 ATCATTGAATGAAAGGTCCTTCTCTAGCCTA 12 52 0 GAAAGTCCTT 0.948087 -110 AGAGCCTTGAGAAAGCGCCTTTTTTCGCTGA 12 99 0 GAAAGGCCTT 0.976275 -63 CATCATGAAAGAAAGAGCCTTGAGAAAGCGC 12 112 0 GAAAGGCCTT 0.976275 -50 TAATTTTAACGAAAGTTCCATCTGATTTAAC 14 66 1 GAAAGTCCAT 0.927249 -94 GGGGACGATTGAAAGTCCCCTTGAAATTTGA 19 239 1 GAAAGCCCCT 0.900042 -62 ***** ***** Masking position 4 Map Score: 2.50484 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 30 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 TAAAAAATATTGCCCTGAGCAAGGAGCCAG 2 25 0 TGCCCTGAGC 0.957985 -35 TTTTTTCGGGCGCCCCGAGCCTTGTAGAGA 6 95 0 CGCCCCGAGC 0.981686 -67 GCGCGTGTGACCCGTCCTGAATAGCGT 7 8 1 TGACCCGTCC 0.916094 -293 AATTCATTGCCCCGTCCCCATCAATTG 35 65 0 TGCCCCGTCC 0.982755 -17 TGTTCCGGGCTGCCCCGAGCTTGCTCACAA 36 24 1 TGCCCCGAGC 0.991666 -158 ********** Masking position 5 Map Score: 1.29089 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 32 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 CGAACACCTTTTGTGTTTCGACAAGAAAGGAGTTTTTC 9 47 1 TTTGTTAGAA 0.735992 -32 CAAGTCTTTCTTCCGTTTCTCAGTGTATTTCAGGATAA 10 109 1 TTCGTTTGAT 0.890194 -47 AAATAAAAACTTTTGTATATTCATGAAACTTTTTCTTA 11 101 0 TTTGTTTGAA 0.956403 -44 TTTCGGTAAATTATGTATCATTATGTAAAATAAAAAAC 13 43 0 TTTGTTTGAA 0.956403 -168 ATTCAGCCCATTATGTATTTATATCCAAAATAAAAAAA 15 43 0 TTTGTTTCAA 0.719347 -105 AGGGGGGTTGTTCCGTTTGCTGATGAATTTTTTCAGAC 22 124 0 TTCGTTTGAT 0.890153 -177 CAATGCATTGTTCTGTCTTCCATTGTAACAGGTTTTAC 22 250 0 TTTGTTTGAA 0.956433 -51 AGATATCTTTTTGTGTTTTTAGCTGAAAGGAGAAGATC 23 188 0 TTTGTTTGAA 0.956403 -94 TATAGTGGTATTATATATAAGTCTGAATAAGTAAATGA 30 18 1 TTTATTTGAT 0.666013 -283 AAAGCTGTTATTTTGTTTCACGGTGTAACGTAGATTTT 30 196 0 TTTGTTTGAA 0.956433 -105 AAACAGTTTTTTCATATGAACCTGTATTAAATGGAAC 31 10 1 TTCATTTGAT 0.554472 -180 ** *** * ** ** Masking position 17 Map Score: 2.98685 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 29 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863