AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_ecoli_reg_100.orf -o00010_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 aceE 160 pyruvate dehydrogenase (decarboxylase component) #2 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #3 yadI 104 putative PTS enzyme II B component #4 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #5 yaiN 166 putative alpha helix chain #6 nagE 300 PTS system, N-acetylglucosamine-specific enzyme IIABC #7 seqA 184 negative modulator of initiation of replication #8 pgm 25 phosphoglucomutase #9 hrsA 108 protein modification enzyme, induction of ompC #10 gpmA 201 phosphoglyceromutase 1 #11 galE 260 UDP-galactose-4-epimerase #12 b0968 181 orf, hypothetical protein #13 agp 292 periplasmic glucose-1-phosphatase #14 ptsG 294 PTS system, glucose-specific IIBC component #15 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #16 gapC_1 300 glyceraldehyde 3-phosphate dehydrogenase C, interrupted #17 malX 174 PTS system, maltose and glucose-specific II ABC #18 pykF 300 pyruvate kinase I (formerly F), fructose stimulated #19 pfkB 286 6-phosphofructokinase II; suppressor of pfkA #20 celF 104 phospho-beta-glucosidase; cryptic #21 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #22 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #23 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #24 gapA 300 glyceraldehyde-3-phosphate dehydrogenase A #25 manX 300 PTS enzyme IIAB, mannose-specific #26 pykA 127 pyruvate kinase II, glucose stimulated #27 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #28 gatZ 28 putative tagatose 6-phosphate kinase 1 #29 gatY 197 tagatose-bisphosphate aldolase 1 #30 fruB 300 PTS system, fructose-specific IIA/fpr component #31 glk 203 glucokinase #32 ptsH 300 PTS system protein HPr #33 ptsI 44 PEP-protein phosphotransferase system enzyme I #34 crr 40 PTS system, glucose-specific IIA component #35 srlA 255 PTS system, glucitol/sorbitol-specific IIC component, one of two #36 ascF 256 PTS system enzyme II ABC (asc), cryptic, transports specific beta-glucosides #37 eno 87 enolase #38 pyrG 227 CTP synthetase #39 bglA 38 6-phospho-beta-glucosidase A; cryptic #40 fba 214 fructose-bisphosphate aldolase, class II #41 pgk 49 phosphoglycerate kinase #42 epd 284 D-erythrose 4-phosphate dehydrogenase #43 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #44 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #45 tdcC 21 anaerobically inducible L-threonine, L-serine permease #46 tdcB 98 threonine dehydratase, catabolic #47 tdcA 188 transcriptional activator of tdc operon #48 agaZ 248 putative tagatose 6-phosphate kinase 2 #49 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #50 ptsN 117 phosphotransferase system enzyme IIA, regulates N metabolism #51 yiaY 189 putative oxidoreductase #52 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #53 yibO 244 putative 2,3-bisphosphoglycerate-independent phosphoglycerate mutase #54 glvB 24 PTS system, arbutin-like IIB component #55 glvC 34 PTS system, arbutin-like IIC component #56 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #57 frvA 300 PTS system, fructose-specific IIA component #58 pfkA 180 6-phosphofructokinase I #59 tpiA 107 triosephosphate isomerase #60 frwC 300 PTS system, fructose-like enzyme II component #61 pflD 50 formate acetyltransferase 2 #62 pgi 300 glucosephosphate isomerase #63 sgaT 291 orf, hypothetical protein #64 fbp 175 fructose-bisphosphatase #65 treB 118 PTS system enzyme II, trehalose specific #66 sgcA 130 putative PTS system enzyme II A component #67 gpmB 42 phosphoglyceromutase 2 Motif number 1 GTAATTAATGGCTAAAACGAGTAAAGTTCA 14 30 1 GCTAAAACGA 0.648368 -265 GAAAAGCGATGCTGAAAGGTGTCAGCTTTG 15 37 1 GCTGAAAGGT 0.664284 -264 TCGCCTACCTGCTGAAACATGATTCAAACT 16 84 1 GCTGAAACAT 0.805514 -217 CGCGCAATTTACTGAATCCAGATTGTTCTC 17 139 1 ACTGAATCCA 0.456095 -36 AGTCCAAAGTGCTGAAACCATTCAAGAGTC 18 86 0 GCTGAAACCA 0.878107 -215 TTTTTTTGTGGCTGAAAGGAGTATACGGTA 23 185 0 GCTGAAAGGA 0.858711 -114 GTAGCCCTTATCTGAATCGATTCGATTGTG 25 219 1 TCTGAATCGA 0.604644 -82 TACTCCGTTGACTGAAACAACCAGGTGTTG 26 104 0 ACTGAAACAA 0.694763 -24 TGCTGACGCTGCTGAAATGAAATTGCTGAT 30 64 1 GCTGAAATGA 0.849173 -237 TTCCTTGCGTGCTGAAACAGAAGTATTATG 30 175 1 GCTGAAACAG 0.802359 -126 ACAAGATCGCGCTGAAACGTTTCAAGAAAG 30 205 0 GCTGAAACGT 0.94547 -96 TCTCATAGAGGCTGAATCGTTTCAATTCAG 30 266 1 GCTGAATCGT 0.918569 -35 CTCCTCTCTTGCTGAATTGAAACGATTCAG 30 277 0 GCTGAATTGA 0.785542 -24 TGCAATTGGTGCTGAAACGATAAAGTAATT 31 70 1 GCTGAAACGA 0.981569 -134 GTTCCGACAGGCTGAATCAA 32 1 0 GCTGAATCAA 0.892203 -300 AAAAGCCAAAGCTGAATCGATTTTATGATT 32 82 1 GCTGAATCGA 0.971948 -219 AAATGCCGATGCTGAAACGGAATTAAGAAA 36 178 0 GCTGAAACGG 0.944428 -79 CTAAAAGCGCGCTGAAACAAGGGCAGGTTT 40 28 0 GCTGAAACAA 0.927123 -187 GCTTATCCTAGCTGAAGCGTTTCAGTCGAT 42 148 1 GCTGAAGCGT 0.701714 -137 AATGAAAGTCACTGAAACGAGAGTAGCTTG 48 103 0 ACTGAAACGA 0.90502 -146 CGCAGTATCAACTGAAACAAAACGAAAGAT 48 197 1 ACTGAAACAA 0.694763 -52 GAAATCTGGCACTGAATCGGTTAACTGTCC 52 184 0 ACTGAATCGG 0.664232 -117 TTTTACTACAGCTGAATCGATAAAATAGCC 53 187 0 GCTGAATCGA 0.971948 -58 ATCACTTCCTGCTGAATTGATTCAGGTCAG 58 66 0 GCTGAATTGA 0.785542 -115 ********** Masking position 3 Map Score: 27.2704 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 335 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 GGAGAGGAGTTTTGACGGCTATCACCCTTTATCAACAAT 3 38 1 TTGATCACCT 0.899829 -67 GCGTGTCTTTTGTGAGTTTTGTCACCAAATATCGTTATT 6 125 0 TTGATCACAA 0.890152 -176 TATGTGATCAATTTCACTTGATTGAAATTAT 9 88 0 TTGATCACTA 0.94473 -21 ACAGAGGGTTTATGAATGATTGCGCTTTTTATCTGAAAA 11 96 0 TTGAGCGCTT 0.831601 -165 TGCCAATTTGTTTGACGGCTATCACGTTTCAACTTCAGA 14 141 0 TTGATCACTT 0.970982 -154 TTTGCAAAAATTTGATTTGGATCACGTAATCAGTACCCA 15 63 1 TTGATCACTA 0.94473 -238 GACCTGTGGTTATGACCCTCTTCACATTTCGGGCAAATA 23 98 0 TTGATCACTT 0.970982 -201 ACGATAAAAATGTGATTTTCATCACGATTTAGGTGCAGC 24 75 0 TTGATCACAT 0.9407 -226 GTAGCCCTTATCTGAATCGATTCGATTGTGGACGACGAT 25 219 1 TTGATCGATT 0.659579 -82 TGAGCAAAAGTTTGATGTGCTGCACAATTTTTTGCCATT 30 123 0 TTGAGCACAT 0.818487 -178 AAAGTAATTGTGTGACCCAGATCGATATTTACAGGGAGC 31 91 1 TTGATCGAAT 0.478773 -113 GAATCGATTTTATGATTTGGTTCAATTCTTCCTTTAGCG 32 95 1 TTGATCAATT 0.788668 -206 TTTTTATATTTGTGAAACCGGTCACCTGAATATTTTTCC 36 80 0 TTGATCACTA 0.94473 -177 AAGACATTTATCTGACTCACATCACACTTTTATCCCCTT 42 72 0 TTGATCACCT 0.899829 -213 AAAGTTAATTTGTGAGTGGTCGCACATATCCTGTTCATT 47 110 1 TTGAGCACTT 0.904867 -79 ATAATGGTTTTCTGATCTGATTCACAAAAGAAACATAAT 48 130 0 TTGATCACAA 0.890152 -119 AAAACAAAAATGTGACACTACTCACATTTAAATGCCATT 52 25 1 TTGATCACTT 0.970982 -276 ACAAGCGTTTTGTGATGAACGTCACGTCAATTACCTCTC 52 98 1 TTGATCACTA 0.94473 -203 CGGCCTTTTGTGTGATATCAATCACATAAATATAGGGGG 52 139 0 TTGATCACTA 0.94473 -162 AACAGCGTCTTGTGAGACGCGTCGCAAATTGACGGTTAC 60 99 0 TTGATCGCAT 0.891728 -202 TATCGCAAGTTATGAGGCGGATCGCATTTTTGTACTGAT 60 157 1 TTGATCGCTT 0.945571 -144 * *** **** * * Masking position 3 Map Score: 24.5943 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 26 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 TTGAACTCTCGCCGGAAAGCTCAATAAGAC 1 90 0 GCCGGAAAGC 0.926457 -71 CGTCTTTCAGGCCGCAGCGGCGTTAGCTTC 2 242 0 GCCGCAGCGG 0.931846 -59 CTCTGGATTTGGGGGAGAGGAGTTTTGACG 3 25 1 GGGGGAGAGG 0.798806 -80 CGGATAGCGGGCGGCAGAAGGAA 5 4 0 GCGGCAGAAG 0.816662 -163 CGAACCGTTGGCCGGAGAGGGTGCTAAGGC 11 39 0 GCCGGAGAGG 0.968146 -222 GCGTGGCAAGGGGGGAGAGCCTCGCCGTGT 14 230 0 GGGGGAGAGC 0.78334 -65 TAGCTATAATGGCGAAAAGCGATGCTGAAA 15 24 1 GGCGAAAAGC 0.684758 -277 CGCGGTTTACGCCGAAAAAGAGGCTAAAAA 16 178 1 GCCGAAAAAG 0.701439 -123 TGGGCGCACTGCCGGAAAGCGAATCCGGTA 18 234 0 GCCGGAAAGC 0.926457 -67 TAACAACAACGCCGGAAAGGCAGGCTCCCT 31 123 0 GCCGGAAAGG 0.932586 -81 AAAAGTTAGAGCGGCAACGCGTACCCTGGG 37 15 1 GCGGCAACGC 0.697826 -73 ATAGTGCGCTGGCGAAGAGGAGGGATAATG 38 119 1 GGCGAAGAGG 0.839761 -109 TGTTTGTCCAGCCGAAGAAGACATTTATCT 42 98 0 GCCGAAGAAG 0.837707 -187 AAAAAAGGTCGCCGAAGCACCTTTTTA 44 8 0 GCCGAAGCAC 0.649904 -293 ATTTAATTCAGGCGAAGAGGTTTTATA 46 82 1 GGCGAAGAGG 0.839761 -17 GGCCCGTTGTGCCGCACAACAGACCGCCAT 50 34 0 GCCGCACAAC 0.6608 -84 TGTTAATGTGGCGGCAGAGGTAGCCGGACC 52 227 0 GCGGCAGAGG 0.933809 -74 GGCTGTATTTGCCGCACCGCGCAGGTATAC 53 58 0 GCCGCACCGC 0.709017 -187 TTGGAGTTTTGCCGCAAAGCGGTAGAGGGC 56 109 1 GCCGCAAAGC 0.934851 -25 CCGGAAGCATGCCGCAAAACAGCGTCTTGT 60 125 0 GCCGCAAAAC 0.81919 -176 GCCCTTGCGAGCGGGAGAAGAAC 61 4 0 GCGGGAGAAG 0.796355 -47 ********** Masking position 6 Map Score: 21.321 Number of sites scoring better than the average of aligned sites = 1420 Number in coding regions = 1312 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 TCAAGCGCATATAAAAGCGCGGCAACTAAAC 1 50 1 ATAAAACGCG 0.68801 -111 TTTTATCTGAAAAAAGACGCGGTTTCATGCC 11 78 0 AAAAAGCGCG 0.886287 -183 AATCGCGCATAAAAAACGGCTAAATTCTTGT 11 148 1 AAAAAAGGCT 0.784014 -113 ATACATCTTCAAAAACAGGCAAGGTTTGACG 13 167 0 AAAAACGGCA 0.748624 -126 ATGTATATAGAAAAACAGGCGTTCAACAAGC 13 192 1 AAAAACGGCG 0.965211 -101 CTGTGTAATAAATAAAGGGCGCTTAGATGCC 14 195 1 AATAAAGGCG 0.801802 -100 GTTTACGCCGAAAAAGAGGCTAAAAATATTC 16 182 1 AAAAAGGGCT 0.605485 -119 TCAACGACTCAAAAACAGGCACTCACGTTGG 18 123 1 AAAAACGGCA 0.748624 -178 AACGAATTATAAAAAGGCGCGAATAACTTAG 19 98 1 AAAAAGCGCG 0.886287 -189 TCAGGCCAAAAAAAACCGGCGCAATGGCCGG 23 45 0 AAAAACGGCG 0.965211 -254 CGATATCTAAAATAAATCGCGAAACGCAGGG 25 178 1 AATAAACGCG 0.68801 -123 CATCCGGCATAAAAACACGCGCACTTTGCTA 29 38 1 AAAAACCGCG 0.93798 -160 GTGAAAGGCAAAAAAACGGCCTCCCGATAGG 29 76 0 AAAAAAGGCC 0.91484 -122 CTCTATGAGAAAAAAAGCGCCAACCTGGCTT 30 245 0 AAAAAACGCC 0.85414 -56 CGCGTCTGTTAAAAACTGGCGCTAACAATAC 32 211 1 AAAAACGGCG 0.965211 -90 TCAAGGTAATAAAAAAGGTCGCCGAAGCACC 44 17 0 AAAAAAGTCG 0.713876 -284 CTGAAAGTGTAAAAAAGGGCGGGCAGCTTAC 51 160 0 AAAAAAGGCG 0.971279 -30 CCACATTAACAAAAAACCTCGGGCTTCCAGC 52 246 1 AAAAAACTCG 0.576279 -55 GGGCGCGACGAAAAAAAAGCGTAAATCTGGC 53 116 1 AAAAAAAGCG 0.673046 -129 AAAAACCTGAAAAAAACGGCCTGACGTGAAT 56 76 0 AAAAAAGGCC 0.91484 -58 CAAACAGTGGATAAAAAGGCCATTTACTGGA 60 206 0 ATAAAAGGCC 0.562383 -95 ****** **** Masking position 5 Map Score: 18.2608 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 281 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 GCAGGGAAGGCCGCCCCGGATAGCGGGCGG 5 20 0 CCGCCCCGGA 0.989813 -147 GCGGGCAACGGCCCCGGAAAAGACCCAC 12 9 1 CGGCCCCGGA 0.919011 -173 TTCCGGCAGTGCGCCCAGAAAGCAAGTTTC 18 247 1 GCGCCCAGAA 0.829613 -54 GGCATATCTGCCCCCCCGGACATAAATAAT 20 52 0 CCCCCCCGGA 0.919011 -53 CATGGGGTCGGCGCCCCGAATTTTAAAGGG 24 119 0 GCGCCCCGAA 0.984075 -182 AAATCAAAAGCGCCACGAATAGTCAAAAT 30 10 1 GCGCCACGAA 0.829613 -291 GTAAAGCATCACGCCCCGCACAAGGAAGCG 35 50 1 ACGCCCCGCA 0.960717 -206 TTTTTTCGTCGCGCCCCGCAAAATTGCATT 53 102 0 GCGCCCCGCA 0.993714 -143 AGGAAGATGGCCGCCCCGCAGGGCAGCAGG 59 59 0 CCGCCCCGCA 0.993714 -49 TCGTTGACAACCGCCCCGCTCACCCTTTAT 62 101 0 CCGCCCCGCT 0.952577 -200 TAAATGTGACGCGACCCGCAAATAATTCCA 63 228 0 GCGACCCGCA 0.925685 -64 ********** Masking position 5 Map Score: 14.7589 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 115 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 ATAGACAAATCGGTTGCCGTTTGTTGTTTA 2 55 1 CGGTTGCCGT 0.828133 -246 TTCCTTCTGCCGCCCGCTATCCGGGG 5 7 1 CTGCCGCCCG 0.788659 -160 TTGACGCTATCCGCTGCCGGGATTTATTCA 7 117 1 CCGCTGCCGG 0.966639 -68 GGTGCTAAGGCCGCCTCCGGCAAGGTCAGC 11 20 0 CCGCCTCCGG 0.868467 -241 ATGCGTCGAACCGTTGGCCGGAGAGGGTGC 11 45 0 CCGTTGGCCG 0.838653 -216 TTTTCCGGGGCCGTTGCCCGC 12 2 0 CCGTTGCCCG 0.93904 -180 TTTTGCGAACCTGTTCCCGGAAAAAAGTCA 13 225 1 CTGTTCCCGG 0.703258 -68 GCGCAATGGCCGGTTTCCGTTGTTACTCAA 23 28 0 CGGTTTCCGT 0.788033 -271 TATGTTTACACCGCATCCGGCATAAAAACA 29 25 1 CCGCATCCGG 0.644684 -173 CACTTTGCTACGGCTTCCCTATCGGGAGGC 29 59 1 CGGCTTCCCT 0.831183 -139 GGCAAAAAAACGGCCTCCCGATAGGGAAGC 29 71 0 CGGCCTCCCG 0.814501 -127 GTGTACTGCACCGTTTGCCGATTGTCCTTG 36 39 1 CCGTTTGCCG 0.802081 -218 TTTGCAGACGCTGCTTGCGTC 41 2 0 CTGCTTGCGT 0.561362 -48 CTTGATATGTCCGTTTGCGGACAAGCAATA 44 43 1 CCGTTTGCGG 0.831285 -258 TTCAAAACACCGGTTTCCCTGCTCAATTGC 44 210 1 CGGTTTCCCT 0.753284 -91 AATCTGGCATCGGCTTGCCGCGAGCGGTCG 53 139 1 CGGCTTGCCG 0.822309 -106 AAAATGAAATCTGTTGCCGGAAGTCTTCTT 58 137 0 CTGTTGCCGG 0.898609 -44 TTTCACAGACCTGCTGCCCTGCGGGGCGGC 59 50 1 CTGCTGCCCT 0.799479 -58 ACATGGCAGGCCGTTGCCGTGCGCTCTTAT 60 37 0 CCGTTGCCGT 0.864412 -264 AAGCTGCTCCCGGGCTTGCGAAA 60 288 0 CTGCTCCCGG 0.792604 -13 ********** Masking position 3 Map Score: 16.1915 Number of sites scoring better than the average of aligned sites = 2551 Number in coding regions = 2270 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 7 ATTCCGAGTTTTTCTGCAAGCCAGGCTTGACGCTAT 7 91 1 TTTCAGCGGC 0.983317 -94 TTCCACTAATTTATTCCATGTCACACTTTTCGCATC 11 187 1 TTTCAGCCAC 0.630478 -74 CTATGCCTGATTAGCCCCTGCCTCGCGTACGCCGCT 13 127 0 TTCCCGCCGC 0.773892 -166 ATATTGTTAATTTCTTCACTTTCCGCTGATTCGGTG 19 230 1 TTTCATTCGC 0.694519 -57 CAGCGATGCCTTTTTGCAAGCTGGGCAAACTAAGTA 31 36 0 TTTCAGTGGC 0.949558 -168 TGTGGGAAGCTTTATTCCAGGCTGGCGTAATAATAA 42 35 0 TTTCCGCGGC 0.940558 -250 AACATTCCTTTTATTCCACGTTTCGCTTATCCTAGC 42 124 1 TTTCAGTCGC 0.905933 -161 TCATTTCATTTTGATACACTTCATGCCGTCAATGAG 47 144 1 TTTCATCTGC 0.77511 -45 ATCAAGCAATTTTTTTCAGGTTTTGCCCGCTTAGTG 56 42 0 TTTCAGTTGC 0.823415 -92 AAAAAATTGCTTGATTCACGTCAGGCCGTTTTTTTC 56 63 1 TTTCAGCGGC 0.983317 -71 TCCTGCTGAATTGATTCAGGTCAGGCCAAATGGCGG 58 54 0 TTTCAGCGGC 0.983317 -127 TTTGGCAGATTTGTCACATGGCAGGCCGTTGCCGTG 60 46 0 TTCCAGCGGC 0.961421 -255 AAATGGCCTTTTTATCCACTGTTTGCTCCGCCTGCG 60 212 1 TTTCATTTGC 0.523989 -89 AGGTGTTATCACAGGACTGGCTCCTCCAACA 62 6 1 TTCCAGCGGC 0.961421 -295 ATGCGGATTTTTCATCCACTCCTGGCGGTCAGTAGT 62 138 1 TTTCATCGGC 0.93295 -163 ** * ** * * *** Masking position 2 Map Score: 13.2595 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 281 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 GGGGGGCTAATCGGCAGGGAAGGCCGCCCCGGAT 5 29 0 TGCAGGGGGC 0.923124 -138 TCCGAGTTTTTCTGCAAGCCAGGCTTGACGCTAT 7 93 1 TGCAAGCGGC 0.971998 -92 AAGGCCGCCTCCGGCAAGGTCAGCACTACCGAC 11 10 0 CGCAAGGAGC 0.930112 -251 ATCAGCGGCGTACGCGAGGCAGGGGCTAATCAGG 13 124 1 TGCGAGGGGG 0.892268 -169 TCTGTTTCAGCACGCAAGGAAAGCCGTAAAGTTA 30 162 0 CGCAAGGAGC 0.930112 -139 TCTTTAACCCTAAGCCAGGTTGGCGCTTTTTTTC 30 234 1 TGCCAGGGGC 0.928925 -67 GCGATGCCTTTTTGCAAGCTGGGCAAACTAAGTA 31 36 0 TGCAAGCGGC 0.971998 -168 AACAACAACGCCGGAAAGGCAGGCTCCCTGTAAA 31 118 0 CGAAAGGGGC 0.883003 -86 AAATCAGTCACAAGTAAGGTAGGGTT 33 29 1 CGTAAGGGGG 0.82707 -16 CTTGCGTCAATGGGCAAGGTGGGCTTGCATTTGC 48 73 0 TGCAAGGGGC 0.987035 -176 CTCTTTTTTGCCTGCAAGCCCGGGTA 55 19 1 CGCAAGCGGG 0.968143 -16 GACATGGGCTTTCGCAAGCCCGGGAGCAGCTT 60 279 1 TGCAAGCGGG 0.956515 -22 TCTTCTCCCGCTCGCAAGGGCGGGTTCGCTTTCC 61 13 1 CGCAAGGGGG 0.985218 -38 * ****** *** Masking position 8 Map Score: 12.5041 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 173 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 GGGATTCTGGCGCTTGCTACCTTGCTGCACCCAGAA 2 168 0 CGCTGCTTGT 0.408452 -133 GCGCCAGAATCCCCAGGAGCTTACATAAGTAAGTGA 2 191 1 CCCCGCTACT 0.931747 -110 CACGCCCTCACCCCAGTCACTTACTTATGTAAGCTC 2 207 0 CCCCGCTACT 0.931747 -94 TGCCGATTAGCCCCCCCCCCTTTCCTCTTTGTTTTC 5 47 1 CCCCCCTTCT 0.904555 -120 TTAACCATTATGCCCGATAAATTCATCCTGTAAATA 9 35 1 TGCCGATTCT 0.713555 -74 ACGGACCATTCCCCTGGAGCGTTGATTTTACGGAAG 16 114 1 CCCCGCTTGT 0.958882 -187 ACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAA 19 41 1 TCCCGCTTCT 0.967075 -246 AGGTAAAATATCCTTGTCACATTCGTTTGCAAAGGA 25 81 0 TCCTGCTTCT 0.732453 -220 ACATGACCTGTGCCACAAACTTTCATTATCCCTCCT 38 136 0 TGCCCCTTCT 0.677164 -92 GAGAGTGAATCCCCAGGAGCTTACATAAGTAAGTGA 40 109 1 CCCCGCTACT 0.931747 -106 CGTTCGCTCACCCCAGTCACTTACTTATGTAAGCTC 40 125 0 CCCCGCTACT 0.931747 -90 GGTAAGGTTTCCCCGGACGATTTGCTGGATTACTCT 42 219 1 CCCCGATTGT 0.861614 -66 AACACCGGTTTCCCTGCTCAATTGCTTTCATTAAAC 44 215 1 TCCCGATTGT 0.812659 -86 AAGTTATATTTCCCTGATACATTGTGAGTAAATCAC 57 91 1 TCCCGCTTGG 0.659188 -210 GGGTTCGCTTTCCCACAGGAGTTCCTC 61 34 1 TCCCCATTCT 0.63806 -17 TTTGACTTTTTGCCAGGGAAGTTGTTGTTGATTTTG 63 99 1 TGCCGATTGT 0.579477 -193 CCTTCTGCGATCCCTGCCGCCTTCGTCAAAAGTATC 66 55 1 TCCCGCTTCT 0.967075 -76 **** * * *** * Masking position 12 Map Score: 11.7125 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 204 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 GGCGGCCTTCCCTGCCGATTAGCCCCCCCCC 5 35 1 CCTGCCATTA 0.468796 -132 AAATTAAACGCGTGTCTTTTGTGAGTTTTGT 6 142 0 CGTGTCTTTG 0.617276 -159 AATGATTTTTCGCGCCCTTTGGCTAACACTA 12 54 1 CGCGCCTTTG 0.982657 -128 AGGGCATCTAAGCGCCCTTTATTTATTACAC 14 197 0 AGCGCCTTTA 0.663682 -98 TTTATCTTCTCGCGCAATTTACTGAATCCAG 17 129 1 CGCGCATTTA 0.587103 -46 GCGTATAATGCGCGCCAATTGACTCTTGAAT 18 66 1 CGCGCCATTG 0.919992 -235 CTAAGTTATTCGCGCCTTTTTATAATTCGTT 19 98 0 CGCGCCTTTT 0.858793 -189 CGCACCTGCCATTTAACAAGGAAAA 28 5 1 CCTGCCTTTA 0.813035 -24 CATAAAAACACGCGCACTTTGCTACGGCTTC 29 45 1 CGCGCATTTG 0.876541 -153 ATCCTGTCGTTTGTTTTCGATTT 29 185 0 CCTGTCTTTG 0.641365 -13 GAATATTTTTCCCGCCGATTGTGCAAGGACA 36 61 0 CCCGCCATTG 0.927272 -196 TACGCGGTCAAGCGCCATTTGTGTCATTTTT 38 17 1 AGCGCCTTTG 0.907863 -211 GGCAGGTTTCCCTGCCCTGTGATTTT 40 6 0 CCTGCCTGTG 0.817588 -209 TGCGGCACAACGGGCCATTTGTACGGTTAAT 50 48 1 CGGGCCTTTG 0.91728 -70 CAGTAAGCTGCCCGCCCTTTTTTACACTTTC 51 158 1 CCCGCCTTTT 0.870861 -32 TGTCCAGTCGACGGCCTTTTGTGTGATATCA 52 158 0 ACGGCCTTTG 0.681351 -143 GAGAGCCAGACCCGCATTTTGTGTATAAAAT 58 22 1 CCCGCATTTG 0.887291 -159 TGTATAAAATACCGCCATTTGGCCTGACCTG 58 43 1 ACCGCCTTTG 0.916147 -138 ACGGCAACGGCCTGCCATGTGACAAATCTGC 60 47 1 CCTGCCTGTG 0.817588 -254 ****** **** Masking position 10 Map Score: 14.8151 Number of sites scoring better than the average of aligned sites = 727 Number in coding regions = 655 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 11 TTGCTGTTGCTTCGTCGCGGCAATATAATGA 10 142 1 TTGTCGCGGC 0.87526 -60 GAAGTAATGATTTTTCGCGCCCTTTGGCTAA 12 49 1 TTTTCGCGCC 0.97374 -133 ACAGGTGCAATTATCAGCGGCGTACGCGAGG 13 112 1 TTTCAGCGGC 0.781678 -181 CTTCTTCGCACCAGCATCAAGA 16 289 0 TTTTCGCACC 0.811563 -12 CATTGCTAAGTTATTCGCGCCTTTTTATAAT 19 103 0 TTTTCGCGCC 0.97374 -184 TTCCTCTCTTTTCTTACCGGCACGATTACCC 21 24 0 TTTTACCGGC 0.753052 -27 TTAGCCTGTATTGTTAGCGCCAGTTTTTAAC 32 218 0 TTTTAGCGCC 0.929238 -83 CACCTGAATATTTTTCCCGCCGATTGTGCAA 36 66 0 TTTTCCCGCC 0.954424 -191 GAGTATTTTATTTTTACCGCCGGACGGTACC 44 256 1 TTTTACCGCC 0.881181 -45 GCTGGCTGTATTTGCCGCACCGCGCAGGTAT 53 60 0 TTGCCGCACC 0.567882 -185 ACGCTTTTTTTTCGTCGCGCCCCGCAAAATT 53 107 0 TTGTCGCGCC 0.944643 -138 GAGTAAAGGATTGTTACCGCACTAAGCGGGC 56 23 1 TTTTACCGCA 0.462755 -111 GTTTTTAAATTTTTCCGCGCAATATATTCTG 65 63 1 TTTCCGCGCA 0.740647 -56 AGCAGAGCGCTTATCCCCGGCAAAGAGCAAT 66 21 1 TTTCCCCGGC 0.850961 -110 ** ******** Masking position 2 Map Score: 10.1399 Number of sites scoring better than the average of aligned sites = 736 Number in coding regions = 664 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 12 AGCGCCAGAATCCCCAGGAGCTTACATAAG 2 190 1 TCCCCAGGAG 0.985632 -111 CTCCCCCAAATCCAGAGGAGAGGAAATAGC 3 12 0 TCCAGAGGAG 0.782516 -93 TGAATACAAGTCGCCAGGAGTATATGAATA 7 141 0 TCGCCAGGAG 0.966611 -44 TACGGACCATTCCCCTGGAGCGTTGATTTT 16 113 1 TCCCCTGGAG 0.934396 -188 AGAGAGTGAATCCCCAGGAGCTTACATAAG 40 108 1 TCCCCAGGAG 0.985632 -107 GGTTCGCTTTCCCACAGGAGTTCCTC 61 35 1 CCCACAGGAG 0.926437 -16 GAACTACTGACCGCCAGGAGTGGATGAAAA 62 146 0 CCGCCAGGAG 0.951172 -155 ********** Masking position 9 Map Score: 5.48528 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 21 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 AGCATCAAGATGCGCCTGCGATTTCTCGGCG 16 268 0 TGCGCCGCGA 0.968151 -33 AGAAAGTTTCCGGGACCGCGATGGTCTCTTT 19 35 0 CGGGACGCGA 0.851531 -252 GAAATAACGCCGCGATGGCGATAAATTAATC 26 53 0 CGCGATGCGA 0.923545 -75 GCGGTCAACACCCGCCAGCAATGGACTGTAT 32 164 1 CCCGCCGCAA 0.928571 -137 ATTTCAATAGTGCGCTGGCGAAGAGGAGGGA 38 113 1 TGCGCTGCGA 0.932248 -115 TTCCAGCCTGCGCGACAGCAAACATAAGAAG 52 270 1 CGCGACGCAA 0.923545 -31 CACTGTTTGCTCCGCCTGCGATTGCCTATTG 60 228 1 TCCGCCGCGA 0.913433 -73 AAGCTGCTCCCGGGCTTGCGAAAGCCCATGT 60 280 0 CGGGCTGCGA 0.889489 -21 GTTCTTCTCCCGCTCGCAAGGGCGGGTTC 61 9 1 CCCGCTGCAA 0.854743 -42 TCTTCTGGCCTGCGCTAGCGCAGGTAGTACA 62 63 1 TGCGCTGCGC 0.702568 -238 TCAGGTGAATCGCGCCAGCAAATTACGGATT 64 84 0 CGCGCCGCAA 0.973993 -92 TATGGAGTAAAGCGACCGCAACAATCTTAAC 64 135 0 AGCGACGCAA 0.574273 -41 ****** **** Masking position 9 Map Score: 8.0039 Number of sites scoring better than the average of aligned sites = 1133 Number in coding regions = 1051 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 14 GACAAATCGGTTGCCGTTTGTTGTTTAAAA 2 58 1 TTGCCGTTTG 0.924845 -243 GGGTATTATGTTGACCATTGTGCCACAGGG 7 43 1 TTGACCATTG 0.601777 -142 TGCTTTGTCCTTTGTCTGCAACGT 8 12 0 TTGTCCTTTG 0.566053 -14 TTTATCGTAATTGCCCTTTAAAATTCGGGG 24 106 1 TTGCCCTTTA 0.696986 -195 CATTTCACTGTTGCTGATTGGCTGCTGACG 30 42 1 TTGCTGATTG 0.739462 -259 TTAGATTAGGTTGCCGTTTGGTAATAAAAC 35 213 1 TTGCCGTTTG 0.924845 -43 ACTGCACCGTTTGCCGATTGTCCTTGCACA 36 43 1 TTGCCGATTG 0.934452 -214 TCATTTCGTTTTGCCTATTAACGCCTTTCT 48 38 1 TTGCCTATTA 0.466192 -211 CAAGCCCACCTTGCCCATTGACGCAAGCTA 48 80 1 TTGCCCATTG 0.954671 -169 TTGCCCAATGTGCCAGAGAT 57 1 1 TTGCCCAATG 0.691477 -300 CACAAAGGCTTTGCTTTTTG 59 1 0 TTGCTTTTTG 0.542588 -107 CCGCCTGCGATTGCCTATTGTTTCCTCCAT 60 239 1 TTGCCTATTG 0.873457 -62 AGAAGGGTTATTGCTCTTTGCCGGGGATAA 66 31 0 TTGCTCTTTG 0.783521 -100 ********** Masking position 2 Map Score: 5.84763 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 187 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 15 CATTGAACTCTCGCCGGAAAGCTCAATAAG 1 92 0 TCGCCGGAAA 0.512969 -69 GTATTTTTATTTTGCTGCAAATTGTACTGC 6 239 0 TTTGCTGCAA 0.481438 -62 CTGTTGCTTCGTCGCGGCAATATAATGAGA 10 145 1 GTCGCGGCAA 0.643228 -57 GCTAAGGCCGCCTCCGGCAAGGTCAGCACT 11 17 0 CCTCCGGCAA 0.814831 -244 GCGGGCAACGGCCCCGGAAAAGACCCACGG 12 11 1 GCCCCGGAAA 0.502569 -171 TGCGAACCTGTTCCCGGAAAAAAGTCATAT 13 228 1 TTCCCGGAAA 0.704779 -65 TCTGGGCGCACTGCCGGAAAGCGAATCCGG 18 236 0 CTGCCGGAAA 0.688181 -65 GACCATCGCGGTCCCGGAAACTTTCTTAAG 19 40 1 GTCCCGGAAA 0.657968 -247 ACGGGTAATCGTGCCGGTAAGAAAAGAGAG 21 22 1 GTGCCGGTAA 0.629887 -29 GAATAAAAGGTTGCCTGTAAAATTACAAAA 24 257 0 TTGCCTGTAA 0.561221 -44 GAAAGGCAGGCTCCCTGTAAATATCGATCT 31 109 0 CTCCCTGTAA 0.698911 -95 AGCTTTGGCTTTTCCTGTAACGATTAATTT 32 65 0 TTTCCTGTAA 0.566864 -236 GGTACTATTTCCTGTAAGAATTGACTC 39 8 1 TTTCCTGTAA 0.566864 -31 CTCTTGTCGCCTTCCTGCAACTCGAATTAT 40 82 0 CTTCCTGCAA 0.777941 -133 AGATCTCCTGCAAGGTTTTCCCT 42 272 0 TCTCCTGCAA 0.600787 -13 AGGGTACCGTCCGGCGGTAAAAATAAAATA 44 259 0 CCGGCGGTAA 0.388034 -42 TATACGACCGCTCGCGGCAAGCCGATGCCA 53 143 0 CTCGCGGCAA 0.798154 -102 GGGATCCAGTTTTGCGGTAAAAC 54 4 0 TTTGCGGTAA 0.503711 -21 GATCTCTTTTTTGCCTGCAAGCCCGGGTA 55 16 1 TTGCCTGCAA 0.704539 -19 CCTCTACCGCTTTGCGGCAAAACTCCAAAA 56 107 0 TTTGCGGCAA 0.678926 -27 CATATTACATCTCCCGGTAAGTTATATTTC 57 73 1 CTCCCGGTAA 0.847988 -228 TGCAAGAAGACTTCCGGCAACAGATTTCAT 58 134 1 CTTCCGGCAA 0.869767 -47 TGGTCATTGCCTTCCTGAAAAAATAGTGTC 63 66 0 CTTCCTGAAA 0.547793 -226 AAAACTTTCCCTGCAATGTTTATGGA 64 160 0 TTCCCTGCAA 0.80651 -16 AGAGCGCTTATCCCCGGCAAAGAGCAATAA 66 24 1 TCCCCGGCAA 0.839179 -107 ********** Masking position 9 Map Score: 15.1 Number of sites scoring better than the average of aligned sites = 1738 Number in coding regions = 1491 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867