AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -igalR_ecoli_bsub_100.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 galE 260 UDP-galactose-4-epimerase #2 mglA 60 ATP-binding component of methyl-galactoside transport and galactose taxis #3 mglB 279 galactose-binding transport protein; receptor for galactose taxis #4 galS 141 mgl repressor, galactose operon inducer #5 galR 300 repressor of galETK operon #6 galP 300 galactose-proton symport of transport system #7 ydjK 300 similar to sugar transporter #8 yfiG 174 similar to metabolite transport protein #9 yhjM 103 similar to transcriptional regulator (LacI family) #10 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #11 yjmC 104 similar to malate dehydrogenase #12 yjmE 24 similar to D-mannonate hydrolase #13 yjmG 47 similar to hexuronate transporter #14 yjmH 87 similar to transcriptional regulator (LacI family) #15 ccpA 274 transcriptional regulator (Lacl family) #16 yufN 300 similar to ABC transporter (lipoprotein) #17 yufO 75 similar to ABC transporter (ATP-binding protein) #18 araE 137 permease #19 ywtG 300 similar to metabolite transport protein #20 rbsR 300 transcriptional regulator (LacI family) #21 galK 80 galactokinase #22 ywcC 300 alternate gene name: ipa-33d #23 galE 114 UDP-glucose 4-epimerase #24 yxcC 238 similar to metabolite transport protein Motif number 1 TAAATTCTTGTGTAAACGATTCCACTAATTTAT 1 168 1 TGTAACGTTC 0.995168 -93 ACAAAACGGCTGTAACCGTTTCCATTGCTGTGA 4 32 1 TGTAACGTTC 0.995092 -110 ACTGAAAGAATGTAAGCGTTTACCCACTAAGGT 5 272 1 TGTAACGTTC 0.995168 -29 TTGTGGTTGGTGTAATCGGTTTCAGTTGTGATG 6 23 0 TGTAACGTTC 0.995168 -278 TAAATGTTAGTGTAAGCGATTACACTGATGTGA 6 204 1 TGTAACGTTC 0.995168 -97 TAACGAGAAATGAAATCGCTTCCATAGGGATTG 7 129 1 TGAAACGTTC 0.990724 -172 TACCCCTTGTTGTAACCGCTTTCTAAAAAGATT 8 76 0 TGTAACGTTC 0.995168 -99 GTTGTTGACATGTTACCGATTTCAGAAACTAGG 9 61 0 TGTTACGTTC 0.963191 -43 TTATAGATGATGAAAACGTATACTTGGTTTTTA 15 71 0 TGAAACGATC 0.925216 -204 CGGAAAACCGTGACATCGTTTTCTGAAGTAAGA 16 45 0 TGACACGTTC 0.952641 -256 AAGGTTTAAATGAAAACGCTTTACTCAACATTC 18 101 1 TGAAACGTTA 0.88458 -37 TCCTTGTTTATGTAACCGTTTACATAGATAGAT 20 269 0 TGTAACGTTC 0.995167 -32 ***** ** ** * Masking position 5 Map Score: 31.6599 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 23 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 CGTTTACACAAGAATTTAGCCGTTTTTTATGCGCGATTA 1 147 0 ATTCTTTTTA 0.724707 -114 ATTCCATGTCACACTTTTCGCATCTTTGTTATGCTATGG 1 199 1 ATTCTTTTGT 0.92675 -62 GTGTAACCAAAGGTTTGCAATCTCTTTTTTTGTCTTACT 5 162 1 ATTTTTTTTT 0.895648 -139 TTCGGTTTTCACAGTTGTTACATTTCTTTTCAGTAAAGT 6 89 1 ATTCTTCTTT 0.883999 -212 GGCTTCAGAAAATAGTTGTTCATGTTTTTATCCAATAAC 7 191 0 AGTCTTTTTT 0.795988 -110 ACTGTTTCCCCCAGTCTTTTTCAAAATGC 7 282 0 ATTCATCTTT 0.622295 -19 TAAGACAACGAGATTTCTCGCGTCTTTATCATATGAAGA 8 36 0 ATTCTTTTAT 0.761016 -139 AAACTAGGATAAATTTGTAATAAATTTTTAGATTATAAA 9 30 0 ATTTATTTTT 0.649812 -74 TTCTGAAGTAAGACTTATGACTTAGTTTTTCGGGATCAA 16 19 0 ATTCTGTTTT 0.795984 -282 TGGCCGGATCAGCTTTGAACCAAATTTTTCTGGGGGGTT 16 240 1 ATTCATTTTT 0.882636 -61 AGGAGGTCGAGCCCTTATCCCTTGTTTTTCTTTTATTTT 17 25 1 GTTCTTTTTT 0.795988 -51 AAATGCAAACAAGATTATTCTATATTTGTACGTACTAAT 18 18 1 ATTTTTTTGT 0.757381 -120 AAGTTTTCCAATCATTTACTTGTATTTTTTTCAATGTCG 19 162 0 ATTTTTTTTT 0.895647 -139 TTTTTTTAGAAATCTTTTAGCCTCTTTTTCCGGCCATTA 19 224 0 ATTCTTTTTT 0.972055 -77 TTGTTCAAGAAATCTTCATCCATATTTGTGAAGACTTTG 20 129 1 ATTCTTTTGT 0.92675 -172 GAAAAATTTAAGGTTTTCACTCTTTTTTTGACAAAGTCT 20 160 0 ATTTTTTTTT 0.895648 -141 TCGTTTATTAATAGTTTTTTCATATTTTTTAGC 23 5 0 ATTCTTTTTT 0.972055 -110 CTAATCTATTAACTTTGTTACATATTTTTAGATACTTCA 24 181 1 ATTCTTTTTT 0.972055 -58 * ** * * ***** Masking position 6 Map Score: 14.0981 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 80 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 TTATCTGAAAAAAGACGCGGTTTCATGCCTG 1 76 0 AAAGAGCGGT 0.919778 -185 ATAGCATAACAAAGATGCGAAAAGTGTGACA 1 205 0 AAAGAGCGAA 0.959803 -56 CCATAAGCCTAATGGAGCGAATT 1 248 1 AATGGGCGAA 0.655462 -13 TACGACGTAAAAAGATGTGAAGCAAATCACA 6 232 0 AAAGAGTGAA 0.824615 -69 GACATGCTAAGAAGAAGGGAAGGTTATGAGG 7 161 1 GAAGAGGGAA 0.856365 -140 TTCATATGATAAAGACGCGAGAAATCTCGTT 8 38 1 AAAGAGCGAG 0.803883 -137 GGGTATTGCTGAAGGAGGGATGCATTGGCTT 8 104 1 GAAGGGGGAT 0.629778 -71 GCCATTCTTGAAAGAAGGGGAAGAAAGCC 8 156 1 AAAGAGGGGA 0.967832 -19 CAACTTTTTTAAGGAAGGGAAAAT 9 90 1 AAGGAGGGAA 0.909873 -14 CCGGTATGATAAGGAAGGGAATTAG 14 73 1 AAGGAGGGAA 0.909873 -15 GTATCCAGTAAAAGGAGTGGTTTTAGG 15 258 1 AAAGGGTGGT 0.6283 -17 CGGGGAAGAGAAGGATGCGGAAGGCGTTCCG 16 80 0 AAGGAGCGGA 0.927118 -221 ATTTCCTTCGAAAGGCGGGGAAGAGAAGGAT 16 95 0 AAAGGGGGGA 0.957494 -206 ATTTTGAAATAAAGGAGCGGTCAATCA 17 59 1 AAAGGGCGGT 0.895662 -17 ATGGCCGGAAAAAGAGGCTAAAAGATTTCTA 19 226 1 AAAGAGCTAA 0.557931 -75 TTCTATGAAGAAATAAGGGGAATAAAAAATA 21 38 1 AAATAGGGGA 0.613943 -43 ***** ***** Masking position 2 Map Score: 12.1146 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 564 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 AATCGCGCATAAAAAACGGCTAAATTCTTG 1 148 1 AAAAAACGGC 0.95777 -113 GTAACGCTCCAGAAAACGGCTTTAATTGTT 3 138 0 AGAAAACGGC 0.858929 -142 CCTGCATAAGAAAAACCGGAGATACC 3 264 1 AAAAACCGGA 0.948297 -16 ACATTCGTTAACAAAACGGCTGTAACCGTT 4 22 1 ACAAAACGGC 0.767897 -120 CCGGCAAAAAAAACCTGCGCATCTGCGC 5 9 1 AAAAACCTGC 0.89112 -292 GTTATTGGATAAAAACATGAACAACTATTT 7 191 1 AAAAACATGA 0.711415 -110 GAGAGTGCCCAAAAAACTGAAAAGGAAGGA 11 76 1 AAAAAACTGA 0.864393 -29 GAGAAAGCATAAAAAAAGGCCGCACGGCGG 15 28 0 AAAAAAAGGC 0.895918 -247 TGAATAAACGAAAAATCGGATTGGCG 16 285 1 AAAAATCGGA 0.833429 -16 ATCAATTTTCAAAAACAAGAACTTATAAAT 19 75 0 AAAAACAAGA 0.517474 -226 TAATGGCCGGAAAAAGAGGCTAAAAGATTT 19 224 1 AAAAAGAGGC 0.667902 -77 ATTTCTTCATAGAAAACGGCAGATCATATG 21 22 0 AGAAAACGGC 0.858929 -59 AATAAAAAATAAAAACCAGAAAGGTGATTG 21 58 1 AAAAACCAGA 0.738607 -23 CCTATTCCCTAAAAAAATGACTAATATAAC 22 93 1 AAAAAAATGA 0.707536 -208 GCTAAAAAATATGAAAAAACTATT 23 5 1 AAAAATATGA 0.402089 -110 ATTTGTTTTGAAAAAACGGAAACTTTATAG 24 125 0 AAAAAACGGA 0.947367 -114 ********** Masking position 5 Map Score: 12.3291 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 624 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 5 ATTCACTACCTGTTATGAGATTGCAGTAAATGACTGCTTG 4 112 0 TTATAATAAA 0.608076 -30 AACCGAATAATAATATGAAAATATTACAAATCTTTGTCTG 6 56 0 TAATAAATAA 0.748667 -245 CAATTAAGACTTTACTGAAAAGAAATGTAACAACTGTGAA 6 96 0 TTCTAAAAAA 0.705773 -205 TTTCATGCACTTAAATCATAACTAAGATAAATGTTAGTGT 6 177 1 TAATAAAAAA 0.868858 -124 TATGATAATATCAGATATAACAAAAATGTC 7 1 1 TTATAATAAA 0.607999 -300 TCCATTTCCTTATAATAAAAAGGGATAGAAACGATACTTC 10 58 1 TTATAAAAAA 0.924813 -66 ACGTGTATAATTTCATGAGAAGTAATTAAATTTGATGAAT 15 106 1 TTATAAAAAA 0.903937 -169 ACTTACGCTTACAAATCATAAACGACATAAATTCGGACAT 15 170 1 AAATAAAAAA 0.700866 -105 GATAAAATTTTCTGATAATAACAAATGGAATGCGCTGAGA 16 162 0 TTATAAAAAA 0.924813 -139 GTCCTGAACAATTTCTTAGAATCGATAAAATTTTCTGATA 16 185 0 ATCTAAAAAA 0.454301 -116 CTCCTTTATTTCAAAATAAAAGAAAAACAAGGGATAAGGG 17 36 0 TAAAAAAAAA 0.640952 -40 TTGTACGTACTTATATTAAAATTTAACGAAAATTACATTT 18 58 0 TAATAAAAAA 0.871049 -80 TTTCGGCGACATTGAAAAAAATACAAGTAAATGATTGGAA 19 156 1 ATAAAAAAAA 0.529929 -145 TTTTTATTTTTCTGATCATAAGTTTTCCAATCATTTACTT 19 180 0 TTATAAATAA 0.844326 -121 AAATATTAAGTTTTATTAAAATTGTTTCAAAGTCATGCGT 20 91 0 TTATAAATAA 0.844205 -210 GTGAAGACTTTGTCAAAAAAAGAGTGAAAACCTTAAATTT 20 156 1 TTAAAAATAA 0.589028 -145 TTAGCAATAAAAATATCAAAAGAAATCTAATTGTAAATTG 20 210 0 AAATAAAAAA 0.700866 -91 GGACCTTATTTATAATAATAAACAATTAAATACTGACTGG 22 127 1 TTATAAAAAA 0.924808 -174 GCTAAAAAATATGAAAAAACTATTAATAAACGATTA 23 7 1 AAATAAATAA 0.50815 -108 GTTTCCGTTTTTTCAAAACAAATGTTTCAAATGAGATAGG 24 132 1 TTAAAAATAA 0.58899 -107 * * ** * ** * ** Masking position 10 Map Score: 11.0872 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 54 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 GTCGGTAGTGCTGACCTTGCCG 1 3 1 CGGTAGTGCT 0.962095 -258 CTTCCATGCCCGGTAACGCTCCAGAAAACG 3 150 0 CGGTAACGCT 0.937363 -130 TTCTTATGCAGGGTAGTGCTTGAGATAAAT 3 246 0 GGGTAGTGCT 0.953469 -34 GGTATCTCCGGTTTTTCTTATGCAGGGT 3 262 0 CGGTTTTTCT 0.65168 -18 TTACAACAAGGGGTATTGCTGAAGGAGGGA 8 94 1 GGGTATTGCT 0.949955 -81 GGGATGCATTGGCTTATGCTTGGTGTCGGG 8 120 1 GGCTTATGCT 0.744566 -55 GTGTTTGTAGGGGTTTCGCTTGGAGAGTGC 11 54 1 GGGTTTCGCT 0.882782 -51 TTTCTTTAAACGGTTATGCTATTCGGTTTC 22 218 0 CGGTTATGCT 0.961315 -83 TTTCTCCTGGCGGTAATGATTACCCTTATC 22 278 0 CGGTAATGAT 0.750087 -23 ********** Masking position 4 Map Score: 3.00809 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 474 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 AAAATTCGTTCTTCCATGCCCGGTAACGCT 3 160 0 CTTCCATGCC 0.928136 -120 ATTAACTCTACTGCCCCGCCGAGCATTTAT 3 222 1 CTGCCCCGCC 0.978081 -58 ACCTCATAACCTTCCCTTCTTCTTAGCATG 7 163 0 CTTCCCTTCT 0.92946 -138 GTCGGGTGCTCTGCCATTCTTGAAAGAAGG 8 144 1 CTGCCATTCT 0.681542 -31 GGCTTTCTTCCCCTTCTTTCAAGAAT 8 159 0 CTTCCCCTTC 0.844016 -16 ATTTTCCCTTCCTTAAAAAAGT 9 92 0 TTTCCCTTCC 0.881968 -12 CTAATTCCCTTCCTTATCATACC 14 75 0 ATTCCCTTCC 0.881968 -13 GCATCCTTCTCTTCCCCGCCTTTCGAAGGA 16 93 1 CTTCCCCGCC 0.981851 -208 TTCCCTGCCCTCCCGAATGTTGAG 18 124 0 CTGCCCTCCC 0.952789 -14 ********** Masking position 2 Map Score: 4.30412 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 214 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 GTTATGCTATGGTTATTTCATACCATAAGC 1 226 1 GGTTATTTCA 0.906011 -35 CAGATGCGCAGGTTTTTTTTGCCGG 5 6 0 GGTTTTTTTT 0.751422 -295 CCTCCAATATGGTTATTTTTTATTGTGAAT 6 276 0 GGTTATTTTT 0.924145 -25 GTGACATTTTTGTTATATCTGATATTATCA 7 13 0 TGTTATATCT 0.500788 -288 AAAGAACAATGGTCATTTCTTTGTGCATAA 7 99 0 GGTCATTTCT 0.938613 -202 GACATTGTTTTGTCATTTCAGGACATC 8 8 0 TGTCATTTCA 0.581389 -167 TTTTCTGGGGGGTTATATCTTGAATAAACG 16 265 1 GGTTATATCT 0.866881 -36 AAGGTCCATTGGTTATATTAGTCATTTTTT 22 104 0 GGTTATATTA 0.741012 -197 GTTTCCCAGGGGTCATTTTTAATAGGCTAA 22 193 0 GGTCATTTTT 0.919314 -108 AATGAAAACAGGTCATTTTTTAGGAGGGTT 23 89 1 GGTCATTTTT 0.919314 -26 GCGCGGGTAAGGTTTTTTTAATGGTTTCTC 24 36 1 GGTTTTTTTA 0.640585 -203 ********** Masking position 6 Map Score: 4.52427 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 240 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 9 GACTGATTGGGCGCAGTCTATTACTG 2 5 1 GATTGGCGCG 0.988642 -56 ATCACTCACAGATTGAAAGCGG 3 1 0 GATTGAAGCG 0.94375 -279 AATGAAGTGTTACTGAACGCCGAAGCTCACTT 3 193 0 TACTGACGCG 0.915665 -87 ACGCTGTTGCGATTGACCGCTGGTGGCGTTTG 5 122 0 GATTGACGCG 0.992327 -179 TATCATCATAGATTAAACGCTGTTATCTGCAA 6 133 0 GATTAACGCG 0.94375 -168 TGATTGACCGCTCCTTTATTTCA 17 63 0 GATTGACGCC 0.961317 -13 AATCACCTTATATTGGACGCCGCAGCAGGTAA 19 120 1 TATTGGCGCG 0.959587 -181 ****** *** * Masking position 2 Map Score: 3.97524 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 110 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 GTGCTAAGGCCGCCTCCGGCAAGGTCAGCA 1 19 0 CGCCTCCGGC 0.976876 -242 TGAAGCCAAACGCCACCAGCGGTCAATCGC 5 116 1 CGCCACCAGC 0.912548 -185 CCAGGGCTGCTGCCTTCCTCACATTTCGTA 7 234 0 TGCCTTCCTC 0.925298 -67 CATAAGCCAATGCATCCCTCCTTCAGCAAT 8 108 0 TGCATCCCTC 0.854854 -67 GCAAGTGCCTCCTTCCTTTTCAGTT 11 90 0 TGCCTCCTTC 0.919539 -15 CCGCCCGGAACGCCTTCCGCATCCTTCTCT 16 75 1 CGCCTTCCGC 0.968646 -226 TTGTTGTACTCGCCTCCATCATCGCGCTGG 22 13 0 CGCCTCCATC 0.976538 -288 ********** Masking position 7 Map Score: 2.14346 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 274 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ACCTTGCCGGAGGCGGCCTTAGCACCCTCT 1 24 1 AGGCGGCCTT 0.938175 -237 CAGTCTATTACTGCGCCCTTATTGTATGGC 2 24 1 CTGCGCCCTT 0.949042 -37 AAAAAGTGAGCTTCGGCGTTCAGTAACACT 3 190 1 CTTCGGCGTT 0.905366 -90 TATTCCAGGGCTGCTGCCTTCCTCACATTT 7 238 0 CTGCTGCCTT 0.963541 -63 CTTATCATACCGGCTGCGATTATTTACTGT 14 56 0 CGGCTGCGAT 0.834557 -32 AAAGGCCGCACGGCGGCCTTTTGGATTGTT 15 14 0 CGGCGGCCTT 0.991525 -261 ATTTTACCTGCTGCGGCGTCCAATATAAGG 19 125 0 CTGCGGCGTC 0.957797 -176 ********** Masking position 4 Map Score: 1.57595 Number of sites scoring better than the average of aligned sites = 974 Number in coding regions = 922 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 12 CAATTAAAGCCGTTTTCTGGAGCGTTACCGGG 3 140 1 CGTTTTCTGG 0.965663 -140 AGCAAGCAGTCATTTACTGCAATCTCATAACA 4 110 1 CATTTACTGA 0.719907 -32 AACCAACGGGCGTTTTCCGTAACACTGAAAGA 5 249 1 CGTTTTCCGA 0.704659 -52 TATTACAAATCTTTGTCTGTTGTGGTTGGTGT 6 43 0 CTTTGTCTGG 0.79771 -258 CATGAACAACTATTTTCTGAAGCCTGCTTACG 7 206 1 TATTTTCTGG 0.8737 -95 AAATTTATCCTAGTTTCTGAAATCGGTAACAT 9 53 1 TAGTTTCTGA 0.540345 -51 TATGTTGGTTCAGTTTCTGTTGCACCGCTTTC 13 12 0 CAGTTTCTGG 0.93415 -36 ACCGTGACATCGTTTTCTGAAGTAAGACTTAT 16 40 0 CGTTTTCTGG 0.965663 -261 GAATCGATAAAATTTTCTGATAATAACAAATG 16 175 0 AATTTTCTGA 0.788177 -126 TTTGAACCAAATTTTTCTGGGGGGTTATATCT 16 253 1 ATTTTTCTGG 0.65788 -48 ATCTTGTTTGCATTTTCTGTCA 18 1 0 CATTTTCTGA 0.960242 -137 GCTGCAATGACATTGTCTGTGGGATTTTTTTA 19 255 0 CATTGTCTGG 0.93415 -46 CATAATTAAACATTTTCTGGGATGATAGTCTT 20 31 1 CATTTTCTGA 0.960242 -270 ********* * Masking position 4 Map Score: 7.31114 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 468 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 13 AATTCATGTGCTCAACCCGAAGTTGACTTCACCTA 5 49 1 CTACCCAGTG 0.986037 -252 GCGTTTGGCTCACATTCCCACGATGAAAACACGCC 5 206 1 CAATCCAGTG 0.917419 -95 ATGTCAAAAACTTATTCCAGGGCTGCTGCCTTCCT 7 245 0 CTATCCGGTG 0.986075 -56 ATGACTGAATCCGGAGGTGCGAGC 12 5 1 CTATCCGGTG 0.986037 -20 CTCAACCTCACCCCTATGTTGGTTCAGTTTC 13 27 0 CTACCCAGTG 0.986075 -21 GCTCGACCTCCTTATCCCTGCGATTC 17 2 0 CTACCCGGTT 0.945139 -74 ** * *** * * ** Masking position 4 Map Score: 0.693276 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 28 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 AATTAAGACTTTACTGAAAAGAAATGTAAC 6 105 0 TTACTGAAAA 0.673974 -196 CATTGTTCTTTTAACGAGAAATGAAATCGC 7 118 1 TTAACGAGAA 0.821704 -183 TATAACTAAATAAACGAGAAAGCATAAAAA 15 43 0 TAAACGAGAA 0.821754 -232 AATTTGATGAATAATGAAAAATAATGTACA 15 134 1 ATAATGAAAA 0.689533 -141 ATATCTTGAATAAACGAAAAATCGGATTGG 16 279 1 TAAACGAAAA 0.930081 -22 TATTTCAAAATAAAAGAAAAACAAGGGATA 17 40 0 TAAAAGAAAA 0.67298 -36 ATATTAAAATTTAACGAAAATTACATTTAA 18 56 0 TTAACGAAAA 0.930024 -82 ATTGAAGGTTTAAATGAAAACGCTTTACTC 18 97 1 TAAATGAAAA 0.908363 -41 ATAGGAATATTTATCGAAAAATGTCTTTCG 19 45 0 TTATCGAAAA 0.765568 -256 ATTGTATATATAATTGAAAAATTTAAGGTT 20 184 0 TAATTGAAAA 0.710941 -117 GGATAGTATGTAAATGAAAATAAATCATTT 22 165 1 TAAATGAAAA 0.908363 -136 TAAACACTATATAATGAAAACAGGTCATTT 23 77 1 ATAATGAAAA 0.689533 -38 ********** Masking position 7 Map Score: 5.68424 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 81 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 15 AACTCTACTGCCCCGCCGAGCATTTATCTC 3 225 1 CCCCGCCGAG 0.946199 -55 GACAAAATAGCCGCCAGCAAGCAGTCATTT 4 95 1 CCGCCAGCAA 0.823028 -47 TCACGGTTTTCCGCCCGGAACGCCTTCCGC 16 65 1 CCGCCCGGAA 0.988842 -236 CAAGATATAACCCCCCAGAAAAATTTGGTT 16 257 0 CCCCCCAGAA 0.928246 -44 TTCCCTGCCCTCCCGAATGTTGAGTAA 18 121 0 CCCTCCCGAA 0.820698 -17 GTAATCATTACCGCCAGGAGAAAAAT 22 285 1 CCGCCAGGAG 0.966879 -16 AAAACCTTACCCGCGCGGAGTAAGGTTTGA 24 22 0 CCGCGCGGAG 0.971205 -217 ********** Masking position 9 Map Score: 0.760572 Number of sites scoring better than the average of aligned sites = 429 Number in coding regions = 394 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097