AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_ecoli_reg_100.orf -o00051_ecoli_100.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 yabB 300 orf, hypothetical protein #2 yadI 104 putative PTS enzyme II B component #3 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #4 nagE 300 PTS system, N-acetylglucosamine-specific enzyme IIABC #5 hrsA 108 protein modification enzyme, induction of ompC #6 ycaI 129 orf, hypothetical protein #7 msbA 36 ATP-binding transport protein; multicopy suppressor of htrB #8 ycaQ 36 orf, hypothetical protein #9 ycaR 51 orf, hypothetical protein #10 ptsG 294 PTS system, glucose-specific IIBC component #11 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #12 prfA 41 peptide chain release factor RF-1 #13 kdsA 35 2-dehydro-3-deoxyphosphooctulonate aldolase #14 rspA 205 starvation sensing protein #15 manA 198 mannose-6-phosphate isomerase #16 malX 174 PTS system, maltose and glucose-specific II ABC #17 pfkB 286 6-phosphofructokinase II; suppressor of pfkA #18 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #19 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #20 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #21 manX 300 PTS enzyme IIAB, mannose-specific #22 cpsG 104 phosphomannomutase #23 gmd 25 GDP-D-mannose dehydratase #24 wcaA 34 putative regulator #25 BIME92 24 BIME #26 wza 300 putative polysaccharide export protein #27 gatD 47 galactitol-1-phosphate dehydrogenase #28 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #29 gatZ 28 putative tagatose 6-phosphate kinase 1 #30 gatY 197 tagatose-bisphosphate aldolase 1 #31 fruB 300 PTS system, fructose-specific IIA/fpr component #32 pdxB 98 erythronate-4-phosphate dehyrogenase #33 glk 203 glucokinase #34 ptsH 300 PTS system protein HPr #35 ptsI 44 PEP-protein phosphotransferase system enzyme I #36 crr 40 PTS system, glucose-specific IIA component #37 srlA 255 PTS system, glucitol/sorbitol-specific IIC component, one of two #38 ascF 256 PTS system enzyme II ABC (asc), cryptic, transports specific beta-glucosides #39 fucA_fucP 546 fucA: L-fuculose-1-phosphate aldolase, fucP: fucose permease #40 fucI 32 L-fucose isomerase #41 fucK 78 L-fuculokinase #42 fba 214 fructose-bisphosphate aldolase, class II #43 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #44 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #45 agaZ 248 putative tagatose 6-phosphate kinase 2 #46 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #47 agaC 38 PTS system N-acetylgalactosamine-specific IIC component 1 #48 ptsN 117 phosphotransferase system enzyme IIA, regulates N metabolism #49 xylA 300 D-xylose isomerase #50 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #51 BIME180 41 BIME #52 mtlD 88 mannitol-1-phosphate dehydrogenase #53 rfaD 288 ADP-L-glycero-D-mannoheptose-6-epimerase #54 rfaS 36 lipopolysaccharide core biosynthesis #55 rfaQ 300 lipopolysaccharide core biosynthesis #56 glvB 24 PTS system, arbutin-like IIB component #57 glvC 34 PTS system, arbutin-like IIC component #58 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #59 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #60 yifM_2 241 orf, conceptual translation in SwissProt is fused with b4404 #61 frvA 300 PTS system, fructose-specific IIA component #62 rhaD 85 rhamnulose-phosphate aldolase #63 rhaB 287 rhamnulokinase #64 pfkA 180 6-phosphofructokinase I #65 tpiA 107 triosephosphate isomerase #66 frwC 300 PTS system, fructose-like enzyme II component #67 pflD 50 formate acetyltransferase 2 #68 sgaT 291 orf, hypothetical protein #69 fbp 175 fructose-bisphosphatase #70 treB 118 PTS system enzyme II, trehalose specific #71 sgcA 130 putative PTS system enzyme II A component Motif number 1 ACGATATTTGGTGACAAAACTCACAAAAGACACGCGT 4 129 1 GTGATCACAA 0.98005 -172 TTTCAATCAAGTGAAATTGATCACATA 5 92 1 GTGATCACAA 0.98005 -17 AAGTTGAAACGTGATAGCCGTCAAACAAATTGGCACT 10 145 1 GTGATCAAAA 0.629752 -150 ACCTGTGGTTATGACCCTCTTCACATTTCGGGCAAAT 20 99 0 ATGATCACAT 0.686835 -200 TTTAAATATCGAGATAACGATCACAAAAACGACAATA 30 124 0 GAGATCACAA 0.734103 -74 ATTTAAAAGTGTTATTTTGATCGCAAAATGAAAGATA 37 164 0 GTTATCGCAA 0.582206 -92 AAATATTCAGGTGACCGGTTTCACAAATATAAAAAAT 38 84 1 GTGATCACAA 0.98005 -173 GCTCTGTAATATGACGGCGGTCACACTTATTAGCTAG 39 150 1 ATGATCACAT 0.686835 -397 GATTATTAAAGTGATGGTAGTCACATAAAGTCACCTT 39 187 0 GTGATCACAA 0.98005 -360 CTGTGATTAGTTGAACCAGGTCACAAAATATAAGCTT 39 407 1 TTGATCACAA 0.672713 -140 TAGATAAGGCGTGTTGTAGATCACAAATATTTATATG 44 71 1 GTGTTCACAA 0.760115 -230 ACCGCATATCGTGATGCATATTACATAATTGATATTT 44 112 0 GTGATTACAA 0.629752 -189 TAATGGTTTTCTGATCTGATTCACAAAAGAAACATAA 45 131 0 CTGATCACAA 0.752866 -118 ATTCACAAGTGTGCGCTCGCTCGCAAAATAAAATGGA 49 168 0 GTGCTCGCAA 0.911616 -133 AAACAAAAATGTGACACTACTCACATTTAAATGCCAT 50 26 1 GTGATCACAT 0.954015 -275 GGTAATTGACGTGACGTTCATCACAAAACGCTTGTGT 50 96 0 GTGATCACAA 0.98005 -205 GGCCTTTTGTGTGATATCAATCACATAAATATAGGGG 50 140 0 GTGATCACAA 0.98005 -161 AACCGATTCAGTGCCAGATTTCGCAGTATCTACAAGG 50 192 1 GTGCTCGCAT 0.813284 -109 TAACCATTATGTGCATTACTCCGCAAATCTGACCTTT 61 172 1 GTGCCCGCAA 0.715841 -129 TTGTGGTGATGTGATGCTCACCGCATTTCCTGAAAAT 63 127 0 GTGACCGCAT 0.805875 -161 AAAGATGAACGTGATGATGTTCACAATTTGCTGAATT 63 162 0 GTGATCACAT 0.954015 -126 ACAGCGTCTTGTGAGACGCGTCGCAAATTGACGGTTA 66 100 0 GTGATCGCAA 0.975757 -201 ATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGA 66 158 1 ATGATCGCAT 0.642458 -143 ATGATTAAATGTGACGCGACCCGCAAATAATTCCACA 68 226 0 GTGACCGCAA 0.907667 -66 **** ***** * Masking position 15 Map Score: 29.4897 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 85 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 CTCCGTAAACTCCTTTCAGTGGGAAATTGT 1 249 1 TCCTTTCAGT 0.732434 -52 TGAACTTTACTCGTTTTAGCCATTAATTAC 10 30 0 TCGTTTTAGC 0.667959 -265 TACCGTATACTCCTTTCAGCCACAAAAAAA 20 185 1 TCCTTTCAGC 0.922692 -114 CACAATCGAATCGATTCAGATAAGGGCTAC 21 219 0 TCGATTCAGA 0.815083 -82 ATCAGCAATTTCATTTCAGCAGCGTCAGCA 31 64 0 TCATTTCAGC 0.924108 -237 CATAATACTTCTGTTTCAGCACGCAAGGAA 31 175 0 CTGTTTCAGC 0.820223 -126 CTTTCTTGAAACGTTTCAGCGCGATCTTGT 31 205 1 ACGTTTCAGC 0.924701 -96 CTGAATTGAAACGATTCAGCCTCTATGAGA 31 266 0 ACGATTCAGC 0.87702 -35 CTGAATCGTTTCAATTCAGCAAGAGAGGAG 31 277 1 TCAATTCAGC 0.876102 -24 AATTACTTTATCGTTTCAGCACCAATTGCA 33 70 0 TCGTTTCAGC 0.981513 -134 TTGATTCAGCCTGTCGGAAC 34 1 1 TTGATTCAGC 0.817431 -300 AATCATAAAATCGATTCAGCTTTGGCTTTT 34 82 0 TCGATTCAGC 0.968584 -219 TTTCTTAATTCCGTTTCAGCATCGGCATTT 38 178 1 CCGTTTCAGC 0.969152 -79 ATCCATGAGTTCATTTCAGACAGGCAAATA 39 101 0 TCATTTCAGA 0.635153 -446 AATTTCATGCCCGTTTCAGAAAATAAATCA 39 226 1 CCGTTTCAGA 0.817903 -321 AAACCTGCCCTTGTTTCAGCGCGCTTTTAG 42 28 1 TTGTTTCAGC 0.885191 -187 CAAGCTACTCTCGTTTCAGTGACTTTCATT 45 103 1 TCGTTTCAGT 0.924108 -146 ATCTTTCGTTTTGTTTCAGTTGATACTGCG 45 197 0 TTGTTTCAGT 0.638773 -52 ATTGGGCACTCCCTTTCAGTTGCTCAATTA 49 231 0 CCCTTTCAGT 0.618298 -70 GGACAGTTAACCGATTCAGTGCCAGATTTC 50 184 1 CCGATTCAGT 0.807111 -117 TCACATCACCACAATTCAGCAAATTGTGAA 63 150 1 ACAATTCAGC 0.620581 -138 CTGACCTGAATCAATTCAGCAGGAAGTGAT 64 66 1 TCAATTCAGC 0.876102 -115 ********** Masking position 5 Map Score: 22.676 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 350 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 3 ACTCCATCAATCGAACGCTGCCGCGGCGTAA 8 9 0 TCACGCGCCG 0.810568 -28 GGGGCGGTGCGAATGCAGGCGTCG 25 4 0 GCATGCGGCG 0.813659 -21 ATCCAGACACGCTACCGCCCCTGGCTTTTTAGC 26 107 0 GCACGCCCTG 0.944317 -194 CTGATTGGCTGCTGACGCTGCTGAAATGAAATT 31 55 1 GCGCGCGCTG 0.863074 -246 AGGCATCGCTGCAATTGGTGCTGAAACGATAAA 33 61 1 GCATGGGCTG 0.533485 -143 AGGACAATCGGCAAACGGTGCAGTACACTGCGT 38 34 0 GCACGGGCAG 0.88079 -223 GGTCGCTCCGGCTACCGGGCCTGAACAAGCAAG 41 36 1 GCACGGCCTG 0.836606 -43 ACTGGGGTGAGCGAACGCAGACGCAGCACATGC 42 144 1 GCACGCGACG 0.918483 -71 TTAAGCAAATGCAAGCCCACCTTGCCCATTGAC 45 69 1 GCACCCCCTT 0.592274 -180 TATTTTGCGAGCGAGCGCACACTTGTGAATTAT 49 175 1 GCACGCCACT 0.436467 -126 ACAAGGTCCGGCTACCTCTGCCGCCACATTAAC 50 223 1 GCACTCGCCG 0.94948 -78 TTCTTTCGCAGCAATCCGACCCGAATGATTTTT 55 122 0 GCACCGCCCG 0.904934 -179 AAAAAAGCACGCTACCGCCCCAGGCTCAACAGC 55 202 0 GCACGCCCAG 0.920531 -99 TCCTAACATCGCCAGCGCGGCATTAAGATTACA 59 65 0 GCACGCGCAT 0.780408 -175 CCACACTGTGGCTGGCTCTGCTGAGTGGTGGCA 60 49 1 GCGCTCGCTG 0.511959 -193 CTGTGTATTTGCCACCCGCGGCGATTTGAGCTT 60 197 1 GCACCGGGCG 0.880317 -45 CGAGAAGGTCGCGAATTCAGGCGCTTTTTAGAC 63 234 1 GCATTCGGCG 0.420857 -54 GAAACAATAGGCAATCGCAGGCGGAGCAAACAG 66 230 0 GCACGCGGCG 0.976361 -71 ATGGGCTTTCGCAAGCCCGGGAGCAGCTT 66 282 1 GCACCCGGAG 0.840747 -19 CTGTGGGAAAGCGAACCCGCCCTTGCGAGCGGG 67 19 0 GCACCCCCCT 0.820745 -32 TAACCCTTCTGCGATCCCTGCCGCCTTCGTCAA 71 51 1 GCACCCGCCG 0.985209 -80 TAATCTGGTAGCGATCCCCGTCGATACTTTTGA 71 80 0 GCACCCGTCG 0.790306 -51 ** * *** **** Masking position 2 Map Score: 17.7638 Number of sites scoring better than the average of aligned sites = 2655 Number in coding regions = 2545 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 TTGATAAAGGGTGATAGCCGTCAAAACTCCTCTC 2 39 0 GTGATATCAA 0.514345 -66 ACGATATTTGGTGACAAAACTCACAAAAGACACG 4 129 1 GTGACATCAC 0.920002 -172 TATGTGATCAATTTCACTTGATTGAAA 5 92 0 GTGATCTCAC 0.784253 -17 AAGTTGAAACGTGATAGCCGTCAAACAAATTGGC 10 145 1 GTGATATCAA 0.514345 -150 ACCTGTGGTTATGACCCTCTTCACATTTCGGGCA 20 102 0 ATGACCTCAC 0.751233 -197 TGTCGTTTTTGTGATCGTTATCTCGATATTTAAA 30 127 1 GTGATCTCTC 0.50161 -71 AAATATTCAGGTGACCGGTTTCACAAATATAAAA 38 84 1 GTGACCTCAC 0.80266 -173 GCTCTGTAATATGACGGCGGTCACACTTATTAGC 39 150 1 ATGACGTCAC 0.596389 -397 GATTATTAAAGTGATGGTAGTCACATAAAGTCAC 39 190 0 GTGATGTCAC 0.65655 -357 CTTATATTTTGTGACCTGGTTCAACTAATCACAG 39 407 0 GTGACCTCAA 0.870754 -140 TAGATAAGGCGTGTTGTAGATCACAAATATTTAT 44 71 1 GTGTTGTCAC 0.468406 -230 TAATGGTTTTCTGATCTGATTCACAAAAGAAACA 45 134 0 CTGATCTCAC 0.797042 -115 AAACAAAAATGTGACACTACTCACATTTAAATGC 50 26 1 GTGACATCAC 0.920002 -275 GGTAATTGACGTGACGTTCATCACAAAACGCTTG 50 99 0 GTGACGTCAC 0.505173 -202 GGCCTTTTGTGTGATATCAATCACATAAATATAG 50 143 0 GTGATATCAC 0.680898 -158 AAAAAACGGCCTGACGTGAATCAAGCAATTTTTT 58 63 0 CTGACGTCAA 0.616821 -71 AAAGATGAACGTGATGATGTTCACAATTTGCTGA 63 165 0 GTGATGTCAC 0.695311 -123 GCCATTTGGCCTGACCTGAATCAATTCAGCAGGA 64 56 1 CTGACCTCAA 0.616821 -125 CCGTCAATTTGCGACGCGTCTCACAAGACGCTGT 66 103 1 GCGACGTCAC 0.764662 -198 ****** **** Masking position 11 Map Score: 18.3332 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 172 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 5 ATACCGAGGTAAAAAACCCGATGTTTACGGC 1 185 0 AAAAAACCGA 0.74823 -116 CTTGAACGAGAGAAAAGCACCTGTCGGGTGC 6 25 1 AGAAAAGCCC 0.618877 -105 TAGAGAAATGAAAAAAGCACCCGACAGGTGC 6 41 0 AAAAAAGCCC 0.946872 -89 TCAAAAAACCAGCATTTGTTGAA 7 24 0 AAAAAACCGC 0.895821 -13 TGAGAACGTAAAAAAAGCACCCATACTCAGG 10 261 1 AAAAAAGCCC 0.946872 -34 ATAAAGATCGAAAAAAGCCGGAGTGATCACA 14 118 0 AAAAAAGCGG 0.826719 -88 TAACGAATTATAAAAAGGCGCGAATAACTTA 17 97 1 TAAAAAGGGC 0.696687 -190 AAAATACCCTTAAAAACCGCAATTTAAATAT 19 61 0 TAAAAACCCA 0.665783 -24 CTCAGGCCAAAAAAAACCGGCGCAATGGCCG 20 46 0 AAAAAACCGC 0.895821 -253 GTGAAAGGCAAAAAAACGGCCTCCCGATAGG 30 76 0 AAAAAACGCC 0.895821 -122 CTCTATGAGAAAAAAAGCGCCAACCTGGCTT 31 245 0 AAAAAAGCCC 0.946872 -56 TAAAAAGGTGCTTCGGCGACC 44 1 1 TAAAAAGGGC 0.696687 -300 TCAAGGTAATAAAAAAGGTCGCCGAAGCACC 44 17 0 AAAAAAGGCG 0.826719 -284 CCACATTAACAAAAAACCTCGGGCTTCCAGC 50 246 1 AAAAAACCCG 0.873577 -55 AGTTAAGCAGAAAAAAGCACGCTACCGCCCC 55 214 0 AAAAAAGCCG 0.892081 -87 AAAAACCTGAAAAAAACGGCCTGACGTGAAT 58 76 0 AAAAAACGCC 0.895821 -58 AAACTCCAAAAAAAAACCTGAAAAAAACGGC 58 87 0 AAAAAACCGA 0.74823 -47 GCGTTTTGGCAAAAAAGCTCAAATCGCCGCG 60 213 0 AAAAAAGCCA 0.860329 -29 AAAACCACGTAAAAAACGTCGATTTTTCAAG 63 85 1 AAAAAACGCG 0.799527 -203 ACGACCAGTCTAAAAAGCGCCTGAATTCGCG 63 243 0 TAAAAAGCCC 0.87334 -45 AAACAGTGGATAAAAAGGCCATTTACTGGAC 66 205 0 TAAAAAGGCA 0.579022 -96 CGGAAAAATTTAAAAACGGGAACGTTCCCGA 70 49 0 TAAAAACGGA 0.398895 -70 ******** ** Masking position 6 Map Score: 17.2885 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 250 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 6 ACGGCTATCACCCTTTATCAACAATGGTCAGGGTAGACTGAT 2 52 1 CTTTATGCGG 0.617329 -53 ACGGCCTGTCTCATTCTTACGATTGCGGCAGGCCGTGTTATT 3 38 1 TTTCTTGCGG 0.932073 -67 GTTATTATTGTCGTTTCTTATATTTTGACAGGAAGAGTATC 3 74 1 TTTTCTGCGG 0.964998 -31 TGTTCTCTCACTTACTGCCTGGTTTGGTTATG 15 1 1 TTCTCTGCGG 0.9601 -198 GCAGATGACCTACTCCCTGATTATGTGACAGATAAAACGTTT 16 11 1 TTCCCTGCGA 0.85442 -164 TTCTTAATTATCTTCGCGAATTATTTGCCCGAAATGTGAAGA 20 77 1 TTCGCGGCGA 0.492957 -222 ATTTACACCGCGGTTTCGCATTCATTGCCTGATGCGACGT 22 9 0 CTTTCGGCGA 0.568479 -96 GTTTTTTCCTTGTTAAATGGCAGGTGCG 29 5 0 TTTCCTGCGG 0.960472 -24 CAGCGCGATCTTGTCTTTAACCCTAAGCCAGGTTGGCGCTTT 31 221 1 TTCTTTGCGG 0.931452 -80 CAGGTTGGCGCTTTTTTTCTCATAGAGGCTGAATCGTTTCAA 31 249 1 CTTTTTGCGA 0.665832 -52 GTTCTATTCCTTATGCGGGGTCAGATACTTAGTTT 33 4 1 CTTCCTGCGA 0.756682 -200 CGTTTGCCGATTGTCCTTGCACAATCGGCGGGAAAAATATTC 38 50 1 TTCCTTGCGG 0.922937 -207 AAACGGTCATTTTTCTATTCCTCCAAGCCCGGAATGACCGTT 39 300 0 TTCTATGCGG 0.752753 -247 TACATTACTCCCTGATGTGATGCCCGGTCGCTCCGGC 41 6 1 TTCCCTGCGG 0.954972 -73 TATCCTTATTTTATTTTTAGGGTACCGTCCGGCGGTAAAAAT 44 265 0 TTTTTTGCGG 0.939645 -36 GATTTTTGGTTTATTTCTTGATTTATGACCGAGATCTTACTT 49 67 1 TTTTCTGCGA 0.884118 -234 AGCCCGAGGTTTTTTGTTAATGTGGCGGCAGAGGTAGCCGGA 50 229 0 TTTGTTGCGA 0.627525 -72 CCCCTTCTTATGTTTGCTGTCGCGCAGGCTGGAAGCCCGAGG 50 262 0 TTTGCTGCGG 0.915116 -39 CCTTCATCAATGTTTTTACCCGAGAGGGCTGGGGTGAGGCTT 52 49 0 TTTTTAGCGG 0.526933 -40 CTCTAGATCTCTTTTTTGCCTGCAAGCCCGGGTA 57 10 1 TTTTTTGCGG 0.939645 -25 GTTCTTCTCCCGCTCGCAAGGGCGGGTTCGCTTTCC 67 5 1 TTCCCGGCGG 0.887871 -46 AGGCAATGACCATTTTTTGACTTTTTGCCAGGGAAGTTGTTG 68 84 1 CTTTTTGCGG 0.87805 -208 TCCCCGTCGATACTTTTGACGAAGGCGGCAGGGATCGCAGAA 71 57 0 TTTTTGGCGG 0.853217 -74 * ***** * * ** Masking position 4 Map Score: 17.0934 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 301 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 TGCGACGCGAGCGGCATTTTAGGACATATCTTC 1 14 0 GCGCTTTTAG 0.559538 -287 CAAATATAAAGTGTCAGTTTGCGACGCGAGCGG 1 33 0 GTGCGTTTGG 0.882152 -268 GGTCGGATTGACGCCTGTCTGCGCAAATCCAGG 4 37 0 ACGCGTCTGG 0.609401 -264 GCGCAAATATACGCCTTTTTTTGTGATCACTCC 14 97 1 ACGCTTTTTG 0.907598 -109 TGTGATCACTCCGGCTTTTTTCGATCTTTATAC 14 118 1 CCGCTTTTTG 0.740331 -88 TGAGACTAGTACGACTTTTTGCGGCTCCAGGTT 15 113 1 ACGCTTTTGG 0.951577 -86 CGAAACCAACATGACTTTTTTTGTGGCTGAAAG 20 197 0 ATGCTTTTTG 0.858976 -102 TAGCTAGAAGGTGACTTTATGTGACTACCATCA 39 180 1 GTGCTTATGG 0.417014 -367 TCGAAATTTCATGCCCGTTTCAGAAAATAAATC 39 222 1 ATGCGTTTCG 0.515856 -325 CAAGCCCGGAATGACCGTTTTCGGCACAAACAA 39 286 0 ATGCGTTTTG 0.820156 -261 TTACCTTGATATGTCCGTTTGCGGACAAGCAAT 44 39 1 ATGCGTTTGG 0.901224 -262 TCACATTTAAATGCCATTTTTAGCGAAAATCGC 50 46 1 ATGCTTTTTG 0.858976 -255 AAGCAACAAGGCGGCGATTTTCGCTAAAAATGG 50 59 0 GCGCATTTTG 0.754354 -242 TGTCCAGTCGACGGCCTTTTGTGTGATATCAAT 50 156 0 ACGCTTTTGG 0.951577 -145 ACGTAAACACGTGGCGTTTTTGGCATAAGACAA 59 13 0 GTGCTTTTTG 0.833256 -227 TTTGCCACCCGCGGCGATTTGAGCTTTTTTGCC 60 204 1 GCGCATTTGG 0.860021 -38 TCGGTAAACAATGACAATTTGAGACAGAGTGAA 61 207 0 ATGCATTTGG 0.822818 -94 TGTAATGTAACCGTCAATTTGCGACGCGTCTCA 66 93 1 CCGCATTTGG 0.684911 -208 GTCTCACAAGACGCTGTTTTGCGGCATGCTTCC 66 120 1 ACGTTTTTGG 0.451214 -181 CCCATGGCAGATGACATTTTTGGTTGGCTGCAG 70 91 0 ATGCTTTTTG 0.858976 -28 *** * ***** * Masking position 8 Map Score: 9.99252 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 342 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 GCCAGCCTCACCCCTTATTCCCAC 1 287 0 AGCCTCACCC 0.956153 -14 GGCTATTTCCTCTCCTCTGGATTTGGG 2 7 1 TTCCTCTCCC 0.85675 -98 GCCGTCAAAACTCCTCTCCCCCAAATCCAGA 2 26 0 CTCCTCTCCC 0.930918 -79 GTACACGGCGAGGCTCTCCCCCCTTGCCACG 10 228 1 AGGCTCTCCC 0.92349 -67 TGTGGTTATGACCCTCTTCACATTTCGGGCA 20 102 0 ACCCTCTTCC 0.804344 -197 AATTTTTCACACCCTCTCAGCATGCAGTCGT 26 54 0 ACCCTCTCAC 0.886348 -247 GCGTCTGCGTTCGCTCACCCCAGTCACTTAC 42 137 0 TCGCTCACCC 0.705024 -78 TTACTCTCTCCTCTACAGGATAA 43 3 1 ACTCTCTCCC 0.839051 -25 TGTGTAATCCTCACCATAAAGTTGAAT 46 150 0 ATCCTCACCT 0.596076 -17 TCCAATCCCACCCTCTCCACATGGAGAAGG 51 10 1 ACCCTCTCCC 0.986423 -32 CTGCCCCTCTCCTCACGGAGAGGG 52 4 1 CCCCTCTCCC 0.973459 -85 CCTCACCCAAACCCTCTCCGTGAGGAGAGGG 52 15 0 ACCCTCTCCT 0.886348 -74 GTGAGGGAAAAGCCTCACCCCAGCCCTCTCG 52 40 1 AGCCTCACCC 0.956153 -49 ACCGACATATCGCCTCTCATCACTTAATCGC 61 235 1 CGCCTCTCAC 0.696446 -66 TGGTGATGTGATGCTCACCGCATTTCCTGAA 63 130 0 ATGCTCACCC 0.796717 -158 ********* * Masking position 5 Map Score: 11.2166 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 135 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 CGCCTTCCTCCTTAGCCGAAAATCAGTC 2 87 0 CCCTCTAGCG 0.96171 -18 AGGTTGTTCTCCCGGCTTATGAGCTGGTTTGCTT 24 9 0 CCCGCTAGCG 0.989233 -26 CACGCTACCGCCCCTGGCTTTTTAGCTACCAATACACT 26 95 0 CCCGCTAGCA 0.982915 -206 AAAAAACGGCCTCCCGATAGGGAAGCCGTAGCAAAGTG 30 59 0 CCCGTAAGCG 0.795725 -139 AAGCATCACGCCCCGCACAAGGAAGCGGTAGTCACTGC 37 53 1 CCCCCAAGCG 0.981763 -203 TGCCTATTAACGCCTTTCTATTAAGCAAATGCAAGCCC 45 49 1 CCCTCTAGCA 0.940097 -200 CACGCTACCGCCCCAGGCTCAACAGCTACCTGAATACT 55 190 0 CCCGCTAGCA 0.982915 -111 GGCTTAATGCCACCACTCAGCAGAGCCAGCCACAGTGT 60 51 0 CCCCCAAGCA 0.971363 -191 CCCACTACGTCGCCTGGCGCAAAAGCGAGTCGGCTGTG 60 164 1 CCCGCGAGCA 0.938575 -78 GGAAGATGGCCGCCCCGCAGGGCAGCAGGTCTGTGAAA 65 50 0 CCCCCAAGCG 0.98189 -58 TTTAATTCTCCACGCTTATAAGCGAATAAAGGAAG 65 83 0 CCCCCTAGCA 0.982915 -25 GGGAAAGCGAACCCGCCCTTGCGAGCGGGAGAAGAAC 67 10 0 ACCCCTAGCG 0.868533 -41 * ** * ** *** * Masking position 14 Map Score: 14.0927 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 212 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 GTTTCTTATATTTTGACAGGAAGAGTATC 3 86 1 TTACAGGAGA 0.957894 -19 GTATTTGTATTATTTACAGGATGAATTTATCGGG 5 47 0 TTACAGGAGA 0.957894 -62 TCATTTTCTTTTTTTACAGGGTGCATTTACGCCT 12 18 1 TTACAGGGGC 0.913772 -24 TGTTACTCGCTTTTAACAGGGCAACGGAACACCC 15 51 0 TTACAGGGAA 0.957894 -148 ATCCGCAGGCTATTGACAGAATAATTCAGACTGG 26 150 0 TTACAGAAAA 0.738378 -151 GTCCTTTTTATTGTTACAGAGGGAT 28 2 0 TTACAGAGGA 0.879059 -29 CCCAGATCGATATTTACAGGGAGCCTGCCTTTCC 33 106 1 TTACAGGGGC 0.913772 -98 TGCCCCCAGGTATTTACAGTGTGAGAAAGAATTA 33 153 1 TTACAGTGGA 0.742045 -51 GCGAAATTAATCGTTACAGGAAAAGCCAAAGCTG 34 62 1 TTACAGGAAA 0.934107 -239 TCTACCCTACTGATAACAGGATAAAATCCG 38 237 1 TTACAGGAAA 0.934107 -20 TCTCTCTGATTCAAAACAGGGCAATAATGTTGTT 39 515 0 TAACAGGGAA 0.810213 -32 CAATGACAATTTGAGACAGAGTGAAAGGTCAGAT 61 198 0 TAACAGAGGA 0.576979 -103 ACCTTCTCGTTACTGACAGGAAAATGGGCCATTG 63 209 0 TTACAGGAAA 0.934107 -79 TACGGTTTTCTGTTTACAGGATAAGAGCGCACGG 66 17 1 TTACAGGAAA 0.934107 -284 * * ****** ** Masking position 8 Map Score: 9.01694 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 32 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 11 CAGTGGGAAATTGTGGGGCAAAGTGGGAATAAGGG 1 265 1 TTTGGGGCAG 0.920533 -36 CGTATTTTTATTTTGCTGCAAATTGTACTGCCGAT 4 235 0 TTTGCTGCAG 0.863409 -66 CAGGATGAATTTATCGGGCATAATGGTTAAATTCG 5 30 0 TTTCGGGCAG 0.843081 -79 TAGTACGACTTTTTGCGGCTCCAGGTTACTTCCCG 15 119 1 TTTGCGGCCG 0.891032 -80 ACATGACTTTTTTTGTGGCTGAAAGGAGTATACGG 20 187 0 TTTGTGGCAG 0.809358 -112 TGGCAAAAAATTGTGCAGCACATCAAACTTTTGCT 31 125 1 TTTGCAGCAA 0.631592 -176 TCATTAAACATTATGCCGCTAAAGGAAGAATTGAA 34 115 0 TTTGCCGCAG 0.976111 -186 ACCTGAATATTTTTCCCGCCGATTGTGCAAGGACA 38 61 0 TTTCCCGCAG 0.949878 -196 TATTAATTGTTTGTGCCGAAAACGGTCATTCCGGG 39 280 1 TTTGCCGAAG 0.68352 -267 TGCTTATCCGGCTAACCACTCTTGCTTG 41 61 0 TTTCCGGCAA 0.821416 -18 TGGCGGTCTGTTGTGCGGCACAACGGGCCATTTGT 48 35 1 TTTGCGGCAG 0.984725 -83 TTTTTCAGGTTTTGCCCGCTTAGTGCGGTAACAAT 58 32 0 TTGCCCGCAG 0.706171 -102 TTTTTTGGAGTTTTGCCGCAAAGCGGTAGAGGGCA 58 105 1 TTTGCCGCAG 0.976111 -29 CGCGAGCGCCTTATCCGGCCTACGGGTCGTGCATC 62 30 1 TTTCCGGCAG 0.967643 -56 TTATCGCAAGTTATGAGGCGGATCGCATTTTTGTA 66 156 1 TTTGAGGCAG 0.809396 -145 GCGCAATATATTCTGCAGCCAACCAAAAATGTCAT 70 79 1 TTTGCAGCAA 0.631593 -40 ** ****** * * Masking position 2 Map Score: 11.1496 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 331 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 GAAAAGCACCTGTCGGGTGCTTTTTTCATT 6 36 1 TGTCGGGTGC 0.86859 -94 GTTATGCTCTGGGCGGGTGTTCCGTTGCCC 15 37 1 GGGCGGGTGT 0.94029 -162 CACCTCAACGTGCCAGATGTATTTTTGAAT 21 256 0 TGCCAGATGT 0.686628 -45 CCTTGTTAAATGGCAGGTGCG 29 2 0 TGGCAGGTGC 0.935553 -27 CGTGTTTTTATGCCGGATGCGGTGTAAACA 30 27 0 TGCCGGATGC 0.813659 -171 AGTCCATTGCTGGCGGGTGTTGACCGCTGA 34 161 0 TGGCGGGTGT 0.935553 -140 GCTGAAACAAGGGCAGGTTTCCCTGCCCTG 42 18 0 GGGCAGGTTT 0.859203 -197 CTGTTTGAGTGGGCAGGTTCTTAGGTGAAA 48 96 1 GGGCAGGTTC 0.895993 -22 ACCGATTCAGTGCCAGATTTCGCAGTATCT 50 193 1 TGCCAGATTT 0.545172 -108 TAGTCCTTCATGGCGGATGTTGGTTTTGCA 53 129 0 TGGCGGATGT 0.888159 -160 CAGAGTGAAAGGTCAGATTTGCGGAGTAAT 61 186 0 GGTCAGATTT 0.518478 -115 AATTCGGTGTTGTCGGATGCACGACCCGTA 62 50 0 TGTCGGATGC 0.783356 -36 GTAATCACGAGGTCAGGTTCTTACCTTAAA 63 45 1 GGTCAGGTTC 0.735351 -243 GTCCAGCTTTTGGCAGATTTGTCACATGGC 66 60 0 TGGCAGATTT 0.754744 -241 CCGCTCGCAAGGGCGGGTTCGCTTTCCCAC 67 20 1 GGGCGGGTTC 0.924019 -31 ********** Masking position 8 Map Score: 8.59193 Number of sites scoring better than the average of aligned sites = 789 Number in coding regions = 718 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 13 TTTATTTTACGTCCAACGTGCGAAGCAAATTAA 1 138 0 GCAACGGCGA 0.752554 -163 GTTCACCGCCGAAAATTGGGCGGTGAATAACCA 10 55 1 GAATTGGCGG 0.905443 -240 TCTGGATTCAGTAAATTGCGCGAGAAGATAAAA 16 128 0 GAATTGGCGA 0.87391 -47 TGCCGGTACGGGTAATCGTGCCGGTAAGAAAAG 18 15 1 GAATCGGCCG 0.945289 -36 AACGGAAACCGGCCATTGCGCCGGTTTTTTTTG 20 37 1 GCATTGGCCG 0.939106 -262 GAGTTAACCGGACAAGTGTGCCATAATCTCGCG 32 52 0 GAAGTGGCCA 0.801494 -47 CTCCTAAGCAGTAAATTGGGCCGCATCTCGTGG 36 12 0 GAATTGGCCG 0.95455 -29 CTGTTGTGCGGCACAACGGGCCATTTGTACGGT 48 42 1 GCAACGGCCA 0.86963 -76 ATGTAGATTTGAAAATGGGGCCGAGTTTCAATG 55 16 0 GAATGGGCCG 0.830712 -285 TTGCCCAATGTGCCAGAGATGCCTC 61 3 1 GCAATGGCCA 0.890212 -298 GTTACTGACAGGAAAATGGGCCATTGGCAACCA 63 202 0 GAAATGGCCA 0.91696 -86 CGACATATGCGTAAAATGAGCGGCAGATTAAAA 69 25 0 GAAATGGCGG 0.874305 -151 TTGCGCTCAGGTGAATCGCGCCAGCAAATTACG 69 88 0 GAATCGGCCA 0.925957 -88 * ***** **** Masking position 5 Map Score: 9.02367 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 322 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 CGTTCTCACGCGTGGCAAGGGGGGAGAGCCTCGCCGTG 10 231 0 CGGGCGGAAG 0.789633 -64 CATAACCAAACCAGGCAGTAAGTGAGAGAACA 15 5 0 CCGGCAGAAG 0.986799 -194 AAAGCGCCAACCTGGCTTAGGGTTAAAGACAAGATCGC 31 225 0 CCGGCGGAAG 0.969827 -76 CGCAAGTATGCCTGGCCGCGAGATTATGGCACACTTGT 32 36 1 CCGGCAGTTG 0.946107 -63 TAAAGTCTAGCCTGGCGGTTCGACTTTAGCCTGTATTG 34 236 0 CCGGCCGTTA 0.683199 -65 AACGGTCATTCCGGGCTTGGAGGAATAGAAAAATGACC 39 300 1 CCGGCAGAAG 0.986799 -247 TTGTCCGGGCAATTAGCATGTGCATGGCGGTC 48 5 1 CCGGCAGTTG 0.946107 -113 AAACAGTGGAACAGGCTCGGAGCATTAACCGTACAAAT 48 64 0 ACGGCAGTAA 0.646126 -54 TACCCGGGCTTGCAGGCAAAAAAGAGATCTA 57 14 0 CCGGCAGAAA 0.975188 -21 CAACAACTTCCCTGGCAAAAAGTCAAAAAATGGTCATT 68 88 0 CCGGCAGAAA 0.975188 -204 AGCGCTTATCCCCGGCAAAGAGCAATAACCCTTCTGCG 71 26 1 CCGGCAGAAA 0.975188 -105 ** *** ** * ** Masking position 6 Map Score: 5.87255 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 181 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 15 GATCCGTAATTTAACTTTCGATTAGCAGAAATT 21 122 0 TACTTTCGTT 0.967786 -179 TAAAATCGATTCAGCTTTGGCTTTTCCTGTAAC 34 74 0 TACTTTGGTT 0.813612 -227 ATTAAAATATTTATCTTTCATTTTGCGATCAAA 37 153 1 TACTTTCATT 0.746527 -103 GAAACGGGCATGAAATTTCGATTATTAAAGTGA 39 210 0 TAATTTCGTT 0.855403 -337 GTCCTTTCGTAAAACTTTCGTTTCATTTCGTTT 45 16 1 AACTTTCGTT 0.82566 -233 CAGAAAACCATTATCTTTCGTTTTATTTTTATC 45 155 1 TACTTTCGTT 0.967786 -94 ACTGCGATATTAATCTTTCGTTTTGTTTCAGTT 45 206 0 TACTTTCGTT 0.967786 -43 TTACAGATTTTTATCTTTCGATTACGATTTTTG 49 42 1 TACTTTCGTT 0.967786 -259 GCACAATATTTTAAATTTCGATTTGAAAAATTA 61 38 1 TAATTTCGTT 0.855403 -263 * * ****** ** Masking position 7 Map Score: 4.67466 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 15 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493