AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_ecoli_reg_100.orf -o00052_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 yadI 104 putative PTS enzyme II B component #2 lacZ 122 beta-D-galactosidase #3 malZ 155 maltodextrin glucosidase #4 nagE 300 PTS system, N-acetylglucosamine-specific enzyme IIABC #5 seqA 184 negative modulator of initiation of replication #6 pgm 25 phosphoglucomutase #7 hrsA 108 protein modification enzyme, induction of ompC #8 galE 260 UDP-galactose-4-epimerase #9 ptsG 294 PTS system, glucose-specific IIBC component #10 galU 201 glucose-1-phosphate uridylyltransferase #11 rspA 205 starvation sensing protein #12 malX 174 PTS system, maltose and glucose-specific II ABC #13 pfkB 286 6-phosphofructokinase II; suppressor of pfkA #14 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #15 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #16 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #17 manX 300 PTS enzyme IIAB, mannose-specific #18 galF 174 homolog of Salmonella UTP--glucose-1-P uridyltransferase, probably a UDP-gal transferase #19 gatD 47 galactitol-1-phosphate dehydrogenase #20 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #21 gatZ 28 putative tagatose 6-phosphate kinase 1 #22 gatY 197 tagatose-bisphosphate aldolase 1 #23 fruB 300 PTS system, fructose-specific IIA/fpr component #24 pdxB 98 erythronate-4-phosphate dehyrogenase #25 glk 203 glucokinase #26 ptsH 300 PTS system protein HPr #27 ptsI 44 PEP-protein phosphotransferase system enzyme I #28 crr 40 PTS system, glucose-specific IIA component #29 srlA 255 PTS system, glucitol/sorbitol-specific IIC component, one of two #30 ascF 256 PTS system enzyme II ABC (asc), cryptic, transports specific beta-glucosides #31 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #32 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #33 ebgA 147 evolved beta-D-galactosidase, alpha subunit; cryptic gene #34 agaZ 248 putative tagatose 6-phosphate kinase 2 #35 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #36 ptsN 117 phosphotransferase system enzyme IIA, regulates N metabolism #37 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #38 glvB 24 PTS system, arbutin-like IIB component #39 glvC 34 PTS system, arbutin-like IIC component #40 yidW 300 regulator protein for dgo operon #41 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #42 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #43 frvA 300 PTS system, fructose-specific IIA component #44 pfkA 180 6-phosphofructokinase I #45 frwC 300 PTS system, fructose-like enzyme II component #46 pflD 50 formate acetyltransferase 2 #47 melA 282 alpha-galactosidase #48 sgaT 291 orf, hypothetical protein #49 treB 118 PTS system enzyme II, trehalose specific #50 sgcA 130 putative PTS system enzyme II A component Motif number 1 CAACGCAATTAATGTGAGTTAGCTCACTCATTAGGCA 2 14 1 ATGTGATCAC 0.868856 -109 AGCTGTTTCCTGTGTGAAATTGTTATCCGCTCACAAT 2 96 0 TTGTGATATC 0.746519 -27 TCCTTGCGTTCTGTAAGCCGGTTCAGGAGGAAATCC 3 10 1 TTGTAATCAG 0.601485 -146 ACGCGTGTCTTTTGTGAGTTTTGTCACCAAATATCGT 4 129 0 TTGTGATCAC 0.983122 -172 TATGTGATCAATTTCACTTGATTGAAA 7 92 0 TTGTGATCAC 0.983122 -17 AGTGCCAATTTGTTTGACGGCTATCACGTTTCAACTT 9 145 0 TTTTGATCAC 0.688195 -150 ACTCCCTGATTATGTGACAGATAAAACGTTTTACCTT 12 22 1 TTGTGAAAAC 0.661489 -153 TATTGTCGTTTTTGTGATCGTTATCTCGATATTTAAA 22 124 1 TTGTGATCTC 0.908966 -74 TGAGTTGAGTTATGTAAAGTCCGTATCGGGCAGTGAC 29 83 0 TTGTAATATC 0.412976 -173 TATCTTTCATTTTGCGATCAAAATAACACTTTTAAAT 29 164 1 TTGCGATAAC 0.893671 -92 ATTTTTTATATTTGTGAAACCGGTCACCTGAATATTT 30 84 0 TTGTGATCAC 0.983122 -173 CATATAAATATTTGTGATCTACAACACGCCTTATCTA 32 71 0 TTGTGAACAC 0.868856 -230 AAATATCAATTATGTAATATGCATCACGATATGCGGT 32 112 1 TTGTAATCAC 0.932952 -189 TTATGTTTCTTTTGTGAATCAGATCAGAAAACCATTA 34 131 1 TTGTGATCAG 0.863358 -118 ATGGCATTTAAATGTGAGTAGTGTCACATTTTTGTTT 37 26 0 ATGTGATCAC 0.868856 -275 ACACAAGCGTTTTGTGATGAACGTCACGTCAATTACC 37 96 1 TTGTGATCAC 0.983122 -205 CCCCTATATTTATGTGATTGATATCACACAAAAGGCC 37 140 1 TTGTGATCAC 0.983122 -161 AACCATTTGATATGCAAATTGCATAACATGCCAGCAA 42 111 0 TTGCAATAAC 0.667521 -129 ATCCAACGAATGTGCAAATAGTATAACAATCACTTCC 44 87 0 TTGCAATAAC 0.667521 -94 TAACCGTCAATTTGCGACGCGTCTCACAAGACGCTGT 45 100 1 TTGCGATCAC 0.966096 -201 TTTAATGGAATGTGTAATTCAATTAACTAAATGAATT 48 147 1 TTGTAATAAC 0.804081 -145 TGTGGAATTATTTGCGGGTCGCGTCACATTTAATCAT 48 226 1 TTGCGGTCAC 0.721933 -66 * ***** **** Masking position 3 Map Score: 25.6412 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 114 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 CCGTCAAAACTCCTCTCCCCCAAATCCAGAGGAGAGGAAATAGC 1 12 0 TCTCCAGAAG 0.45747 -93 GGTTTATTCCGAGTTTTTCTGCAAGCCAGGCTTGACGCTATCCG 5 86 1 GCGCCAGGTG 0.980977 -99 CAGTGTCTTAGCTGAATACAAGTCGCCAGGAGTATATGAATAAA 5 139 0 GCGCCAGGTA 0.949891 -46 GAGAGGGTGCTAAGGCCGCCTCCGGCAAGGTCAGCACTACCGAC 8 11 0 TCGCAAGGAG 0.898158 -250 ATGCCTGCATGCGTCGAACCGTTGGCCGGAGAGGGTGCTAAGGC 8 39 0 GCGCCGGAGG 0.8329 -222 TACACGGCGAGGCTCTCCCCCCTTGCCACGCGTGAGAACGTAAA 9 229 1 GCGCCACGTG 0.923438 -66 TTAAGACAATTACTTATACGAATGGCGACGATAGTACCACCAGC 10 55 0 TCGCGACGAG 0.690857 -147 TGTGAAGAGGGTCATAACCACAGGTCAAGGAGAAACAATTTATA 16 111 1 GCTCAAGGAA 0.452675 -188 GGTCTATACCGTATACTCCTTTCAGCCACAAAAAAAGTCATGTT 16 179 1 GCGCCACAAA 0.462313 -120 TTATTATCGTTAACACCTCAACGTGCCAGATGTATTTTTGAATC 17 255 0 TCGCCAGATA 0.615142 -46 TGTTCCTAAGTATGACTCCATTTTTCCAGGAATGGTCGCAAAT 18 10 0 TCTCCAGGTG 0.813018 -165 AGCATAATACTTCTGTTTCAGCACGCAAGGAAAGCCGTAAAGTT 23 163 0 TCGCAAGGAG 0.898158 -138 GCGCGATCTTGTCTTTAACCCTAAGCCAGGTTGGCGCTTTTTTT 23 223 1 GCGCCAGGGG 0.982438 -78 GGACAAGTGTGCCATAATCTCGCGGCCAGGCATACTTGCGAAGA 24 32 0 GCGCCAGGTA 0.949891 -67 GTTCTATTCCTTATGCGGGGTCAGATACTTAGTT 25 1 1 GCGCGGGGAG 0.909884 -203 AACAATACAGGCTAAAGTCGAACCGCCAGGCTAGACTTTAGTTC 26 234 1 GCGCCAGGAG 0.985546 -67 GGGCAGTGACTACCGCTTCCTTGTGCGGGGCGTGATGCTTTACC 29 49 0 TCGCGGGGTG 0.814471 -207 AACGAGAGTAGCTTGCGTCAATGGGCAAGGTGGGCTTGCATTTG 34 74 0 GCGCAAGGGG 0.926393 -175 CAGACCGCCATGCACATGCTAATTGCCCGGACAA 36 1 0 TCGCCCGGAA 0.591647 -117 CAAAGTTGCCGCGTTATGCATCGATCGGGGTAAAGTAGAGAAGA 40 243 1 GCTCGGGGAA 0.352484 -58 AGATTACAGATATAAAAGCAAAACGCCACGTAAACACGTGGCGT 42 29 0 TCGCCACGAA 0.771181 -211 TGCTTTTATATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGG 42 53 1 TCGCCGCGGG 0.820456 -187 GTTCTTCTCCCGCTCGCAAGGGCGGGTTCGCTTTC 46 2 1 TCGCAAGGGG 0.878573 -49 AACTCAGATTTACTGCTGCTTCACGCAGGATCTGAGTTTATGGG 47 169 1 TCGCAGGATG 0.372763 -114 CGAATCTGCAGAAAACCTCCGGCTTCCAGGTTGAGCATTCCCAT 47 208 0 GCTCCAGGGA 0.750998 -75 GCAATGACCATTTTTTGACTTTTTGCCAGGGAAGTTGTTGTTGA 48 86 1 TCGCCAGGAG 0.975124 -206 ATCGCAGAAGGGTTATTGCTCTTTGCCGGGGATAAGCGCTCTGC 50 22 0 GCGCCGGGTA 0.920104 -109 * * ****** ** Masking position 9 Map Score: 22.8221 Number of sites scoring better than the average of aligned sites = 2273 Number in coding regions = 2123 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 3 CAGGATTTCCTCCTGAACCGGCTTACAGAACG 3 17 0 TCCTGCCGGC 0.912778 -139 CAGGAGGAAATCCTGATCCGGCTATTCCGAAA 3 34 1 TCCTGCCGGC 0.912778 -122 TTTAAGCGTAACCTGGATTTGCGCAGACAGGC 4 26 1 ACCTGTTTGC 0.407827 -275 CCCTACGAGAACCCTATTTGGCTCGTTTCAAG 4 271 0 ACCCTTTGGC 0.520951 -30 GATAGCGTCAAGCCTGGCTTGCAGAAAAACTC 5 96 0 AGCCTCTTGC 0.78055 -89 GTCGGTAGTGCTGACCTTGCCGGAGGCGGC 8 9 1 TGCTGCTTGC 0.784132 -252 CGGCCTTAGCACCCTCTCCGGCCAACGGTTCG 8 37 1 ACCCTCCGGC 0.911138 -224 CGGCACGATTACCCGTACCGGCATCGA 14 6 0 ACCCGCCGGC 0.977442 -45 GTATGTTTACACCGCATCCGGCATAAAAACAC 22 24 1 ACCGCCCGGC 0.744998 -174 ATACTTAGTTTGCCCAGCTTGCAAAAAGGCAT 25 35 1 TGCCCCTTGC 0.835918 -169 ACAGGGAGCCTGCCTTTCCGGCGTTGTTGTTA 25 121 1 TGCCTCCGGC 0.871411 -83 AGCAAATGCAAGCCCACCTTGCCCATTGACGC 34 72 1 AGCCCCTTGC 0.849436 -177 TACCCGGGCTTGCAGGCAAAAAA 39 22 0 ACCCGCTTGC 0.953674 -13 GTAATCTTAATGCCGCGCTGGCGATGTTAGGA 42 66 1 TGCCGCTGGC 0.960469 -174 ATACACAAAATGCGGGTCTGGCTCTCTTTTAT 44 16 0 TGCGGCTGGC 0.813607 -165 ATCCACTGTTTGCTCCGCCTGCGATTGCCTAT 45 225 1 TGCTCCCTGC 0.616416 -76 AAGCTGCTCCCGGGCTTGCGAAAGCCCAT 45 282 0 TCCCGCTTGC 0.948952 -19 GGGAAAGCGAACCCGCCCTTGCGAGCGGGAGA 46 16 0 ACCCGCTTGC 0.953674 -35 TACCAGATTAACCCGAATCGGCATGGAGTCAA 50 103 1 ACCCGTCGGC 0.844783 -28 ***** ***** Masking position 3 Map Score: 19.1703 Number of sites scoring better than the average of aligned sites = 1653 Number in coding regions = 1558 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 TGAACTTTACTCGTTTTAGCCATTAATTAC 9 30 0 TCGTTTTAGC 0.732351 -265 CAGTCTGGCACCGAATCAGCGGAAAGTGAA 13 244 0 CCGAATCAGC 0.705095 -43 TACCGTATACTCCTTTCAGCCACAAAAAAA 16 185 1 TCCTTTCAGC 0.832715 -114 CACAATCGAATCGATTCAGATAAGGGCTAC 17 219 0 TCGATTCAGA 0.749864 -82 ATCAGCAATTTCATTTCAGCAGCGTCAGCA 23 64 0 TCATTTCAGC 0.894583 -237 CATAATACTTCTGTTTCAGCACGCAAGGAA 23 175 0 CTGTTTCAGC 0.826629 -126 CTTTCTTGAAACGTTTCAGCGCGATCTTGT 23 205 1 ACGTTTCAGC 0.918494 -96 CTGAATTGAAACGATTCAGCCTCTATGAGA 23 266 0 ACGATTCAGC 0.909573 -35 CTGAATCGTTTCAATTCAGCAAGAGAGGAG 23 277 1 TCAATTCAGC 0.883377 -24 AATTACTTTATCGTTTCAGCACCAATTGCA 25 70 0 TCGTTTCAGC 0.982198 -134 TTGATTCAGCCTGTCGGAAC 26 1 1 TTGATTCAGC 0.875635 -300 AATCATAAAATCGATTCAGCTTTGGCTTTT 26 82 0 TCGATTCAGC 0.980099 -219 TTTCTTAATTCCGTTTCAGCATCGGCATTT 30 178 1 CCGTTTCAGC 0.970888 -79 CAAGCTACTCTCGTTTCAGTGACTTTCATT 34 103 1 TCGTTTCAGT 0.894583 -146 ATCTTTCGTTTTGTTTCAGTTGATACTGCG 34 197 0 TTGTTTCAGT 0.548175 -52 GGACAGTTAACCGATTCAGTGCCAGATTTC 37 184 1 CCGATTCAGT 0.82074 -117 CTGACCTGAATCAATTCAGCAGGAAGTGAT 44 66 1 TCAATTCAGC 0.883377 -115 ********** Masking position 6 Map Score: 18.7392 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 230 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 5 GCAAATTAAACGCGTGTCTTTTGTGAGTTTTG 4 143 0 CGCGTCTTTT 0.838245 -158 GGCATGAAACCGCGTCTTTTTTCAGATAAAAA 8 78 1 CGCGTTTTTT 0.976113 -183 GGCATCTAAGCGCCCTTTATTTATTACACAGA 9 194 0 CGCCTTATTT 0.888275 -101 CCTGAGTATGGGTGCTTTTTTTACGTTCTCAC 9 260 0 GGTGTTTTTT 0.71237 -35 CGCAAATATACGCCTTTTTTTGTGATCACTCC 11 98 1 CGCCTTTTTG 0.834505 -108 GGACCGCGATGGTCTCTTTTTTTGTTGTACGG 13 22 0 GGTCTTTTTT 0.659597 -265 CTAAGTTATTCGCGCCTTTTTATAATTCGTTA 13 97 0 CGCGTTTTTA 0.916581 -190 CCGGCCATTGCGCCGGTTTTTTTTGGCCTGAG 16 45 1 CGCCTTTTTT 0.96967 -254 TAATTATCTTCGCGAATTATTTGCCCGAAATG 16 81 1 CGCGTTATTT 0.910411 -218 CCCTGCGTTTCGCGATTTATTTTAGATATCGA 17 177 0 CGCGTTATTT 0.910411 -124 TAGCAAAGTGCGCGTGTTTTTATGCCGGATGC 22 37 0 CGCGTTTTTA 0.916581 -161 CCTATCGGGAGGCCGTTTTTTTGCCTTTCACT 22 76 1 GGCCTTTTTT 0.95103 -122 AAGCCAGGTTGGCGCTTTTTTTCTCATAGAGG 23 245 1 GGCGTTTTTT 0.961274 -56 GTATTGTTAGCGCCAGTTTTTAACAGACGCGA 26 210 0 CGCCTTTTTA 0.895794 -91 AAGGTGCTTCGGCGACCTTTTTTATTACCTTG 32 15 1 GGCGCTTTTT 0.758918 -286 ATTCACGTCAGGCCGTTTTTTTCAGGTTTTTT 41 76 1 GGCCTTTTTT 0.95103 -58 **** ****** Masking position 10 Map Score: 14.8518 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 215 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 CGCCTTCCTCCTTAGCCGAAAATCAGTCTACC 1 83 0 GCCCTGCGAA 0.877486 -22 ACAGAACATCGGCAGTACAATTTGCAGCAAAATAAAAATAC 4 228 1 GGCATGCGAA 0.980578 -73 GGTTATTCACCGCCCAATTTTCGGCGGTGAACTTTACTCGT 9 46 0 CGCTTGCGAA 0.957933 -249 ATAAATAAAGGGCGCTTAGATGCCCTGTACACGGCGAGGCT 9 202 1 GGCATCCGCA 0.817612 -93 CACAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGACAA 11 81 0 GGCTTGCGAA 0.992172 -125 TAGGAAAAATGGCAAAAAATTGTGCAGCACATCAAACTTTT 23 116 1 GGCTTGCGCA 0.991401 -185 CACACTGTCCGGCAATCGTTTTTGCCGGACAGTGCTGCCGT 33 20 1 GGCTTGCGCA 0.991401 -128 GCATGTGCATGGCGGTCTGTTGTGCGGCACAACGGGCCATT 36 26 1 GGCTTGCGCA 0.991401 -92 AAAGCAACAAGGCGGCGATTTTCGCTAAAAATGGCATTTAA 37 52 0 GGCTTGCAAA 0.893032 -249 TCACACAAAAGGCCGTCGACTGGACAGTTAACCGATTCAGT 37 163 1 GGCCTACGAA 0.839458 -138 CGGGATCCAGTTTTGCGGTAAAAC 38 3 0 GGGTTGCGAA 0.919585 -22 AGTATCATGAGGCCGAAAACTCTGCTTTTCAGGTAATTTAT 47 121 1 GGCCTGCTCA 0.826267 -162 ACTTCATCATGGCAGGCGAATCTGCAGAAAACCTCCGGCTT 47 227 0 GGCATGCGAA 0.980578 -56 AATTTTTCCGCGCAATATATTCTGCAGCCAACCAAAAATGT 49 70 1 CGCTTGCGAA 0.957933 -49 *** ** ** * ** Masking position 21 Map Score: 12.5635 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 188 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 TTGATAAAGGGTGATAGCCGTCAAAACTCCTCTC 1 39 0 GTGATATCAA 0.657938 -66 TGCCTAATGAGTGAGCTAACTCACATTAATTGCG 2 17 0 GTGAGCTCAC 0.776953 -106 ACGATATTTGGTGACAAAACTCACAAAAGACACG 4 129 1 GTGACATCAC 0.797722 -172 TATGTGATCAATTTCACTTGATTGAAA 7 92 0 GTGATCTCAC 0.727225 -17 AAGTTGAAACGTGATAGCCGTCAAACAAATTGGC 9 145 1 GTGATATCAA 0.657938 -150 ACCTGTGGTTATGACCCTCTTCACATTTCGGGCA 16 102 0 ATGACCTCAC 0.712802 -197 TGTCGTTTTTGTGATCGTTATCTCGATATTTAAA 22 127 1 GTGATCTCTC 0.653188 -71 AAGTAATTGTGTGACCCAGATCGATATTTACAGG 25 92 1 GTGACCTCGA 0.842887 -112 AAATATTCAGGTGACCGGTTTCACAAATATAAAA 30 84 1 GTGACCTCAC 0.732823 -173 ATAAATATTTGTGATCTACAACACGCCTTATCTA 32 71 0 GTGATCACAC 0.642764 -230 TAATGGTTTTCTGATCTGATTCACAAAAGAAACA 34 134 0 CTGATCTCAC 0.82642 -115 AAACAAAAATGTGACACTACTCACATTTAAATGC 37 26 1 GTGACATCAC 0.797722 -275 GGTAATTGACGTGACGTTCATCACAAAACGCTTG 37 99 0 GTGACGTCAC 0.504002 -202 GGCCTTTTGTGTGATATCAATCACATAAATATAG 37 143 0 GTGATATCAC 0.677422 -158 AACCGATTCAGTGCCAGATTTCGCAGTATCTACA 37 192 1 GTGCCATCGC 0.744897 -109 TAGTACCAGCGTGATGACGTTCGCGTTTGCCGTG 40 209 0 GTGATGTCGC 0.813199 -92 GCCATTTGGCCTGACCTGAATCAATTCAGCAGGA 44 56 1 CTGACCTCAA 0.543381 -125 ACAGCGTCTTGTGAGACGCGTCGCAAATTGACGG 45 103 0 GTGAGATCGC 0.69203 -198 GGTGAAAACCGTGCTCCCACTCGCAGTCATCCTC 47 57 0 GTGCTCTCGC 0.822311 -226 ****** **** Masking position 2 Map Score: 14.3625 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 290 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 8 TTTTATTTTGCTGCAAATTGTACTGCCGATGTTCT 4 230 0 CGAATTGACG 0.827926 -71 GGGTATTATGTTGACCATTGTGCCACAGGGCTGCA 5 43 1 TGCATTGGCA 0.902162 -142 AAGTTCACCGCCGAAAATTGGGCGGTGAATAACCA 9 53 1 CGAATTGGCG 0.987394 -242 AATCTGGATTCAGTAAATTGCGCGAGAAGATAAAA 12 128 0 CGAATTGGCA 0.97402 -47 ACAACGGAAACCGGCCATTGCGCCGGTTTTTTTTG 16 35 1 CGCATTGGCG 0.98808 -264 GGAAAAATGGCAAAAAATTGTGCAGCACATCAAAC 23 118 1 CAAATTGGCG 0.920111 -183 GAGAGTTAACCGGACAAGTGTGCCATAATCTCGCG 24 52 0 CGCAGTGGCA 0.881714 -47 TTCTCCTAAGCAGTAAATTGGGCCGCATCTCGTGG 28 12 0 CGAATTGGCG 0.98519 -29 AATATTTTTCCCGCCGATTGTGCAAGGACAATCGG 30 56 0 CGCATTGGCA 0.969989 -201 ATGTGCATGGCGGTCTGTTGTGCGGCACAACGGGC 36 28 1 CGCGTTGGCG 0.942752 -90 GAGGCATCTCTGGCACATTGGGCAA 43 1 0 TGAATTGGCA 0.741631 -300 AATCGAAATTTAAAATATTGTGCCGGAGGCATCTC 43 26 0 TAAATTGGCG 0.717733 -275 * * * **** ** * Masking position 9 Map Score: 10.3593 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 334 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 AACCGGCTTACAGAACGCAAGGA 3 4 0 CAGAACGCAA 0.733321 -152 TTTTCAGATAAAAAGCGCAATCATTCATAA 8 96 1 AAAAGCGCAA 0.926641 -165 TTCATAAATCAATACCGCAATATTTAAATT 15 42 1 AATACCGCAA 0.642396 -43 AATACCCTTAAAAACCGCAATTTAAATATT 15 60 0 AAAACCGCAA 0.865994 -25 AAATCAAAAGCGCCACGAATAGTCA 23 6 1 AAAAGCGCCA 0.953078 -295 CTATGAGAAAAAAAGCGCCAACCTGGCTTA 23 244 0 AAAAGCGCCA 0.953078 -57 GCGACGCACGAAGAGCGCAATACAGTCCAT 26 184 0 AAGAGCGCAA 0.938844 -117 TGCCGCACAACAGACCGCCATGCACATGCT 36 25 0 CAGACCGCCA 0.875212 -93 ACGCTTGTGTAAAAAAGCAACAAGGCGGCG 37 76 0 AAAAAAGCAA 0.468903 -225 GTCTTATGCCAAAAACGCCACGTGTTTACG 42 15 1 AAAAACGCCA 0.867575 -225 GATATAAAAGCAAAACGCCACGTAAACACG 42 35 0 CAAAACGCCA 0.784404 -205 TCAGTATAAAAGAGAGCCAGACCCGCATT 44 10 1 AAGAGAGCCA 0.842507 -171 TTGTGTATAAAATACCGCCATTTGGCCTGA 44 40 1 AATACCGCCA 0.74284 -141 TTTACAGGATAAGAGCGCACGGCAACGGCC 45 29 1 AAGAGCGCAC 0.660657 -272 TATTCCAGGAAAGAGAGCCATCC 47 4 0 AAGAGAGCCA 0.842507 -279 TTATCCCCGGCAAAGAGCAATAACCCTTCT 50 31 1 CAAAGAGCAA 0.603199 -100 ********** Masking position 4 Map Score: 11.4852 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 695 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 10 GAATGGTTGACAAAAGATGAAATAGAATACCTTT 11 60 0 CAAATAAATA 0.947284 -146 CATGCTTATTCAAAAAATGAAATAAGAATACATT 13 130 0 CAAATAAATA 0.947284 -157 TATTTATCTGCAAAATTTTAAATAAAGCTCCAAT 13 191 1 CAAATAAATA 0.947284 -96 TCTTTGACGGGAAAATTTAAAATAAA 15 3 0 GAAATAAATA 0.812943 -82 GCAGAAATTTCGAAAGGTAAAATATCCTTGTCAC 17 97 0 CAAATAAATA 0.947284 -204 TTCTGCTAATCGAAAGTTAAATTACGGATCTTCA 17 125 1 CAAATAATTA 0.743641 -176 ATAATTTTTTCGATATCTAAAATAAATCGCGAAA 17 168 1 CATATAAATA 0.605924 -133 AACTGCTCCGCTAAAGTCAAAATAATTCTTTCTC 25 175 0 CAAACAAATA 0.81775 -29 CCGTCCGGCGGTAAAAATAAAATACTCGTGCGGT 32 249 0 GAAATAAATA 0.812943 -52 GGACGGTACCCTAAAAATAAAATAAGGATAATTT 32 277 1 CAAATAAATA 0.947284 -24 AAGGAGATAACTAAACCTTAATAAATACATCACT 35 77 1 CAAATAATAA 0.576612 -90 ACTAAGCGGGCAAAACCTGAAAAAAATTGCTTGA 41 43 1 CAAATAAAAA 0.894031 -91 CGCTTTGCGGCAAAACTCCAAAAAAAAACCTGAA 41 96 0 CAAACAAAAA 0.678107 -38 TTTTTCAAATCGAAATTTAAAATATTGTGCCGGA 43 34 0 CAAATAAATA 0.947284 -267 ACTTCCCTGGCAAAAAGTCAAAAAATGGTCATTG 48 87 0 CAAATAAAAA 0.894031 -205 ATATTGCGCGGAAAAATTTAAAAACGGGAACGTT 49 54 0 GAAATAAAAA 0.671098 -65 * *** * ***** Masking position 5 Map Score: 15.1506 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 26 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 CGCACCTGCCATTTAACAAGGA 21 3 1 CACCTGCCAT 0.970584 -26 GCACGGCAACGGCCTGCCATGTGACAAATC 45 45 1 GGCCTGCCAT 0.934607 -256 CTGTTTGCTCCGCCTGCGATTGCCTATTGT 45 230 1 CGCCTGCGAT 0.969107 -71 TCCTCCCTCACTCCTGCCATAATTCTGATA 47 32 0 CTCCTGCCAT 0.970584 -251 TCTGCAGATTCGCCTGCCATGATGAAGTTA 47 240 1 CGCCTGCCAT 0.986727 -43 CCAAAAATGTCATCTGCCATGGGGCTTT 49 101 1 CATCTGCCAT 0.90001 -18 AGCAATAACCCTTCTGCGATCCCTGCCGCC 50 46 1 CTTCTGCGAT 0.791584 -85 ********** Masking position 9 Map Score: 4.78515 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 64 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 GCTTTTTATCTGAAAAAAGACGCGGTTTCATG 8 80 0 TGAAAAAGCG 0.731389 -181 GGAGTGATCACAAAAAAAGGCGTATATTTGCG 11 98 0 CAAAAAAGCG 0.626748 -108 GTATAAAGATCGAAAAAAGCCGGAGTGATCAC 11 119 0 CGAAAAAGCG 0.953244 -87 CATTACGCAACGATAATAGCGGGTATAAGATA 12 64 0 CGATAAAGGG 0.53299 -111 GAACTCAGGCCAAAAAAAACCGGCGCAATGGC 16 48 0 CAAAAAAACG 0.739422 -251 AAATAAATCGCGAAACGCAGGGGTTTTTGGTT 17 187 1 CGAAACCAGG 0.623975 -114 GAGGTGTTAACGATAATAAAGGAGGTAGCAA 17 280 1 CGATAAAAGG 0.658548 -21 TTGATGCTGGCGAAAAAAATCGAACAAGCTAT 18 120 1 CGAAAAAACG 0.971782 -55 ATTTTGAAATCGAAAACAAACGACAGGAT 22 179 1 CGAAAAAACG 0.971794 -19 AGCCTCTATGAGAAAAAAAGCGCCAACCTGGC 23 247 0 AGAAAAAACG 0.645528 -54 TTTTGATGCGCGAAATTAATCGTTACAGGAAA 26 53 1 CGAAATAACG 0.89544 -248 AACTGGATCACGAAAATAAACGGCAGCACTGT 33 48 0 CGAAAAAACG 0.971793 -100 ATAGGCAAAACGAAATGAAACGAAAGTTTTAC 34 24 0 CGAAATAACG 0.895484 -225 CAGTATCAACTGAAACAAAACGAAAGATTAAT 34 199 1 TGAAACAACG 0.642771 -50 AGGCACTCCCCGATATTAATCGGGAAGTACAT 35 37 0 CGATATAACG 0.633443 -130 CCATTTTTAGCGAAAATCGCCGCCTTGTTGCT 37 59 1 CGAAAACGCG 0.901025 -242 AAAAAAAACCTGAAAAAAACGGCCTGACGTGA 41 78 0 TGAAAAAAGG 0.559325 -56 GGAAGCATGCCGCAAAACAGCGTCTTGTGAGA 45 121 0 CGCAAACACG 0.619963 -180 GGAACGTTCCCGAAACGCAGCGAAGATCACAA 49 30 0 CGAAACCACG 0.857463 -89 ****** ** ** Masking position 5 Map Score: 13.5228 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 449 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 GATAAAGGGTGATAGCCGTCAAAACTCCTCTC 1 39 0 GATAGCGCAA 0.932847 -66 GATTTGCGCAGACAGGCGTCAATCCGACCTGA 4 41 1 GACAGGGCAA 0.808247 -260 GTTGAAACGTGATAGCCGTCAAACAAATTGGC 9 147 1 GATAGCGCAA 0.932847 -148 AAGAGGAAGTGTCAGCTGACAAAAGGTATTCT 11 39 1 GTCAGCGCAA 0.975671 -167 TTTCAGCAGCGTCAGCAGCCAATCAGCAACAG 23 49 0 GTCAGCGCAA 0.975671 -252 CGTACGAAACGTCAGCGGTCAACACCCGCCAG 26 150 1 GTCAGCGCAA 0.975671 -151 TGATATGTCCGTTTGCGGACAAGCAATAGATA 32 45 1 GTTTGCGCAA 0.921197 -256 TACCCGGGCTTGCAGGCAAAAAAGAGATC 39 16 0 GCTTGCGCAA 0.810404 -19 TGTGCAAGAAGACTTCCGGCAACAGATTTCAT 44 132 1 GACTTCGCAA 0.660155 -49 GCGCAATATATTCTGCAGCCAACCAAAAATGT 49 79 1 TTCTGCGCAA 0.705294 -40 ****** * *** Masking position 11 Map Score: 5.48216 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 173 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 TGAGTAACAACGGAAACCGGCCATTGCGCC 16 29 1 CGGAAACCGG 0.813893 -270 CCTCCCGATAGGGAAGCCGTAGCAAAGTGC 22 58 0 GGGAAGCCGT 0.977889 -140 CTTCCCTATCGGGAGGCCGTTTTTTTGCCT 22 72 1 GGGAGGCCGT 0.969221 -126 CAGCACGCAAGGAAAGCCGTAAAGTTATGA 23 159 0 GGAAAGCCGT 0.831615 -142 TTTTATATTTGTGAAACCGGTCACCTGAAT 30 88 0 GTGAAACCGG 0.894653 -169 TCATGATTTTGTGAAACCGGTTTCTTAATT 30 158 1 GTGAAACCGG 0.894653 -99 CAATTGAGCAGGGAAACCGGTGTTTTGAAA 32 209 0 GGGAAACCGG 0.967844 -92 CTTGATTCACGTCAGGCCGTTTTTTTCAGG 41 72 1 GTCAGGCCGT 0.730187 -62 TTTGTCACATGGCAGGCCGTTGCCGTGCGC 45 43 0 GGCAGGCCGT 0.905583 -258 ATGCTCAACCTGGAAGCCGGAGGTTTTCTG 47 214 1 TGGAAGCCGG 0.873645 -69 ********** Masking position 4 Map Score: 5.85068 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 281 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 TTATTCATATACTCCTGGCGACTTGTATTCAGCT 5 140 1 ACTCCGGCTT 0.367694 -45 CGTCGAACCGTTGGCCGGAGAGGGTGCTAAGGCC 8 38 0 TTGGCGGGGG 0.625004 -223 TTAAATTCTCCTGGACTGTTCGTGTTTTGA 10 182 0 TCTCCGGGTT 0.905497 -20 CTTAAGAAAGTTTCCGGGACCGCGATGGTCTCTT 13 36 0 TTTCCGGGCG 0.926759 -251 ATTCGTTACCTTTCCAGGGACGCTAATCTTTGAT 13 71 0 TTTCCGGGCT 0.939155 -216 TGACTCCATTTTTCCAGGAATGGTCGCAAAT 18 8 0 TTTCCGGGGT 0.904645 -167 ACTTTACGGCTTTCCTTGCGTGCTGAAACAGAAG 23 164 1 TTTCCTGGCT 0.380352 -137 GGAGCCTGCCTTTCCGGCGTTGTTGTTATGCCCC 25 125 1 TTTCCGCGTT 0.855358 -79 AATACAGTCCATTGCTGGCGGGTGTTGACCGCTG 26 162 0 ATTGCGGGTG 0.788736 -139 TTTCCCGGGTTCTTTTAAAAATCA 27 1 1 TTTCCGGCTT 0.855358 -44 GGCAAAAACGATTGCCGGACAGTGTGTAAGGGGA 33 12 0 ATTGCGGGTG 0.788736 -136 GGCAATCGTTTTTGCCGGACAGTGCTGCCGTTTA 33 30 1 TTTGCGGGTG 0.937478 -118 AGTTTGTGTAATTGCTGGGGAGTTTAGTAAAATT 33 115 0 ATTGCGGGTT 0.819955 -33 TTTTCAGGTTTTGCCCGCTTAGTGCGGTAACAAT 41 32 0 TTGCCGCGTG 0.579486 -102 TTTTTGGAGTTTTGCCGCAAAGCGGTAGAGGGCA 41 106 1 TTTGCGCGCG 0.699266 -28 ATTCCTGGAATTTGCTGGCATGTTATGCAATTTG 42 100 1 TTTGCGGGTT 0.948161 -140 ACATATTACATCTCCCGGTAAGTTATATTTCCCT 43 72 1 TCTCCGGGTT 0.905497 -229 AAGACGCTGTTTTGCGGCATGCTTCCGGTTTATC 45 127 1 TTTGCGCCTT 0.520771 -174 GCAGATCTCCTGGCTTGCTTGAATAACTT 47 264 0 TCTCCGGGCT 0.859074 -19 TTTTGACTTTTTGCCAGGGAAGTTGTTGTTGATT 48 98 1 TTGCCGGGTT 0.873361 -194 TGTGGAATTATTTGCGGGTCGCGTCACATTTAAT 48 226 1 TTTGCGGCGT 0.635483 -66 ***** ** *** Masking position 5 Map Score: 14.9361 Number of sites scoring better than the average of aligned sites = 964 Number in coding regions = 876 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161