AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_bsub_reg_300.orf -o02010_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 mrcB 195 peptidoglycan synthetase; penicillin-binding protein 1B #2 fhuA 219 outer membrane protein receptor for ferrichrome, colicin M, and phages T1, T5, and phi80 #3 fhuC 50 ATP-binding component of hydroxymate-dependent iron transport #4 ykfD 183 putative amino acid/amine transport protein #5 ybaE 87 orf, hypothetical protein #6 glnP 138 glutamine high-affinity transport system; membrane component #7 glnH 300 periplasmic glutamine-binding protein; permease #8 hyaA 300 hydrogenase-1 small subunit #9 appC 133 probable third cytochrome oxidase, subunit I #10 appA 184 phosphoanhydride phosphorylase; pH 2.5 acid phosphatase; periplasmic #11 yceA 224 orf, hypothetical protein #12 oppA 300 oligopeptide transport; periplasmic binding protein #13 oppB 85 oligopeptide transport permease protein #14 ydbK 300 putative oxidoreductase, Fe-S subunit #15 hisQ 89 histidine transport system permease protein #16 hisJ 220 histidine-binding periplasmic protein of high-affinity histidine transport system #17 argT 265 lysine-, arginine-, ornithine-binding periplasmic protein #18 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #19 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #20 cvpA 165 membrane protein required for colicin V production #21 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #22 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #23 dedA 82 orf, hypothetical protein #24 usg 65 putative PTS system enzyme II A component #25 pdxB 98 erythronate-4-phosphate dehyrogenase #26 trxC 206 putative thioredoxin-like protein #27 yfiP 44 orf, hypothetical protein #28 yfiQ 31 orf, hypothetical protein #29 pssA 110 phosphatidylserine synthase; phospholipid synthesis #30 yfiM 96 orf, hypothetical protein #31 yfiL 170 orf, hypothetical protein #32 b2603 149 orf, hypothetical protein #33 ygaM 139 orf, hypothetical protein #34 ygbA 286 orf, hypothetical protein #35 yhaP 119 putative L-serine dehydratase #36 yhaQ 65 putative L-serine dehydratase #37 tdcE 33 probable formate acetyltransferase 3 #38 tdcC 21 anaerobically inducible L-threonine, L-serine permease #39 tdcB 98 threonine dehydratase, catabolic #40 tdcA 188 transcriptional activator of tdc operon #41 yhcF 207 putative transcriptional regulator #42 yhcG 184 orf, hypothetical protein #43 yhcJ 47 putative enzyme #44 nanT 78 sialic acid transporter #45 nanA 121 N-acetylneuraminate lyase (aldolase); catabolism of sialic acid; not K-12? #46 yhcK 300 putative FADA-type transcriptional regulator #47 dppB 172 dipeptide transport system permease protein 1 #48 BIME174 101 BIME #49 dppA 300 dipeptide transport protein #50 rbsD 300 D-ribose high-affinity transport system; membrane-associated protein #51 rbsB 24 D-ribose periplasmic binding protein Motif number 1 TTGGTTTTCTCCCTCTCCCTGTGGGAGAGG 1 13 1 CCCTCTCCCT 0.992784 -183 CTCACCCCGGCCCTCTCCCACAGGGAGAGG 1 24 0 CCCTCTCCCA 0.950878 -172 CGCGCTGATGCCCTCACCCCGGCCCTCTCC 1 36 0 CCCTCACCCC 0.981177 -160 CGCACGTTCACCCTCACCCTAACCCTCTCC 1 64 1 CCCTCACCCT 0.989389 -132 CTCACCCTAACCCTCTCCCTCAAGGGAGAG 1 76 1 CCCTCTCCCT 0.992784 -120 TCGATCGGTCCCCTCTCCCTTGAGGGAGAG 1 88 0 CCCTCTCCCT 0.992784 -108 GACGCAGATGCCCGCGCCGGGCGCTTAATA 4 98 0 CCCGCGCCGG 0.871877 -86 ACTGGCAGTTCCCTCTCCCCTATGGGGAGA 6 33 1 CCCTCTCCCC 0.987165 -106 CTCACCCTAATCCTCTCCCCATAGGGGAGA 6 46 0 TCCTCTCCCC 0.782242 -93 GGGTTTGCGCCCCTCACCCTAATCCTCTCC 6 58 0 CCCTCACCCT 0.989389 -81 GGGGCGCAAACCCGCTCCGGGGCCATTAAT 6 75 1 CCCGCTCCGG 0.971421 -64 TGAAAGAAAGCCCGCTCCCTTCGGGTAACC 15 21 1 CCCGCTCCCT 0.994423 -69 GGCAAAATATCCCGCCCCGTTAGACGTATT 16 121 0 CCCGCCCCGT 0.934944 -100 GGGTGCCAGACCGGCACCCTCAGCGAAGGC 18 12 0 CCGGCACCCT 0.89323 -83 CGACAATAAACCCGCCGCCGACAGAGTAAT 35 20 0 CCCGCCGCCG 0.893838 -100 TTACGACCGTCCCGCTCACGAGGCT 36 6 0 CCCGCTCACG 0.883381 -60 CGTTTATTTCCCCTCACCCGGTAGGGGCGA 44 26 0 CCCTCACCCG 0.988346 -53 TCTATAGTGACCCGCAGCCTGGAACTGCGT 47 142 0 CCCGCAGCCT 0.942354 -31 ********** Masking position 5 Map Score: 37.8251 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 96 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 GATGGCAACTCGCCATCCGGTATTTCACGCTT 2 16 0 CGCCATCGGA 0.988092 -204 GATGGCGAGTTGCCATCCGGTAAAATAACATC 2 31 1 TGCCATCGGA 0.940151 -189 GATTATTAATCCCCACCCGCTATTAAGCGCCC 4 78 1 CCCCACCGCA 0.89426 -106 CTAATCCTCTCCCCATAGGGGAGAGGGAACTG 6 38 0 CCCCATAGGA 0.834899 -101 GGGCGCAAACCCGCTCCGGGGCCATTAATTAC 6 76 1 CCGCTCCGGC 0.506219 -63 CACGTTTTTGCCGCATCTCGAAAAATCAAGGA 7 199 1 CCGCATCCGA 0.867326 -102 TTATGAATATCGCAATCGGCGAATACCTCTGG 9 37 1 CGCAATCGCA 0.487572 -97 TGCTAATGCGCCGCATCAGGCCTACGTTCGTT 10 114 0 CCGCATCGGC 0.941892 -71 CGCATTAGCATCGCATCAGGCAATCAATAATG 10 136 1 TCGCATCGGA 0.922816 -49 ATTTTTACTTTCCCATCTCGCAGGAACCGTAC 11 200 1 TCCCATCCGA 0.722881 -25 CGAGTAAGAACCGCATTTGGTACTTTCCGGGC 12 12 1 CCGCATTGGA 0.705598 -289 TGTGCAGGGTCCCAATCCGGGATTACACATGC 12 238 1 CCCAATCGGA 0.933894 -63 TCGCCATCGGTGAAAGAAAGCCC 15 2 1 CGCCATCGTA 0.767428 -88 GAAAGCCCGCTCCCTTCGGGTAACCGGAGGGA 15 26 1 TCCCTTCGGA 0.732799 -64 ATGATGATCATTCCATCAGGTACAGCTTCCCA 16 19 0 TTCCATCGGA 0.730853 -202 TATGCCTTTGCGGCATCGGGCAATGCGT 20 7 0 CGGCATCGGA 0.975171 -159 GTTGTGAATGCGCAATCAGGTAAGGTAGGCCC 33 37 0 CGCAATCGGA 0.897667 -103 TTTGCCTCCACCAGGACCGTCAGATTG 41 191 0 CTCCACCGGC 0.682003 -17 GTTTATTTCCCCTCACCCGGTAGGGGCGAGCG 44 23 0 CCTCACCGGA 0.804732 -56 AGAGGCACAGCGCCACCGGGTATACAGATTGT 47 33 0 CGCCACCGGA 0.979762 -140 CTGCGTGCAGCGCCATCCGGCAGCAATACTTC 47 63 1 CGCCATCGGA 0.988089 -110 GATAAGCGGAGCGCATCAGGCATTTTTGCCTT 48 37 0 GCGCATCGGA 0.814059 -65 ATAACGTTGACCCGACCGGGCAAAAAACAAAA 49 213 1 CCCGACCGGA 0.828617 -88 ******* ** * Masking position 5 Map Score: 21.4499 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 412 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 TGCCCTCACCCCGGCCCTCTCCCACAGGGAGAG 1 25 0 CCGGCCCCCC 0.580681 -171 ATTCGAAACGCTGGCGGGTTCGCAAGCGGTACG 2 130 0 CTGGCGGCGC 0.946905 -90 ACGCAGATGCCCGCGCCGGGCGCTTAATAGCGG 4 94 0 CCGCGCCCGC 0.901758 -90 AAAGTCAACCCTGCACCAGACGCAGATGCCCGC 4 113 0 CTGCACCCGC 0.654353 -71 GCCCGGTGTCCTGCCGGTGTCGCAAGGAGGAGA 8 268 1 CTGCCGGCGC 0.974361 -33 AACTTTTCAGACGCGGGTCCAGCCATACCAACA 10 81 0 ACGCGGGAGC 0.702271 -104 AAAGAATCGTCTGGCGGTTGCCCGGAAAGTACC 12 30 0 CTGGCGGCCC 0.85903 -271 GAGAGCTGTCCTGCGCGTTGCCCCGCATTTTTA 14 107 1 CTGCGCGCCC 0.977862 -194 AAGATTACTACTGGGCGCGCAGCAATTTCGTGC 14 247 1 CTGGGCGAGC 0.942972 -54 TGCCTTCGCTGAGGGTGCCGGTCTGGCACCC 18 9 1 CTGAGGGCGG 0.539871 -86 ATTTTTATTGATGCGCGGGAAGGAAATCCCTAC 20 73 1 ATGCGCGAGG 0.43556 -93 TCCACCAGCGCTGCGCGAAGCGCGCAGATTACC 26 18 1 CTGCGCGCGC 0.992323 -189 TACCCGAAGTCCGCGCGGTTCGCCATGATTTCG 26 47 1 CCGCGCGCGC 0.988994 -160 TCGGTCACTTCTGCGGGAGACCGGT 28 17 1 CTGCGGGCCG 0.868215 -15 TTATTATCAACCGCGGGCCTACCTTACCTGATT 33 23 1 CCGCGGGACC 0.872267 -117 GAGCTATACTCTGGGGGGTGAGCACTGAACAAT 42 122 0 CTGGGGGAGC 0.930021 -63 GGTCTATGTACCGGGCCTTTCGCTAAGGGAAGA 43 22 1 CCGGGCCCGC 0.917219 -26 CGCTGTGCCTCTGCGTGCAGCGCCATCCGGCAG 47 53 1 CTGCGTGCGC 0.947258 -120 AAAGGCAAAAATGCCTGATGCGCTCCGCTTATC 48 36 1 ATGCCTGCGC 0.436727 -66 GTATTTGCGTCTGCGCGGCAAGCTGTACTTGCT 50 60 1 CTGCGCGAGC 0.972402 -241 ******* *** Masking position 3 Map Score: 22.3244 Number of sites scoring better than the average of aligned sites = 672 Number in coding regions = 633 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 AACGTGCGCGCTGATGCCCTCACCCCGGCC 1 42 0 CTGATGCCCT 0.62169 -154 GAAAATCGGGCTTTTGCGCCTGAATATTGC 1 165 1 CTTTTGCGCC 0.71495 -31 GCGTTATGAGCTGGCGGCCCTTTTTGTATC 4 47 1 CTGGCGGCCC 0.735991 -137 CCGGAGCGGGTTTGCGCCCCTCACCCTAAT 6 65 0 TTTGCGCCCC 0.82789 -74 GGGCACCAATCTGGTGCGCTAAAATTGTGC 7 126 0 CTGGTGCGCT 0.707325 -175 GCGCACCAGATTGGTGCCCCAGAATGGTGC 7 137 1 TTGGTGCCCC 0.934641 -164 ACCTATTTTTCTTTTGGCCGGGCGGTGGGG 8 52 0 CTTTTGGCCG 0.717322 -249 TCCTTCTGCACTGGCGCACGTCGCCAGAAA 8 162 0 CTGGCGCACG 0.82339 -139 TTGTCGCATTTTTTCGCCCGCAACCAAAAT 11 51 1 TTTTCGCCCG 0.849939 -174 AATCGTCTGGCGGTTGCCCGGAAAGTACCA 12 29 0 CGGTTGCCCG 0.889277 -272 TATGGCTATTTTTTTGCCCTCTGTTTGATC 14 146 1 TTTTTGCCCT 0.752518 -155 GCAGCAATTTCGTGCGCCCCTCATTTGCGC 14 265 1 CGTGCGCCCC 0.687688 -36 CACGCCAGGTTTGTTGCACTATCGTGGTGC 16 55 1 TTGTTGCACT 0.509079 -166 CTCCGCTGTTGCCCTGTTTCAGGGC 17 6 1 CTGTTGCCCT 0.939181 -260 CATAATGCCATTTTTGCCCCCAACAGACCA 22 83 0 TTTTTGCCCC 0.870426 -73 CGGGGCGCATCTTGTGCCCCGTTTTCTCCT 27 17 1 CTTGTGCCCC 0.949708 -28 ACTGGTGTTATTATTGCCCGCTTATGTCGT 29 45 1 TTATTGCCCG 0.547134 -66 ACACTTCGGCCTGTCGCACGATGTCGAAAC 35 57 1 CTGTCGCACG 0.833182 -63 TCCTGTTGCCCGGTCTATGTAC 43 3 1 CTGTTGCCCG 0.977577 -45 CCTTTTTTGTTTTTTGCCCGGTCGGGTCAA 49 219 0 TTTTTGCCCG 0.895684 -82 TCAAATTGATCTGGTGCACGCAGCGCATTA 50 102 0 CTGGTGCACG 0.891466 -199 ********** Masking position 6 Map Score: 14.8592 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 503 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 ACGCCTCCGGAAGGTGCGAACAAGTCCCTGA 4 20 0 AAGGTGGAAC 0.792864 -164 CGATTGTGTGATGATGTGGATACAAAAAATT 7 39 0 ATGATGGGAT 0.653608 -262 TTTTGGCCGGGCGGTGGGGATGTTTAGCCGG 8 40 0 GCGGTGGGAT 0.958875 -261 AACAATACAAACTGTGTGGATTTATCTTTTA 8 95 0 ACTGTGGGAT 0.912007 -206 TGTAGCGTAAAATGTGTGGATGTTAATTATC 11 145 1 AATGTGGGAT 0.840647 -80 CTGATTCGTTACGGTGAGAATAGCAAAAGGG 21 41 0 ACGGTGGAAT 0.955946 -29 TCGAGCGAAGATGGTGGGGATCCCTGA 32 133 1 ATGGTGGGAT 0.963367 -17 AGTACTAAGGAAGGTGCGAACAAGTCCCTGA 41 20 0 AAGGTGGAAC 0.792864 -188 GCTATTTATGGTGCGGATGTCGTGTTTT 46 8 1 ATGGTGGGAT 0.963367 -293 ATTTACACCAACGGTGAGAATCCACACACAA 49 65 0 ACGGTGGAAT 0.955946 -236 CATCAGTGTAACAGTGCGGATCCTCCATAAA 49 157 0 ACAGTGGGAT 0.854603 -144 TCAACGTTATGAGGTGGGGATGCCGTACTAA 49 192 0 GAGGTGGGAT 0.922285 -109 ****** **** Masking position 10 Map Score: 9.0636 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 97 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 CACGGATTTCCGTGCCCATTTCACAAGTTGGCTG 3 25 1 CTGCATTCAC 0.71756 -26 ATGAAAAAATCGTGCCAGTTTTGCAACTCCTTGA 7 224 0 CTGCGTTTGC 0.983242 -77 CGCCCGGTGTCCTGCCGGTGTCGCAAGGAGGAGA 8 267 1 CTGCGTTCGC 0.94454 -34 TGGCTGAAGACTGGGCGAAATTGCCGCGCTTGTA 11 84 1 CGGCAATTGC 0.942567 -141 TGCCCTGTTTCAGGGCAATTTTGCAACCGCGATC 17 20 1 CGGCATTTGC 0.972565 -246 TCTTCAACTTCAGGACAATAATGCAACGTCTTAT 17 119 1 CGGCATATGC 0.777239 -147 AAATAGTTGCCCTGTCAGACTTGCAGGCAGACTT 18 71 0 CTGCGATTGC 0.964492 -24 AGCAAAGCTCCCTGCCAATGTTACAGCAGAGAGC 24 23 0 CTGCATTTAC 0.897464 -43 GGGTTGAAAGCGCGACTAAATTGCCTGTGTAAAT 31 116 0 CCGCAATTGC 0.823354 -55 TTATCAACCGCGGGCCTACCTTACCTGATTGCGC 33 26 1 CGGCACTTAC 0.572713 -114 AAATAATCCACCTGTCTGTCTTGCAGGTGTCGGT 39 33 1 CTGCGTTTGC 0.983242 -66 ATTACCACTTCTTGACCATTTTGCATAAACACCA 41 67 0 CTGCATTTGC 0.979707 -141 CCTGGAACTGCGTGTCTGTATTGCTCACAAATCA 47 121 0 CTGCGTTTGC 0.983242 -52 AGTTTAATCCTGACTGAGTTGGGAAAACCATC 50 279 0 CTGCGATTGG 0.710197 -22 * ** * ** **** Masking position 6 Map Score: 12.9451 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 197 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 GACCGATCGAGCACAAATTTTGAGAGATAT 1 108 1 GCACAAATTT 0.900299 -88 AGGCGCAAAAGCCCGATTTTCTGTTCTTCT 1 156 0 GCCCGATTTT 0.848692 -40 CTCTTTTGGGGCACGGATTTCCGTGCCCAT 3 14 1 GCACGGATTT 0.877738 -37 TGTGTTGAGTGCACAATTTTAGCGCACCAG 7 116 1 GCACAATTTT 0.933913 -185 AAAACGTGATGCACGATTTATAGGGCAATA 7 177 0 GCACGATTTA 0.79099 -124 TGCAAAACTGGCACGATTTTTTCATATATG 7 233 1 GCACGATTTT 0.972649 -68 CAGTCTTCAGCCACAAATTTTGGTTGCGGG 11 67 0 CCACAAATTT 0.638632 -158 AATGAGGGGCGCACGAAATTGCTGCGCGCC 14 260 0 GCACGAAATT 0.707451 -41 ATGTGTCCCACGATTTTACGCCCTGTC 20 149 0 CCACGATTTT 0.874371 -17 GGGGAAAATGGCAGGGTTTTCTCTTTGTGC 46 223 0 GCAGGGTTTT 0.687387 -78 TCAATACATTGCAGAATTTTCGTAGGCCTG 48 68 0 GCAGAATTTT 0.734446 -34 TATTGAATTTGCACGATTTT 48 92 1 GCACGATTTT 0.972649 -10 TGGAGTAGCACAAATTTCTCTGCTGCA 49 8 1 GCACAAATTT 0.900299 -293 ********** Masking position 9 Map Score: 9.71813 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 200 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 GATCTCATATCAGGGACTTGTTCGC 4 6 1 CATATCAGGG 0.975346 -178 GTAAATAATCAAATTCAGGGTAATTAATGG 6 97 0 AAATTCAGGG 0.867728 -42 TTACATTGCGCAAATGAGGGGCGCACGAAA 14 272 0 CAAATGAGGG 0.823499 -29 GCGGGAGTTGCAAGTCAGGGTGCCAGACCG 18 29 0 CAAGTCAGGG 0.921514 -66 ATGCTCGGAACATTTCAGGCTGTAGCCAAC 23 19 1 CATTTCAGGC 0.78181 -64 CACCCCATTTAATATCAGGGAACCGGACAT 34 17 0 AATATCAGGG 0.928396 -270 CGGAGTTAATCATTTCAGGGGAAGAAGCGA 34 93 1 CATTTCAGGG 0.96103 -194 TTTTTTGACAAAAATCAGGGTTTATGCTGA 40 12 1 AAAATCAGGG 0.913225 -177 GATCTCATATCAGGGACTTGTTCGC 41 6 1 CATATCAGGG 0.975346 -202 ********** Masking position 5 Map Score: 7.03281 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 60 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 TCTGTCTTGTAACAGAAGAACAGAAAATCGGGCT 1 143 1 ACAGAAAAGA 0.895992 -53 TTAATAAACAACCAGATGAAAAGAAAGGGTTAAT 2 74 0 ACAGAAAAGA 0.895992 -146 GGGATTAATAATCAGATACAAAAAGGGCCGCCAG 4 57 0 ACAGACAAAA 0.729108 -127 TGCTATCTCCAGCTGATTAAGTAAATTTTTTGTA 7 16 1 ACTGAAATAA 0.709566 -285 TTAGCGTAAAACCTGATGAAAAAACAATCTTTAT 7 74 0 ACTGAAAAAA 0.792678 -227 GTGGAGAGCGAACACATCAACAAAATGCCGACGA 10 42 0 ACACAAAAAA 0.769571 -143 CGTCTGAATCACCAGAATAAATAAAGTCGGTGAT 12 156 1 ACAGAAATAA 0.915996 -145 TGGCTTGAAGATCAGAGGAAGAAAAGATGCGAGC 14 30 0 ACAGAAAAAA 0.944643 -271 GGCGCATTCTAACAGAAAAAGAAAACGTTTGCGT 20 104 0 ACAGAAAAAA 0.944643 -62 AACAATAGCGAACAGACAAAAAGAATACGCAAAA 30 54 0 ACAGAAAAGA 0.895992 -43 ACGTAACGATAACACATAAAGTAAAGTTTTCAAT 31 63 1 ACACAAATAA 0.680925 -108 TACCTGTTATACCAGATCAATTAAGCAACACCCC 45 53 0 ACAGAAATAA 0.915996 -69 TACCATAATTAACGGAATAATTAACTATTGCGAA 46 181 0 ACGGAAATAA 0.672504 -120 * **** ** *** Masking position 6 Map Score: 7.58236 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 113 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 AACGCTCAGATTGCGTACCGCTTGCGAACCCG 2 117 1 TTGCGCCGCT 0.915551 -103 ATAAGATAATATTCGAAACGCTGGCGGGTTCG 2 141 0 ATTCGACGCT 0.969791 -79 TGTGCAAAAGTTTCACTACGCTTTATTAACAA 8 127 1 TTTCAACGCT 0.874341 -174 CACATTATTCTTTCGCGACGCTCTTTAATTGT 12 83 0 TTTCGACGCT 0.942968 -218 TGATCAAAACATTCATTACGCTGATGTGGGGG 14 171 1 ATTCAACGCT 0.931081 -130 TCTGCCATTCAATCGAAACGCTGCGATTCAAC 17 73 1 AATCGACGCT 0.746119 -193 GTATCCGCTGATTCGTTACGGTGAGAATAGCA 21 47 0 ATTCGACGGT 0.893629 -23 GGGGCACAAGATGCGCCCCGGTAAGA 27 5 0 ATGCGCCGGT 0.846357 -40 ATCGATATTTTTTCAGAATGCTCATTAAAATA 32 96 0 TTTCAATGCT 0.689661 -54 CTGATTGCGCATTCACAACGCTTTCAGAAAAG 33 50 1 ATTCAACGCT 0.931081 -90 TTTGCAGCTTTTGCGTGATGCTTATGAAGCAA 34 162 1 TTGCGATGCT 0.851379 -125 GCTGGTGTTTATGCAAAATGGTCAAGAAGTGG 41 65 1 ATGCAATGGT 0.550541 -143 AAAGCTTATAATGCGATCTGCTTCACTAAAGT 45 15 0 ATGCGCTGCT 0.870518 -107 CATTCATAATATTCATAATGCTCGTGAATAGT 46 101 1 ATTCAATGCT 0.811847 -200 AAAATGCCTGATGCGCTCCGCTTATCAGGCCT 48 43 1 ATGCGCCGCT 0.954649 -59 ***** ***** Masking position 12 Map Score: 11.72 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 275 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 GATGCCCGCGCCGGGCGCTTAATAGCGGGT 4 92 0 CCGGGCGCTT 0.976365 -92 GATTAGGGTGAGGGGCGCAAACCCGCTCCG 6 64 1 AGGGGCGCAA 0.862586 -75 CGGCAGGACACCGGGCGCTTATGGTCGGCA 8 254 0 CCGGGCGCTT 0.976365 -47 TGCGCAAATGAGGGGCGCACGAAATTGCTG 14 266 0 AGGGGCGCAC 0.902939 -35 TCATCCTGTTCGGGGCGCATTCTAACAGAA 20 121 0 CGGGGCGCAT 0.987466 -45 TTTTATCTTTGGGGACGCATAATGCCATTT 22 100 0 GGGGACGCAT 0.836644 -56 TCTTACCGGGGCGCATCTTGTGCCCC 27 7 1 CGGGGCGCAT 0.987466 -38 CACATTGATGACGGTCGCATGAAAAAATGA 32 66 1 ACGGTCGCAT 0.757024 -84 ATCGTAAGGTACGGACGTTTCGACATCGTG 35 73 0 ACGGACGTTT 0.468364 -47 GCCTGATAAGCGGAGCGCATCAGGCATTTT 48 43 0 CGGAGCGCAT 0.84969 -59 CGCAAATACCACGGGCGTTTGCGAGGATCA 50 39 0 ACGGGCGTTT 0.851157 -262 TTCTTCATAAGGGGGCGTTTTTGTTTTCAT 50 196 1 GGGGGCGTTT 0.842044 -105 ********** Masking position 6 Map Score: 9.50045 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 159 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 ACCACGGTAACAGGAACAACAT 6 127 1 CAGGAACAAC 0.655535 -12 GTGTCGCAAGGAGGAGAGACGTGCGAT 8 284 1 GAGGAGAGAC 0.794151 -17 CGTAGAGTTTCAGGATAAAGAGGGAGATCT 9 70 1 CAGGATAAAG 0.841086 -64 GGAGCAGAAACAATGTGGTAT 10 2 1 GAGCAGAAAC 0.907969 -183 AGTAACCTGACAGCAGAAAGTCTCCGAGCC 12 208 1 CAGCAGAAAG 0.894667 -93 GTGGCTTAACGAGGAAAAAGACGT 19 23 1 GAGGAAAAAG 0.625821 -14 GCCAATGTTACAGCAGAGAGCATGAAGAAG 24 14 0 CAGCAGAGAG 0.768592 -52 TGTCGCAGAGGAGAAAACGGGGCACAA 27 28 0 GAGGAGAAAA 0.73571 -17 TATCGCAAACGAGCATAAACAGGATCGCCA 31 13 0 GAGCATAAAC 0.860096 -158 CATCCTCGCTGAGGATCAACTATCGCAAAC 31 33 0 GAGGATCAAC 0.857594 -138 TGATAATAACGAGGATCAAAT 33 2 0 GAGGATCAAA 0.629521 -138 TTCCCGGAACCAGCATCAAGAACTCGCCGT 34 123 0 CAGCATCAAG 0.838309 -164 GTATAAAAATCAGCATAAACCCTGATTTTT 40 21 0 CAGCATAAAC 0.860096 -168 CAGCTATTTGCAGCAGAGAAATTTGTGCTA 49 16 0 CAGCAGAGAA 0.521198 -285 GGGCGTTTGCGAGGATCAACGACTCATGCG 50 27 0 GAGGATCAAC 0.857594 -274 CATTACGTTGCAGCAGCAAGTACAGCTTGC 50 77 0 CAGCAGCAAG 0.892707 -224 ********** Masking position 5 Map Score: 5.92856 Number of sites scoring better than the average of aligned sites = 509 Number in coding regions = 460 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 13 AAAACGCACTGGCAGTTCCCTCTCCCCTAT 6 26 1 GGCAGTTCCC 0.74483 -113 ACTTTTCAGACGCGGGTCCAGCCATACCAA 10 83 0 CGCGGGTCCA 0.807787 -102 AGAATCGTCTGGCGGTTGCCCGGAAAGTAC 12 31 0 GGCGGTTGCC 0.870707 -270 CTCCGCTGTTGCCCTGTTTCAGG 17 4 1 CGCTGTTGCC 0.766091 -262 AGGATTTGATCGCGGTTGCAAAATTGCCCT 17 31 0 CGCGGTTGCA 0.94039 -235 AAAGTAACTCCGCGGTTCGACCACTTTTTT 22 11 1 CGCGGTTCGA 0.964529 -145 TCTGTCTGAACCTGGTTCGATGCCAGTTTT 22 126 0 CCTGGTTCGA 0.522198 -30 GGGTAATCTGCGCGCTTCGCGCAGCGCTGG 26 22 0 CGCGCTTCGC 0.844207 -185 CCGAAGTCCGCGCGGTTCGCCATGATTTCG 26 50 1 CGCGGTTCGC 0.98476 -157 AACATACCGGCGTCGTTGCCGATAAGTCTC 26 165 1 CGTCGTTGCC 0.48951 -42 GGGGTTATGTCCGGTTCCCTGATATTAAA 34 10 1 TCCGGTTCCC 0.644792 -277 ATCAAGAACTCGCCGTTCGCTTCTTCCCCT 34 109 0 CGCCGTTCGC 0.939017 -178 AATACAGACACGCAGTTCCAGGCTGCGGGT 47 133 1 CGCAGTTCCA 0.87241 -40 TGGTGTAAATCCCGGTTGGCTGTATTGACG 49 86 1 CCCGGTTGGC 0.924942 -215 GACCTGAGTACCCAGTTCGATAACCCTGTT 50 142 0 CCCAGTTCGA 0.692087 -159 ********** Masking position 7 Map Score: 8.17733 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 369 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 TCTCCCTCTCCCTGTGGGAGAGGGCCGGGGT 1 20 1 CCTGTGGAGA 0.825119 -176 GGGCGCAAACCCGCTCCGGGGCCATTAATTA 6 76 1 CCGCTCGGGG 0.656298 -63 GCGCACTCCTGTAGGCGAAGAGAGAAAA 9 116 0 CCTGTGGCGA 0.879494 -18 AGTCTCCGAGCCTGTGCAGGGTCCCAATCCG 12 226 1 CCTGTCAGGG 0.882345 -75 ACTTTTTATGCCTTTGCGGCATCGGGCAATG 20 14 0 CCTTTCGGCA 0.504043 -152 GCCCTGTCATCCTGTTCGGGGCGCATTCTAA 20 126 0 CCTGTCGGGG 0.991293 -40 ACATTCATGGTCTGTTGGGGGCAAAAATGGC 22 76 1 TCTGTGGGGG 0.938815 -80 GTTTGTGTTACCTGTATGAGACGAGAGTTAA 25 78 0 CCTGTTGAGA 0.695537 -21 ACAACCCCGTCCTGTACGGGGTTTGTTTTTT 30 13 1 CCTGTCGGGG 0.991293 -84 AACCTATTACTCTGTCGGCGGCGGGTTTATT 35 15 1 TCTGTGGCGG 0.785247 -105 TGATAGTACTCCTGTCCGGCATTGTTA 42 7 0 CCTGTCGGCA 0.934055 -178 TTATAAGCTTTCTGTATGGGGTGTTGCTTAA 45 36 1 TCTGTTGGGG 0.881366 -86 GTTCGATAACCCTGTTTGGCGGGATTTCAAA 50 127 0 CCTGTTGGCG 0.921148 -174 ***** ***** Masking position 5 Map Score: 6.05698 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 199 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 TAACGCTACACCTGTAAAACGCAC 6 2 1 ACTACACCTG 0.968703 -137 AAGGCAAACCATCGCTTCACGTGAGATGCTGAA 8 204 0 ACTTCACGTG 0.806126 -97 CTGCGATTCAACCGCTATACCTGCTATCTTCAA 17 93 1 ACTATACCTG 0.960066 -173 TACGTATCCTTATACCTGAAATCTTCGC 25 6 1 ACTATACCTG 0.960066 -93 TTTCAGCAGTTCACCTGCTGAGTGGAA 35 103 0 ACTTCACCTG 0.961719 -17 TATAAAACCTCTTCGCCTGAATTAAATAT 39 80 0 ACTTCGCCTG 0.854434 -19 TAAACGATATACCTTTATACCTGTTATACCAGA 45 71 0 ACTATACCTG 0.960066 -51 TTTGTCAACAATCTGTATACCCGGTGGCGCTGT 47 26 1 ACTATACCCG 0.848875 -147 TCAACCTCGAAACGTTTTACATGGTGATTAACC 50 226 0 ACTTTACATG 0.685442 -75 * * ******** Masking position 6 Map Score: 3.12717 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 41 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701