AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02060_ecoli_reg_300.orf -o02060_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e 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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 nagE 300 PTS system, N-acetylglucosamine-specific enzyme IIABC #2 hrsA 108 protein modification enzyme, induction of ompC #3 yceD 159 orf, hypothetical protein #4 rpmF 51 50S ribosomal subunit protein L32 #5 plsX 110 glycerolphosphate auxotrophy in plsB background #6 fabH 67 3-oxoacyl-[acyl-carrier-protein] synthase III; acetylCoA ACP transacylase #7 acpP 210 acyl carrier protein #8 fabF 87 3-oxoacyl-[acyl-carrier-protein] synthase II #9 pabC 119 4-amino-4-deoxychorismate lyase #10 ptsG 294 PTS system, glucose-specific IIBC component #11 malX 174 PTS system, maltose and glucose-specific II ABC #12 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #13 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #14 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #15 osmE 201 activator of ntrL gene #16 manX 300 PTS enzyme IIAB, mannose-specific #17 manY 62 PTS enzyme IIC, mannose-specific #18 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #19 gatZ 28 putative tagatose 6-phosphate kinase 1 #20 gatY 197 tagatose-bisphosphate aldolase 1 #21 BIME96 27 BIME #22 b2097 184 orf, hypothetical protein #23 fruB 300 PTS system, fructose-specific IIA/fpr component #24 b2383 24 putative PTS system enzyme IIA component, enzyme I #25 b2386 21 putative transport protein #26 b2387 218 putative PTS system enzyme IIB component #27 glk 203 glucokinase #28 ptsH 300 PTS system protein HPr #29 ptsI 44 PEP-protein phosphotransferase system enzyme I #30 crr 40 PTS system, glucose-specific IIA component #31 yfeU 163 putative regulator #32 srlA 255 PTS system, glucitol/sorbitol-specific IIC component, one of two #33 ascF 256 PTS system enzyme II ABC (asc), cryptic, transports specific beta-glucosides #34 ygdP 300 putative invasion protein #35 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #36 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #37 agaZ 248 putative tagatose 6-phosphate kinase 2 #38 BIME157 76 BIME #39 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #40 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #41 agaC 38 PTS system N-acetylgalactosamine-specific IIC component 1 #42 yrbG 209 orf, hypothetical protein #43 rpoN 47 RNA polymerase, sigma(54 or 60) factor; nitrogen and fermentation regulation #44 yhbH 22 probable sigma-54 modulation protein #45 ptsN 117 phosphotransferase system enzyme IIA, regulates N metabolism #46 yhbJ 45 orf, hypothetical protein #47 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #48 glvB 24 PTS system, arbutin-like IIB component #49 glvC 34 PTS system, arbutin-like IIC component #50 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #51 bglG 285 positive regulation of bgl operon #52 BIME185 97 BIME #53 pstC 86 high-affinity phosphate-specific transport system, cytoplasmic membrane component #54 pstS 300 high-affinity phosphate-specific transport system; periplasmic phosphate-binding protein #55 frvA 300 PTS system, fructose-specific IIA component #56 frwC 300 PTS system, fructose-like enzyme II component #57 pflD 50 formate acetyltransferase 2 #58 sgaT 291 orf, hypothetical protein #59 treB 118 PTS system enzyme II, trehalose specific #60 treR 300 repressor of treA,B,C #61 sgcA 130 putative PTS system enzyme II A component #62 sgcC 286 putative PTS system enzyme IIC component #63 sgcX 300 putative lyase/synthase Motif number 1 CTCGTAATTAATGGCTAAAACGAGTAAAGTTC 10 27 1 AGCTAAAACG 0.566384 -268 CCAATGATCTGAAGTTGAAACGTGATAGCCGT 10 134 1 GGTTGAAACG 0.871557 -161 GACTTTTTTTGTGGCTGAAAGGAGTATACGGT 14 186 0 GGCTGAAAGG 0.927088 -113 CTAACCCGTTGCTACTGAAACGACAAGCGACA 15 50 1 GACTGAAACG 0.911689 -152 CAAGCGACAGCGGGCTGAATGGTGGTTAAAAC 15 73 1 CGCTGAATGG 0.769294 -129 GGCTGCTGACGCTGCTGAAATGAAATTGCTGA 23 61 1 GGCTGAAATG 0.921745 -240 GCTTTCCTTGCGTGCTGAAACAGAAGTATTAT 23 172 1 CGCTGAAACA 0.789633 -129 AAGACAAGATCGCGCTGAAACGTTTCAAGAAA 23 206 0 CGCTGAAACG 0.978529 -95 TTTTCTCATAGAGGCTGAATCGTTTCAATTCA 23 263 1 GGCTGAATCG 0.975036 -38 GTTCTCCTCTCTTGCTGAATTGAAACGATTCA 23 278 0 CGCTGAATTG 0.755437 -23 CGCTGCAATTGGTGCTGAAACGATAAAGTAAT 27 67 1 GGCTGAAACG 0.988008 -137 CCAGTTCCGACAGGCTGAATCAA 28 2 0 CGCTGAATCA 0.640224 -299 AGGAAAAGCCAAAGCTGAATCGATTTTATGAT 28 79 1 AGCTGAATCG 0.8317 -222 GAAAAATGCCGATGCTGAAACGGAATTAAGAA 33 179 0 GGCTGAAACG 0.988008 -78 CATAATGAAAGTCACTGAAACGAGAGTAGCTT 37 104 0 GACTGAAACG 0.911689 -145 ATCGTACTCTCCTGCTAAAACGTCGCAAACTT 43 19 0 CGCTAAAACG 0.850985 -29 TGCGAAATCTGGCACTGAATCGGTTAACTGTC 47 185 0 GACTGAATCG 0.830342 -116 CTGAGCAGGGACGTTAAAACGTCACGGCCTT 60 10 1 GGTTAAAACG 0.45954 -291 TTGGGCGGTAGTGGCTGAAATGCCCTGTTCAG 62 86 0 GGCTGAAATG 0.921745 -201 * ********* Masking position 6 Map Score: 23.4867 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 440 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 CGCGTGTCTTTTGTGAGTTTTGTCACCAAATATCGT 1 129 0 TTGTGATCAC 0.984464 -172 TATGTGATCAATTTCACTTGATTGAAA 2 92 0 ATGTGATCAC 0.950214 -17 TGACCTGTGGTTATGACCCTCTTCACATTTCGGGCA 14 102 0 TTATGATCAC 0.944191 -197 CGTATTGTGTTGATTATCACTCAGTTTTCA 17 5 1 TTGTGTTCAC 0.899748 -58 ATTGTCGTTTTTGTGATCGTTATCTCGATATTTAAA 20 125 1 TTGTGATCTC 0.87086 -73 GCTTAAGTTCTTATGACGCTCTTCACACTCTGCGAG 31 44 1 TTATGATCAC 0.944191 -120 TTTTTTATATTTGTGAAACCGGTCACCTGAATATTT 33 84 0 TTGTGATCAC 0.984465 -173 ATATAAATATTTGTGATCTACAACACGCCTTATCTA 36 71 0 TTGTGAACAC 0.827457 -230 GATAATGGTTTTCTGATCTGATTCACAAAAGAAACA 37 134 0 TTCTGATCAC 0.860843 -115 CAAAACAAAAATGTGACACTACTCACATTTAAATGC 47 24 1 ATGTGATCAC 0.950211 -277 CACAAGCGTTTTGTGATGAACGTCACGTCAATTACC 47 97 1 TTGTGATCAC 0.984465 -204 CCCTATATTTATGTGATTGATATCACACAAAAGGCC 47 141 1 ATGTGATCAC 0.950213 -160 ACACCCCTTCTTATGTTTGCTGTCGCGCAGGCTGGA 47 271 0 TTATGTTCGC 0.622398 -30 ATTGATAAAAATATGACCATGCTCGCAGTTATTAAC 51 88 0 ATATGATCGC 0.778035 -198 AATGACTGGATTGTTACTGCATTCGCAGGCAAAACC 51 199 1 TTGTTATCGC 0.670621 -87 AAACAGCGTCTTGTGAGACGCGTCGCAAATTGACGG 56 103 0 TTGTGATCGC 0.977574 -198 TTATCGCAAGTTATGAGGCGGATCGCATTTTTGTAC 56 156 1 TTATGATCGC 0.920873 -145 GGTCGAATAATTGTGAGAACGTTCACGTGAAAACGC 63 248 0 TTGTGATCAC 0.984465 -53 ****** **** Masking position 4 Map Score: 25.1031 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 24 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 GCAAATTAAACGCGTGTCTTTTGTGAGTTTT 1 144 0 CGCGGTCTTT 0.639151 -157 GTCCGCTTGCGGGCCTTTTTTCTTAGCTTTT 9 37 1 GGGCTTTTTT 0.860842 -83 GGCATCTAAGCGCCCTTTATTTATTACACAG 10 195 0 CGCCTTTATT 0.740186 -100 CCGGCCATTGCGCCGGTTTTTTTTGGCCTGA 14 45 1 CGCCGTTTTT 0.906515 -254 GAATACATTGGGCGCTTTTTCAAGCCCGTGA 15 142 0 GGCGTTTTTC 0.834831 -60 CCCTGCGTTTCGCGATTTATTTTAGATATCG 16 178 0 CGCGTTTATT 0.756306 -123 TAGCAAAGTGCGCGTGTTTTTATGCCGGATG 20 38 0 CGCGGTTTTT 0.913521 -160 CCTATCGGGAGGCCGTTTTTTTGCCTTTCAC 20 76 1 GGCCTTTTTT 0.947659 -122 GGTCGTTACGGGCGAGTTTTTCCATCTTTTG 22 158 0 GGCGGTTTTT 0.920048 -27 AAGCCAGGTTGGCGCTTTTTTTCTCATAGAG 23 245 1 GGCGTTTTTT 0.951745 -56 GTCTGGTAACGGCGATTTGTTTTGCACGTTC 26 157 1 GGCGTTTGTT 0.664783 -62 GTATTGTTAGCGCCAGTTTTTAACAGACGCG 28 211 0 CGCCGTTTTT 0.906515 -90 GTTTCAGCATCGGCATTTTTCCGTCACGTCG 33 190 1 CGGCTTTTTC 0.592706 -67 GGTGCTTCGGCGACCTTTTTTATTACCTTGA 36 17 1 CGACTTTTTT 0.689413 -284 TCCCCCGTAAGGCCTTTCTTTTTCTTTCGTT 38 39 1 GGCCTTCTTT 0.752219 -38 GCTGGAAGCCCGAGGTTTTTTGTTAATGTGG 47 246 0 CGAGTTTTTT 0.707438 -55 AACATAAGAAGGGGTGTTTTT 47 290 1 GGGGGTTTTT 0.797235 -11 ATTCACGTCAGGCCGTTTTTTTCAGGTTTTT 50 76 1 GGCCTTTTTT 0.947659 -58 CTGGTGAAGTCGGGTTTTTTTGTTTATAAAA 51 253 1 CGGGTTTTTT 0.860842 -33 AGCAAGGACCTTTTTTATAAACAAAA 51 270 0 GGACTTTTTT 0.707438 -16 TGCGTAAGCGGGGCATTTTTCTTCCTGTTAT 54 11 1 GGGCTTTTTC 0.613195 -290 TATTATTTGCGGCGCTTTTTTCACTTACCGG 60 134 0 GGCGTTTTTT 0.951745 -167 TAACAGTTACCGCGTTTTATTCATCCTCATT 63 115 1 CGCGTTTATT 0.756306 -186 **** ****** Masking position 7 Map Score: 21.9258 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 309 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 4 ACGCTTAAAGATGCCTAATCCGCC 1 2 0 AGCCTACCGC 0.645473 -299 AACTGGGGAAAGACCAAACCGGGCGGCGACGAT 5 55 1 AACCAACGGG 0.551561 -56 TCGATGCCGGTACGGGTAATCGTGCC 12 4 1 AGCCGTCGGG 0.973533 -47 GAATCCTCTGAAAGCGGAGCCGTTTCGTTCACG 15 114 1 AAGCGACCGT 0.47379 -88 ACGTATGTTTACACCGCATCCGGCATAAAAACA 20 22 1 AACCGACCGG 0.96861 -176 CATAACAACAACGCCGGAAAGGCAGGCTCCCTG 27 122 0 AGCCGAAGGC 0.579513 -82 AGTTATGTAAAGTCCGTATCGGGCAGTGACTAC 32 80 0 ATCCGACGGG 0.83737 -176 AAAAATGCCGATGCTGAAACGGAATTAAGAAAC 33 177 0 AGCTGACGGA 0.465785 -80 GATTTTCAGAAAGCCGTAACGGATGCTTAATTT 42 147 0 AGCCGACGGA 0.908846 -63 GCGGCGTAAAACACCGTACCCGGCCTGGAGTTT 53 13 0 AACCGACCGG 0.96861 -74 ACGGTGTTTTACGCCGCATCCGGCATTACAAAA 53 29 1 AGCCGACCGG 0.988924 -58 TGTAAACAGAAAACCGTACCGGGA 56 2 0 AACCGACGGG 0.961242 -299 GTCACATGGCAGGCCGTTGCCGTGCGCTCTTAT 56 37 0 AGCCGTCCGT 0.864108 -264 AAGCTGCTCCCGGGCTTGCGAAA 56 288 0 AGCTGTCCGG 0.800089 -13 CTCCTGTGGGAAAGCGAACCCGCCCTTGCGAGC 57 22 0 AAGCGACCGC 0.727121 -29 CCGTCTTTTCACGGCGTTACCGGATGCGTAAGG 60 38 0 AGGCGTCCGG 0.905756 -263 CGTTGACTCCATGCCGATTCGGGTTAATCTGGT 61 104 0 AGCCGTCGGG 0.973533 -27 TGAAGTCGACATGCCGGTACCGCATGCCACAAG 62 19 0 AGCCGTCCGC 0.949542 -268 * **** * **** Masking position 1 Map Score: 16.6437 Number of sites scoring better than the average of aligned sites = 1127 Number in coding regions = 846 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 5 GCTTGCGGGCCTTTTTTCTTAGCTTTTATTCCGAC 9 41 1 CTTTCTTATT 0.63339 -79 AAACGTTTTACCTTTTATTTATCTTATACCCGCTA 11 45 1 CTTTTTTATT 0.865513 -130 ATCGGGAGGCCGTTTTTTTGCCTTTCACTCCTCGA 20 79 1 CTTTTTGCTT 0.882349 -119 ATCCTGTCGTTTGTTTTCGATTTCAAAATATA 20 176 0 CTTTTTTCTT 0.96982 -22 CTTCGGCGACCTTTTTTATTACCTTGATATGTCCG 36 21 1 CTTTATTATT 0.527618 -280 GTAAAACTTTCGTTTCATTTCGTTTTGCCTATTAA 37 24 1 CTTTTTTCTT 0.96982 -225 CAGTGACTTTCATTATGTTTCTTTTGTGAATCAGA 37 119 1 CTTATTTCTT 0.847956 -130 ATCAGAAAACCATTATCTTTCGTTTTATTTTTATC 37 153 1 CTTATTTCTT 0.847956 -96 ATTAATCTTTCGTTTTGTTTCAGTTGATACTGCGT 37 196 0 CTTTTTTCTT 0.96982 -53 TAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGC 38 46 1 CTTTTTTCTT 0.96982 -31 ATCCCTTTTGCTTCCTTTATCTTTTCTT 39 4 1 CTTTCTTCTT 0.896122 -188 TCACAAATTTCGTTTTATTTCTTTTTTCTCCATTG 39 46 1 CTTTTTTCTT 0.96982 -146 CTCCATTGAACTTTCAGTTTCTTTTCTATAGATTT 39 73 1 CTTCTTTCTT 0.896122 -119 ACTTGCCTTTCGTTTCATTTCACTTGGTGATGTCT 39 119 0 CTTTTTTCTT 0.96982 -73 GGCGTTGTCGCTTTCACTTGCCTTTCGTTTCATTT 39 134 0 CTTCTTGCTT 0.668144 -58 CGAAAGCTGGCATTTGTTTTACTTTTTAGCCGCAT 42 105 1 CTTTTTTATT 0.865513 -105 AACAATTATCCATTTAAATTCATTTAGTTAATTGA 58 165 0 CTTTATTCTT 0.847955 -127 * *** **** ** Masking position 9 Map Score: 17.9187 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 52 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 TGGGGAAAGACCAAACCGGGCGGCGACGATA 5 58 1 CCAAACGGGC 0.770219 -53 GCACGATTACCCGTACCGGCATCGA 12 5 0 CCGTACGGCA 0.932435 -46 TGAGTAACAACGGAAACCGGCCATTGCGCCG 14 29 1 CGGAACCGGC 0.870426 -270 AAACGACAAGCGACAGCGGGCTGAATGGTGG 15 67 1 CGACACGGGC 0.799086 -135 TATGTTTACACCGCATCCGGCATAAAAACAC 20 25 1 CCGCACCGGC 0.973721 -173 GCTACGGCTTCCCTATCGGGAGGCCGTTTTT 20 65 1 CCCTACGGGA 0.728592 -133 AAAAACTCGCCCGTAACGACCAGGATT 22 168 1 CCGTACGACC 0.65777 -17 TATGTAAAGTCCGTATCGGGCAGTGACTACC 32 79 0 CCGTACGGGC 0.987405 -177 TATTGCTTGTCCGCAAACGGACATATCAAGG 36 42 0 CCGCAACGGA 0.583874 -259 TGCCGCAAAGCGGTAGAGGGCAAGTT 50 118 1 CGGTAAGGGC 0.783926 -16 GCGTAAAACACCGTACCCGGCCTGGAGTTTT 53 12 0 CCGTACCGGC 0.973235 -75 GTGTTTTACGCCGCATCCGGCATTACAAAAT 53 32 1 CCGCACCGGC 0.973721 -55 AAACAGAAAACCGTACCGGGA 56 1 0 CCGTACGGGA 0.967485 -300 TAAGAGCGCACGGCAACGGCCTGCCATGTGA 56 38 1 CGGCACGGCC 0.945011 -263 CCAGATTAACCCGAATCGGCATGGAGTCAAC 61 105 1 CCGAACGGCA 0.846082 -26 TTGTGGCATGCGGTACCGGCATGTCGACTTC 62 20 1 CGGTACGGCA 0.86488 -267 ***** ***** Masking position 5 Map Score: 15.5052 Number of sites scoring better than the average of aligned sites = 1264 Number in coding regions = 996 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 7 GTAGTGTATAAAATGTTGAAAAATTTGCAACTA 7 145 0 AAATGAAAAA 0.84924 -66 AATTCGTCTGAAAGCTTGAGTAACAACGGAAAC 14 13 1 AAATGAGTAA 0.565595 -286 AGCCAACAGAAAACGCTGAAAAAACATCCAAAA 22 130 1 AAATGAAAAA 0.84924 -55 AAAAACATCCAAAAGATGGAAAAACTCGCCCGT 22 149 1 AAATGGAAAA 0.672004 -36 GGACACAAAGAAAAATTGAATAAACTGTATGAT 26 57 0 AAATGAATAA 0.916229 -162 TTTTAATTTGAAAGTTTGAATAAAAGGATAGCG 32 127 0 AAATGAATAA 0.916229 -129 TCACAAATATAAAAAATGAACAATTCACTCTCT 33 104 1 AAATGAACAA 0.791256 -153 CGGTTTCACAAAATCATGAATAGTTGTCACTAA 33 144 0 AAATGAATAG 0.565595 -113 CTATCCACAGAAAAGGTGAATAAAAACGGCTAT 34 131 1 AAATGAATAA 0.916229 -170 ACACACTAATAACAATTGAATAACTCACAGTTA 34 195 0 AACTGAATAA 0.565595 -106 GGTGTTTTGAAAACAGTGAATTATTAATTTCTT 36 188 0 AAATGAATTA 0.467651 -113 ATCCTCACCATAAAGTTGAATAATATAATTTTT 40 138 0 TAATGAATAA 0.467651 -29 CTAAGCGGGCAAAACCTGAAAAAAATTGCTTGA 50 44 1 AAATGAAAAA 0.84924 -90 ACTCCAAAAAAAAACCTGAAAAAAACGGCCTGA 50 83 0 AAATGAAAAA 0.84924 -51 TAAATCACAAAAATAATGAATAACCCATTAATG 55 119 1 AAATGAATAA 0.916229 -182 CAAATCTGCCAAAAGCTGGACAAATGTAATGTA 56 69 1 AAATGGACAA 0.579598 -232 CAGGCGGAGCAAACAGTGGATAAAAAGGCCATT 56 213 0 AAATGGATAA 0.799117 -88 *** ******* Masking position 7 Map Score: 11.0386 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 85 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 AGCCTCGCCGTGTACAGGGCATCTAAGCGC 10 213 0 TGTACAGGGC 0.87689 -82 ACCGCTTCCTTGTGCGGGGCGTGATGCTTT 32 52 0 TGTGCGGGGC 0.946651 -204 TAAACCACTCTCTGCAGGGCATTACACACT 34 221 0 TCTGCAGGGC 0.884421 -80 TGAAAGCAATTGAGCAGGGAAACCGGTGTT 36 215 0 TGAGCAGGGA 0.923551 -86 GTTGATTTTCTAAGCATGGCGCTCAATTTA 42 30 1 TAAGCATGGC 0.773173 -180 GCAATTAGCATGTGCATGGCGGTCTGTTGT 45 19 1 TGTGCATGGC 0.87689 -99 TGCGTAAGCGGGGCATTTTTCTTC 54 5 1 TAAGCGGGGC 0.894645 -296 CTGAGCAGGGACGTTAAAACG 60 2 1 TGAGCAGGGA 0.923551 -299 GATGGGGATAAGCAGAGCGCTTATCCCC 61 9 1 TAAGCAGAGC 0.635481 -122 AGTTCCTGACTGAACAGGGCATTTCAGCCA 62 77 1 TGAACAGGGC 0.923551 -210 TTGATCCCTGTGAGCAGGGCGGCGCCATTA 62 210 0 TGAGCAGGGC 0.987408 -77 ********** Masking position 1 Map Score: 9.37861 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 295 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 CCTATCAAAACTCGCTTTCGCGATGGTTTTCG 7 177 0 CTCGCTTCGG 0.748197 -34 CCAAAAACCCCTGCGTTTCGCGATTTATTTTA 16 185 0 CTGCGTTCGG 0.908445 -116 CAAAACAAATCGCCGTTACCAGACAAATAATG 26 149 0 CGCCGTTCCG 0.86214 -70 TACAGGGAGCCTGCCTTTCCGGCGTTGTTGTT 27 120 1 CTGCCTTCCG 0.937365 -84 CAGAATGCTCCGGGTTTTCCCGTAGTAATTCC 34 83 1 CGGGTTTCCG 0.696652 -218 AGAAAAAGAAAGGCCTTACGGGGGAAGTGAAG 38 32 0 AGGCCTTCGG 0.866017 -45 GTCCAGTCGACGGCCTTTTGTGTGATATCAAT 47 156 0 CGGCCTTTGG 0.866017 -145 TACCCGGGCTTGCAGGCAAAAAAGAG 49 19 0 CGGGCTTCAG 0.897304 -16 CTGAAAAAAACGGCCTGACGTGAATCAAGCAA 50 69 0 CGGCCTGCGG 0.968288 -65 CGCACGGCAACGGCCTGCCATGTGACAAATCT 56 44 1 CGGCCTGCAG 0.824686 -257 AAGCTGCTCCCGGGCTTGCGAAAGCCCATGTC 56 279 0 CGGGCTTCGA 0.849817 -22 AAAGCGAACCCGCCCTTGCGAGCGGGAGAAGA 57 13 0 CGCCCTTCGG 0.967278 -38 GTGATCTTCGCTGCGTTTCGGGAACGTTCCCG 59 32 1 CTGCGTTCGG 0.908446 -87 TAAAACGTCACGGCCTTACGCATCCGGTAACG 60 25 1 CGGCCTTCGA 0.924248 -276 CGTCTTTTCACGGCGTTACCGGATGCGTAAGG 60 38 0 CGGCGTTCCG 0.962768 -263 CGTGAAAAGACGGGCTTACCGGAAAAGTTTTA 60 58 1 CGGGCTTCCG 0.969711 -243 ******* ** * Masking position 6 Map Score: 14.9563 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 408 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 CGTATTTTTATTTTGCTGCAAATTGTACTGCCGAT 1 235 0 TTTCTGCAAG 0.689815 -66 ATATTAACTTTGTAACGTCATAGAGTCAAAGAAAA 3 126 0 TGTCGTCAAG 0.632065 -34 TATTTTAAATTTTCCCGTCAAAGAGTTATTTCATA 13 13 1 TTTCGTCAAG 0.836163 -72 GCGGTCAAGTTTTCACCGCAAAGGTATTTAAAAGG 22 71 0 TTTCCGCAAT 0.89945 -114 GGTTGGCGCTTTTTTTCTCATAGAGGCTGAATCGT 23 251 1 TTTTCTCAAG 0.376538 -50 TTTTTCTTTGTGTCCCCTCACAAGGTCGACCTGCG 26 75 1 TGTCCTCAAG 0.761116 -144 ACTAAGTATCTGACCCCGCATAAGGAATAGAAC 27 9 0 TGACCGCAAG 0.697703 -195 CAATTCTTCCTTTAGCGGCATAATGTTTAATGACG 28 117 1 TTTCGGCAAG 0.957779 -184 AAAGTGTTATTTTGATCGCAAAATGAAAGATAAAT 32 161 0 TTTTCGCAAG 0.728588 -95 ACCTGAATATTTTTCCCGCCGATTGTGCAAGGACA 33 61 0 TTTCCGCCAG 0.875848 -196 GCATCGGCATTTTTCCGTCACGTCGACTGATAACA 33 196 1 TTTCGTCAGG 0.632065 -61 TTATCTATTGCTTGTCCGCAAACGGACATATCAAG 36 43 0 CTTCCGCAAG 0.777997 -258 ATTGCTTTCATTAAACCGCACGAGTATTTTATTTT 36 235 1 TTACCGCAGT 0.329179 -66 AGTATTTTATTTTTACCGCCGGACGGTACCCTAAA 36 257 1 TTTCCGCCGG 0.703667 -44 TGTTTTACTTTTTAGCCGCATAAAGTCAAAATTAA 42 119 1 TTTCCGCAAG 0.976784 -91 TGGCGGTCTGTTGTGCGGCACAACGGGCCATTTGT 45 35 1 TTGCGGCAAG 0.684402 -83 GTACTGTTTCTCCTCACAACGTCTAAAAGAG 46 25 0 TTTCCTCAAG 0.90445 -21 TTTTTGTTAATGTGGCGGCAGAGGTAGCCGGACCT 47 226 0 TGTCGGCAAT 0.618819 -75 GTTTTACCGCAAAACTGGATCCCG 48 2 1 TTTCCGCAAT 0.89945 -23 TTTTTCAGGTTTTGCCCGCTTAGTGCGGTAACAAT 50 32 0 TTTCCGCTAG 0.721168 -102 TTTTTTGGAGTTTTGCCGCAAAGCGGTAGAGGGCA 50 105 1 TTTCCGCAAG 0.976784 -29 ATTATGTGCATTACTCCGCAAATCTGACCTTTCAC 55 177 1 TTACCGCAAT 0.59314 -124 ATTGTCATTGTTTACCGACATATCGCCTCTCATCA 55 222 1 TTTCGACAAG 0.514456 -79 CAAGACGCTGTTTTGCGGCATGCTTCCGGTTTATC 56 126 1 TTTCGGCAGT 0.618819 -175 *** ***** * * Masking position 9 Map Score: 16.5085 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 591 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 GCAGTAACCCGCAATGTGTGCGAATTATTGG 3 72 1 GCAATGTGGC 0.655102 -88 ACCGTCACTTGCAAACTGCGAGTTCGCTGGC 6 20 0 GCAAACTGGA 0.793483 -48 TCATAACCACGCAGACTGCGCGCAACATGAG 7 30 0 GCAGACTGGC 0.944774 -181 AAAAAGGCCCGCAAGCGGACCTTTTATAAGG 9 26 0 GCAAGCGGCC 0.870666 -94 CTCACGCGTGGCAAGGGGGGAGAGCCTCGCC 10 234 0 GCAAGGGGGA 0.860411 -61 GGAATCCTCTGAAAGCGGAGCCGTTTCGTTC 15 113 1 GAAAGCGGGC 0.813157 -89 GGAAGCCGTAGCAAAGTGCGCGTGTTTTTAT 20 46 0 GCAAAGTGGC 0.930775 -152 ATGCCTTTTTGCAAGCTGGGCAAACTAAGTA 27 36 0 GCAAGCTGGC 0.960265 -168 GTCTACACTCGCAGAGTGTGAAGAGCGTCAT 31 56 0 GCAGAGTGGA 0.707633 -108 AGGACAATCGGCAAACGGTGCAGTACACTGC 33 36 0 GCAAACGGGC 0.971329 -221 TTGCTTGTCCGCAAACGGACATATCAAGGTA 36 40 0 GCAAACGGCA 0.516903 -261 GCGTCAATGGGCAAGGTGGGCTTGCATTTGC 37 73 0 GCAAGGTGGC 0.944604 -176 TAATGTGGCGGCAGAGGTAGCCGGACCTTGT 47 223 0 GCAGAGGTGC 0.519547 -78 TGCGTAAGCGGGGCATTTTTCTTC 54 4 1 GTAAGCGGGC 0.711655 -297 ATAGGCAATCGCAGGCGGAGCAAACAGTGGA 56 226 0 GCAGGCGGGC 0.974969 -75 AGGACGTAATGAAGAGGGAGCGTCCTGCAAC 63 72 1 GAAGAGGGGC 0.685159 -229 TTTTATAGGCGCAGACTGGTCGAATAATTGT 63 270 0 GCAGACTGTC 0.492216 -31 ******** ** Masking position 3 Map Score: 12.1789 Number of sites scoring better than the average of aligned sites = 1314 Number in coding regions = 1242 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 12 GTTTTCTGGTTTAGCCAGTAAAAGGGAGTGA 1 93 1 TTGCCAGTAA 0.650483 -208 CCCGATAAATTCATCCTGTAAATAATACAAA 2 47 1 TCTCCTGTAA 0.882363 -62 TGTACTTCTCCTGTTTACGTAAGACT 17 47 0 TTTCCTGTTT 0.656263 -16 GCGGGATTAATTCTCCAGTAAATGCATTATT 26 125 1 TTTCCAGTAA 0.843014 -94 CAGCTTTGGCTTTTCCTGTAACGATTAATTT 28 65 0 TTTCCTGTAA 0.955836 -236 CGGTTCGACTTTAGCCTGTATTGTTAGCGCC 28 228 0 TTGCCTGTAT 0.650483 -73 CGGATTTTATCCTGTTATCAGTAGGGT 33 240 0 TTTCCTGTTA 0.884987 -17 AATATTATCCTGTAGAGGAGAGAGT 35 13 0 TTTCCTGTAG 0.818628 -15 GGGGCATTTTTCTTCCTGTTATGTTTTTAAT 54 20 1 TCTCCTGTTA 0.72728 -281 CCGTGCGCTCTTATCCTGTAAACAGAAAACC 56 20 0 TTTCCTGTAA 0.955835 -281 AGATTAAAACTTTTCCGGTAAGCCCGTCTTT 60 63 0 TTTCCGGTAA 0.818628 -238 CCTGTTGTCCTGTAACGTGTTGTTT 60 286 0 TTTCCTGTAA 0.955836 -15 ** ******** Masking position 9 Map Score: 6.59625 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 71 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 13 GAAAACTTATTTTATCATTCAAAAAATCAGG 1 68 0 TTTATCTTCA 0.893191 -233 ACAGGATGAATTTATCGGGCATAATGGTTAA 2 35 0 TTTATCGGCA 0.768475 -74 TTACTGCTTTATTTTCGTTCAGTGCTGATAA 3 48 0 ATTTTCTTCA 0.54867 -112 GGTAAAACGTTTTATCTGTCACATAATCAGG 11 26 0 TTTATCGTCA 0.954637 -149 CTCATCGACGATTATCTGTCAGCCAGACACT 14 269 0 ATTATCGTCA 0.871071 -30 AATTAAAATATTTATCTTTCATTTTGCGATC 32 152 1 TTTATCTTCA 0.893191 -104 TGTTCTCTCCTTCAGGATTTATTG 32 242 0 TCTCTCTTCA 0.652908 -14 AGCATCGGCATTTTTCCGTCACGTCGACTGA 33 195 1 TTTTTCGTCA 0.905024 -62 TAAAATATTCATTATCAGTCAATGCATTACA 34 30 0 ATTATCGTCA 0.871071 -271 TCGGCTACTTTTTCTCTGTCACAGAATGAAA 54 89 1 TTTCTCGTCA 0.937436 -212 AGAATGAAAATTTTTCTGTCATCTCTTCGTT 54 111 1 TTTTTCGTCA 0.905024 -190 GAAGACTTTATCTCTCTGTCATAAAACTGTC 54 190 1 TCTCTCGTCA 0.825594 -111 AAGATCACAATTTATCGTTCAGGAAACGA 59 9 0 TTTATCTTCA 0.893191 -110 ****** **** Masking position 11 Map Score: 7.32644 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 167 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 14 AACTCTTTGACGGGAAAATTTAAAATAAA 13 5 0 CGAAATAAAA 0.947355 -80 TAAATCAATACCGCAATATTTAAATTGCGGTTTTT 13 46 1 CGAAATAAAT 0.872735 -39 ATCCCTCTGTAACAATAAAAAGGACTATTT 18 7 1 CGAAATAAAA 0.947355 -24 TCAAAAGCGCCACGAATAGTCAAAATGCCATTTCA 23 14 1 CCAAATAAAA 0.824843 -287 AGCAGCCAATCAGCAACAGTGAAATGGCATTTTGA 23 33 0 CGAAATAAAT 0.872735 -268 ATTGAATAAACTGTATGATTTAAAAGATTATCGGG 26 41 0 CGATATAAAA 0.771525 -178 TTCAACTGCTCCGCTAAAGTCAAAATAATTCTTTC 27 177 0 CGTAATAAAA 0.757466 -27 TCTAATCAGATTGAAAGATTTAAAAGTGTTATTTT 32 183 0 TGAAATAAAA 0.504512 -73 TACCGTCCGGCGGTAAAAATAAAATACTCGTGCGG 36 250 0 CGAAATAAAT 0.872735 -51 CCGGACGGTACCCTAAAAATAAAATAAGGATAATT 36 275 1 CCAAATAAAT 0.642162 -26 ACTTTTTAGCCGCATAAAGTCAAAATTAAGCATCC 42 125 1 CCTAATAAAA 0.449731 -85 TACCGCTTTGCGGCAAAACTCCAAAAAAAAACCTG 50 98 0 CGAAATCAAA 0.709437 -36 AAAATAGTGTCAGGATTAATCAAAACCAATCACAT 58 42 0 CGATATAAAA 0.771525 -250 ATATATTGCGCGGAAAAATTTAAAAACGGGAACGT 59 55 0 CGAAATAAAA 0.947355 -64 ACGCGCAAAGCTGAACAAATAAAAAATTATGTGAG 63 217 0 CGACATAAAA 0.739466 -84 * * ** * * **** Masking position 8 Map Score: 7.19165 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 80 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 15 CAAATACAATACAAATAATTTCAATCAAGT 2 74 1 ACAAATAATT 0.762636 -35 TTACACAGAGTAAAATAATTCAGTGCCAAT 10 173 0 TAAAATAATT 0.610346 -122 CACATTTCGGGCAAATAATTCGCGAAGATA 14 85 0 GCAAATAATT 0.832492 -214 CTTCATCACATAAAATAATTTTTTCGATAT 16 154 1 TAAAATAATT 0.610346 -147 CTTTCACTCCTCGAATAATTTTCATATTGT 20 100 1 TCGAATAATT 0.79601 -98 ATATTTAAAAACAAATAATTTCATTATATT 20 152 1 ACAAATAATT 0.762636 -46 CTATTTACGATCAAATAATTGCAGATGTAT 31 130 0 TCAAATAATT 0.910453 -34 GACGCGACCCGCAAATAATTCCACATGGAT 58 221 0 GCAAATAATT 0.832492 -71 AACGTTAGGCTCAAATAATTAAACAACACG 60 266 1 TCAAATAATT 0.910453 -35 TCCACTCGGCTCACATAATTTTTTATTTGT 63 208 1 TCACATAATT 0.656913 -93 CGCAGACTGGTCGAATAATTGTGAGAACGT 63 262 0 TCGAATAATT 0.79601 -39 ********** Masking position 5 Map Score: 4.46417 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 31 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344