AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_bsub_reg_300.orf -o00561_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 glpQ 98 glycerophosphoryl diester phosphodiesterase #2 glpT 296 glycerol-3-phosphate permease #3 purT 230 phosphoribosylglycinamide formyltransferase 2 #4 mpr 143 extracellular metalloprotease #5 ybfK 165 similar to carboxylesterase #6 pssA 195 phosphatidylserine synthase #7 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #8 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #9 ycbD 29 similar to aldehyde dehydrogenase #10 cwlJ 300 alternate gene name: ycbQ #11 ycbR 105 similar to toxic cation resistance protein #12 phoD 278 phosphodiesterase/alkaline phosphatase D #13 yccC 216 similar to asparaginase #14 lipA 162 lipase #15 ddlA 174 D-alanyl-D-alanine ligase A #16 phoB 300 alkaline phosphatase III #17 lipB 272 lipase #18 yhxA 300 similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase #19 glpP 27 transcription antiterminator #20 glpF 178 glycerol uptake facilitator #21 glpD 140 glycerol-3-phosphate dehydrogenase #22 phoA 300 alkaline phosphatase A #23 yhdW 233 similar to glycerophosphodiester phosphodiesterase #24 ylbQ 159 similar to pyrimidine-thiamine biosynthesis #25 yllA 70 yllA #26 yllB 125 similar to hypothetical proteins #27 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #28 ftsL 39 cell-division protein #29 spoVD 116 penicillin-binding protein #30 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #31 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #32 spoVE 60 spoVE #33 murG 122 UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase #34 flgB 300 flagellar basal-body rod protein #35 fliF 45 flagellar basal-body M-ring protein #36 fliH 117 flagellar assembly protein #37 fliK 160 fliK #38 flgE 21 flagellar hook protein #39 fliL 251 flagellar protein #40 fliM 33 flagellar motor switch protein #41 cheY 25 two-component response regulator #42 flhA 32 flagella-associated protein #43 cheW 21 cheW #44 sigD 22 RNA polymerase sigma-28 factor (sigma-D) #45 ylxL 28 ylxL #46 rpsB 143 ribosomal protein S2 #47 tsf 101 elongation factor Ts #48 smbA 145 uridylate kinase #49 yluA 130 similar to hypothetical proteins #50 pgsA 300 phosphatidylglycerophosphate synthase #51 pksF 300 pksF #52 yphC 300 similar to hypothetical proteins #53 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #54 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #55 yqiS 124 similar to phosphate butyryltransferase #56 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #57 yqfF 78 yqfF #58 yqfC 56 yqfC #59 yqfB 24 yqfB #60 yqfA 21 yqfA #61 yqeZ 130 yqeZ #62 rpsU 163 ribosomal protein S21 #63 blt 116 multidrug-efflux transporter #64 bltD 168 spermine/spermidine acetyltransferase #65 yraG 248 similar to spore coat protein #66 adhA 300 NADP-dependent alcohol dehydrogenase #67 msmR 217 transcriptional regulator (LacI family) #68 msmE 33 multiple sugar-binding protein #69 gbsA 198 glycine betaine aldehyde dehydrogenase #70 tpi 30 triose phosphate isomerase #71 pgk 300 phosphoglycerate kinase #72 yvfL 39 similar to maltodextrin transport system permease #73 yvfK 140 similar to maltose/maltodextrin-binding protein #74 lacR 179 transcriptional regulator (LacI family) #75 yvfI 300 similar to transcriptional regulator (GntR family) #76 tagD 300 glycerol-3-phosphate cytidylyltransferase #77 ywnE 242 similar to cardiolipin synthase #78 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #79 aldX 142 aldehyde dehydrogenase Motif number 1 AGTGCTTATCTATAAGGAGGAGAAATC 1 82 1 TATAAGGAGG 0.831095 -17 TTGTTTTTCGGGAAAGGAGGCACGCCACAC 2 243 1 GGAAAGGAGG 0.934896 -54 GCAATAAATAAAAAAGGCAGTTCCCTTAAA 5 24 0 AAAAAGGCAG 0.663059 -142 AACCCGGAGGAAAAAGAAGAAG 5 154 1 AAAAAGAAGA 0.602665 -12 CGGTTTATTGAAAAAGACGGATATATACTG 7 205 1 AAAAAGACGG 0.639131 -96 TATACACAAATAACAGGAGGTTATGTTG 8 209 1 TAACAGGAGG 0.818529 -18 GAAAAGACAAAAAAAGAAGGATATGACAAC 13 104 1 AAAAAGAAGG 0.903909 -113 AGAAAAGAAGGCGAATAAGCC 14 2 1 GAAAAGAAGG 0.849267 -161 AAAAGCCAAAAAAAAGAAGGCTTATTCGCC 14 20 0 AAAAAGAAGG 0.903909 -143 TTTGTTACAAAAAAAGGAGGATATT 14 148 1 AAAAAGGAGG 0.978889 -15 AAATGGCATTGAAAAGGAGATGTGACAT 15 9 0 GAAAAGGAGA 0.817453 -166 CCTTATTATAGAAAAGGGAGGAAGGGAACA 17 84 1 GAAAAGGGAG 0.669156 -189 TTTCTTCTTGAGAAAGGGGATGTTTTATTA 18 155 1 AGAAAGGGGA 0.555349 -146 TTACCGTGACAACAAGGAGGAAACGTA 21 124 1 AACAAGGAGG 0.675185 -17 ACGGAATACATTAAAGGAGGC 22 290 1 TTAAAGGAGG 0.79001 -11 TATAATAGCAAAAAAGGAGGCGAGATC 23 8 0 AAAAAGGAGG 0.978889 -226 TATTTATTGGAGAAAGGAAGTTCTAGAAG 25 52 1 AGAAAGGAAG 0.843856 -19 TTCATCCTGATAAAAGGTGGGACCAACACA 27 48 1 TAAAAGGTGG 0.718565 -22 AACGCAAAATTAAAAGGAGGTCATCAGCCT 28 20 1 TAAAAGGAGG 0.975689 -20 GAAGGCATAAAAAAAGAAAGCCTGCATAAC 29 24 0 AAAAAGAAAG 0.679532 -93 CGTTTGAAAGAAACAGGAGGAGAAAAGGAC 31 92 1 AAACAGGAGG 0.839003 -21 GCTTCATGTTAGACAGGAGGCTTGGAAATA 33 17 0 AGACAGGAGG 0.72933 -106 AATGCCGAAAAGAAAGGAGAAAAAACAGAA 34 68 1 AGAAAGGAGA 0.794483 -233 AAGTTTGTAGTAAAAGAAGATGAAGAAGCT 39 158 1 TAAAAGAAGA 0.567626 -94 TTTTTCGATTTAAAAGGAGAGAAAAAACAG 42 12 1 TAAAAGGAGA 0.866151 -21 AAAAAGGTGATAAAAGGCAGTCCCTCTTAT 47 26 0 TAAAAGGCAG 0.630076 -76 TGTTTAAACATATAAGGAGGAATACAA 47 85 1 TATAAGGAGG 0.831095 -17 GGCAGCTCTTTAAAAGAAGGAACGCTGAAA 50 52 1 TAAAAGAAGG 0.890614 -249 GATTGTAAATAAAAAGGAAGAAAAGTCATC 50 228 1 AAAAAGGAAG 0.912679 -73 GCGGCTGGATTGAAAGGAAGGGTACT 52 285 1 TGAAAGGAAG 0.82387 -16 TTTTAAAAGCATAAAGGAGGGGCTTGA 54 57 1 ATAAAGGAGG 0.812966 -17 ACTTGCATAATAAAAGGCGGAGTCGAAACA 55 89 1 TAAAAGGCGG 0.883125 -36 AGTCGAAACAAGAAAGGTGGTAACAG 55 109 1 AGAAAGGTGG 0.604003 -16 GTGTATGATTTGAAAGGAGGTTCTAACACT 58 11 0 TGAAAGGAGG 0.954026 -46 ACACATGAGATGAAAGGGGGTTCTTTTTGT 58 37 1 TGAAAGGGGG 0.870203 -20 GCACTTATTATAAAAGGAAGGAGGGATACA 61 105 1 TAAAAGGAAG 0.900464 -26 GTCTATATAATGAAAGAAAGGGGTTG 62 7 0 TGAAAGAAAG 0.486906 -157 TTCAATTGAGTAAAAGGGGAATTCAG 63 101 1 TAAAAGGGGA 0.676447 -16 CGGGATAAGAAAAAAGGAGAATGTAGT 64 152 1 AAAAAGGAGA 0.882026 -17 GTAACGTTGATAAAAGGAGGTTACATCAAT 65 229 1 TAAAAGGAGG 0.975689 -20 GAAGTAAGCGAATAAGGAAGGGTGATGGG 67 10 0 AATAAGGAAG 0.561686 -208 TCATCACGATGATAAGGAGGAAAAG 68 19 1 GATAAGGAGG 0.772986 -15 TTTTCTAAAGGAAAAGAGGGTCAGT 69 6 0 GAAAAGAGGG 0.64543 -193 TCAAAACTGCTATAAGGAAGTGGAACAG 70 13 1 TATAAGGAAG 0.525876 -18 ATGGAAAAAGGGAAAGGGAGTCCGTCCCCT 71 64 0 GGAAAGGGAG 0.511192 -237 GACATTTGTGAAAAAGAAAGTAAAATATTT 74 121 1 AAAAAGAAAG 0.679532 -59 GAAACATCAAATAAAGGGGGAGGATTAT 77 9 0 ATAAAGGGGG 0.584079 -234 CATACCTTACAAAAAGGAGAAACGGA 78 152 1 AAAAAGGAGA 0.882026 -16 ATAGGTCCGAGAAAAGAAGAAAGCAAATGA 79 110 1 GAAAAGAAGA 0.476021 -33 ********** Masking position 5 Map Score: 43.4947 Number of sites scoring better than the average of aligned sites = 1484 Number in coding regions = 866 Number in noncoding regions = 618 Number of orfs with sites within 600 bp upstream = 670 Fraction of orfs with sites within 600 bp upstream = 0.107613 Motif number 2 CTTTAAACAGCCTCCCTCCAGATTTTTAT 2 10 1 GCCTCCCTCC 0.87271 -287 TTTGTCATCTCCCTCCTTTAGTGTCA 4 128 0 ATCTCCCTCC 0.859029 -16 CTTTCACATCCGCTCCTTCCCATATATCCT 8 145 0 CGCTCCTTCC 0.930802 -82 AAAACTTCTCCTGTCCCTCCGTCATCACTT 10 234 1 CTGTCCCTCC 0.858148 -67 TCAAGATCCCCTCTCTCCTCATTGATCG 12 261 0 CCCTCTCTCC 0.980472 -18 CTATTTCTCTCCTTACATCCAT 13 205 0 ATTTCTCTCC 0.426366 -12 ACAATACCTCTTTCCAACGTAATAC 16 6 1 ACCTCTTTCC 0.668627 -295 TTAGTACTATCGCTCTTTCCTTCTAAAACT 16 135 1 CGCTCTTTCC 0.865667 -166 CGGTTGTGTTCCCTTCCTCCCTTTTCTATA 17 90 0 CCCTTCCTCC 0.97233 -183 TACGTTTCCTCCTTGTTGTCAC 21 129 0 CGTTTCCTCC 0.805807 -12 TCTTGCCCCACTTTCTCTCCTTAACTCACC 26 102 0 CTTTCTCTCC 0.836551 -24 TGTCCTTTTCTCCTCCTGTTTCT 31 100 0 CCTTTTCTCC 0.810826 -13 TACTCGCCTCCCCTCCCTCC 39 1 0 CCCTCCCTCC 0.990548 -251 AATCTATCTCTCTCCTTGTGTTTCG 41 11 0 ATCTCTCTCC 0.744855 -15 ATTAAGATGACTTTTCTTCCTTTTTATTTA 50 233 0 CTTTTCTTCC 0.497814 -68 ATCCATAATGCGCTCTCTCCTCAAGGGATT 51 61 0 CGCTCTCTCC 0.958825 -240 ATGAGTTAAGCCCTTCCTCTGAAGGGTTTC 52 194 1 CCCTTCCTCT 0.559755 -107 GGCGGTGTATCCCTCCTTCCTTTTATAATA 61 110 0 CCCTCCTTCC 0.966669 -21 TCTCTTTCCCTCCCTCCGAATACACCA 62 147 0 CCCTCCCTCC 0.990548 -17 CTTTTCCTCCTTATCATCGT 68 24 0 CTTTTCCTCC 0.78176 -10 GACTCCCTTTCCCTTTTTCCATGAAGACCG 71 72 1 CCCTTTTTCC 0.823281 -229 TTAAAGAAACGCTCCTTCCTAATGTTAAA 76 282 0 CGCTCCTTCC 0.930802 -19 TCCGTTTCTCCTTTTTGTAAG 78 157 0 CCGTTTCTCC 0.708209 -11 ********** Masking position 4 Map Score: 25.4067 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 302 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 TTCCAACACGCCGTTTACATCCGTTTTTTA 1 37 1 CCGTTTACAT 0.820326 -62 TGAAAATTACCCGTTTACATTCGCTCCGGA 2 106 1 CCGTTTACAT 0.820326 -191 TATCATGATAGCGCTTTCTTAAATTATCAT 2 138 0 GCGCTTTCTT 0.892782 -159 ATTAATAAAAGCGCTTACAGATAGAGGCCG 8 179 1 GCGCTTACAG 0.908333 -48 GCTGAATGACGCGTTTTCTGCATATCCTGT 12 112 0 GCGTTTTCTG 0.818673 -167 TTAATGTTCAGCGCTTACAATCAGTTCACA 12 190 1 GCGCTTACAA 0.764573 -89 TAGAAGCAACCCGCTTACATCTTGAACAAT 16 41 0 CCGCTTACAT 0.901327 -260 TGAAGCCTAGCCGTTTTCTGTATGATATAG 18 21 0 CCGTTTTCTG 0.818673 -280 CACCGCTTTCATGCACTGATAC 20 3 1 CCGCTTTCAT 0.927971 -176 TTTAAATAAAGCGTTTACAATATATGTAGA 24 33 0 GCGTTTACAA 0.618791 -127 GTAAACATTGCCGTTTTCTATTATGCAAGA 48 112 0 CCGTTTTCTA 0.596727 -34 TTCAATCCAGCCGCTTTCATTTTTACATAA 52 269 0 CCGCTTTCAT 0.927971 -32 ATTATTGTAACCGCTTACTTTTATATGATA 67 138 1 CCGCTTACTT 0.855154 -80 CTTCCCTTGTCCGCTTTCATTATAGCGCTT 71 36 0 CCGCTTTCAT 0.927971 -265 CTATCACAGAGCGTTTTCTGAAAGCCGGTC 71 97 0 GCGTTTTCTG 0.818673 -204 TATCTTTAAAGCGCTTTCATTCCTACCGAA 73 108 1 GCGCTTTCAT 0.927971 -33 CTCTGTTCAGGCGCTTGCTGAGAGCTTTCA 75 220 1 GCGCTTGCTG 0.629778 -81 ACTCATATCTGCGTTTTCAGCAGGAATTTG 78 55 0 GCGTTTTCAG 0.874772 -113 ********** Masking position 5 Map Score: 17.1887 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 403 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 GTGTTTTCTGGCTCTTTTTGTTTTTCGGGAAA 2 226 1 GCTTTTTTTT 0.882049 -71 ATCCCCCTTTGCTGTTTGTGCTGGATGTGTGG 2 267 0 GCTTTTGTCT 0.711762 -30 GGACAAGGCCTGTTTTTTTCTTTCTCCGTAAA 4 33 1 TGTTTTTTTT 0.525486 -111 ATAAGAAATAGGTATTTTTTCTTACGAGACAA 5 95 1 GGTTTTTTCT 0.960647 -71 TCACATCCTCGCTTTTTATTTTGGGGAATCGG 7 156 0 GCTTTTATTT 0.499485 -145 CTGACCAGGCTGTTTTTTTGCTGCGCAGAATC 8 24 1 TGTTTTTTCT 0.76527 -203 CAAATTGAACGGTGTTTTTCTTTGAAAAGATG 11 26 1 GGTTTTTTTT 0.892378 -80 ATCTCCGTCAGCTCTTTTTTCTTTGATTATCT 11 78 0 GCTTTTTTCT 0.956551 -28 GAAATGGCTCGGTGTTTTTGCTTCTTTTTAAG 12 38 1 GGTTTTTTCT 0.960647 -241 CAATATCGTTACTATTTTTTCTGAAAATTAAA 17 196 0 ACTTTTTTCT 0.672343 -77 GGTTTGTTGTGGTTTTTTTATTCTCTTCTTCT 20 117 1 GGTTTTTTTT 0.892378 -62 GGTTATCCGCAGTTTTTTTATTTAAACAAACA 22 97 1 AGTTTTTTTT 0.435937 -204 TAGCAGAATTTCTGTTTTTTCTCCTTTCTTTT 34 75 0 TCTTTTTTCT 0.746211 -226 GCTGTTTTTTCTCTCCTTTTAA 42 21 0 GCTTTTTTCT 0.956551 -12 CTAATATAATGGTTTTTTTCCTCCGCTTAGGT 46 111 0 GGTTTTTTCT 0.960647 -33 AACATGAGAGGGTCTTTTCACTATTATCTATT 49 26 0 GGTTTTTCCT 0.71052 -105 GTTTACAGGGGGTTTTTTTGTTAATACTGTTG 49 55 1 GGTTTTTTTT 0.892378 -76 TTTAAGAATCGCTGTTTTTGCTCGTTCTTATG 65 142 0 GCTTTTTTCT 0.956551 -107 CTGGATCGCCGCTCTTTATTCTTTTAAAATGT 77 127 1 GCTTTTATCT 0.746059 -116 ATATGAGTTTGTTATTTTTTCTGACAAACCTT 78 77 1 GTTTTTTTCT 0.657935 -91 *** ***** ** Masking position 6 Map Score: 16.7559 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 161 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 GATTTCTCCTCCTTATAGATAAG 1 86 0 TTCTCCTCCT 0.873349 -13 GGATTCCTGGCTCTCCTCATCTCCATCCAA 2 178 0 CTCTCCTCAT 0.984092 -119 AAGATCCCCTCTCTCCTCATTGATCGTCTC 12 257 0 CTCTCCTCAT 0.984092 -22 CTATTTCTCTCCTTACATCCATATGA 13 201 0 CTCTCCTTAC 0.804905 -16 GTGCTGTGGTCTCTCCTCATCTCAGGACCG 21 49 0 CTCTCCTCAT 0.984092 -92 ATAACCACAGCTCTCCTCGAATATACTTTA 22 73 0 CTCTCCTCGA 0.925592 -228 GCCCCACTTTCTCTCCTTAACTCACCACTA 26 98 0 CTCTCCTTAA 0.875521 -28 GAGACCGTTCACTCCTTATTTAGGCTTGT 29 98 0 CACTCCTTAT 0.683166 -19 TGTCCTTTTCTCCTCCTGTTTCTTTCA 31 96 0 TTCTCCTCCT 0.873349 -17 AATCTATCTCTCTCCTTGTGTTTCG 41 7 0 CTCTCCTTGT 0.932072 -19 GCTGTTTTTTCTCTCCTTTTAAATCGAAAA 42 13 0 CTCTCCTTTT 0.775463 -20 ATAATGCGCTCTCTCCTCAAGGGATTATTT 51 57 0 CTCTCCTCAA 0.952064 -244 ATAACTTCTCCTCGTTTCTAT 60 7 0 TTCTCCTCGT 0.909456 -15 TGGAATGTTTTTCTCCTCATGAGTACTTAA 76 129 1 TTCTCCTCAT 0.941305 -172 ********** Masking position 4 Map Score: 13.0266 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 41 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TAGCTTGGATGGAGATGAGGAGAGCCAGGA 2 174 1 GGAGATGAGG 0.90887 -123 ACTAAAGGAGGGAGATGACAAA 4 132 1 GGAGATGACA 0.894889 -12 TTTTACAATTGGAGGTTTGGTTACACT 6 179 1 GGAGGTTTGG 0.735883 -17 ACTGTATAATGGAGACTACAGAATCATACA 7 40 1 GGAGACTACA 0.465786 -261 GAGATCAAGGGGAGGTGACGTG 10 289 1 GGAGGTGACG 0.965459 -12 AAGAGCTGACGGAGATGACAGA 11 94 1 GGAGATGACA 0.894889 -12 GCATTGAAAAGGAGATGTGACAT 15 4 0 GGAGATGTGA 0.787246 -171 TAGCAAAAAAGGAGGCGAGATC 23 3 0 GGAGGCGAGA 0.850908 -231 GCCCATACGAGGAGCTGACTTAGC 23 220 1 GGAGCTGACT 0.87535 -14 CAACAAAGGGGGAGATTTGT 24 1 0 GGAGATTTGT 0.495755 -159 ATGTTAGACAGGAGGCTTGGAAATACATTC 33 12 0 GGAGGCTTGG 0.554389 -111 GGAGGGAGGGGAGGCGAGTAATCGCTTCT 39 10 1 GGAGGCGAGT 0.868624 -242 GACAGAATACGGAGGTGAGGAAA 40 21 1 GGAGGTGAGG 0.953396 -13 CCATTCGAGGAGGTGTCTCAC 43 9 1 GGAGGTGTCT 0.923157 -13 CTCAAATCCAGGAGCTGTCTGATGCCTT 50 9 0 GGAGCTGTCT 0.806581 -292 AGTTGAGCTAGGAGCTGACTCTGTAGACAG 51 180 1 GGAGCTGACT 0.87535 -121 TCACAGAATCGGAGATGACGTGTATTTGAT 52 112 1 GGAGATGACG 0.931632 -189 GTTGATAAAAGGAGGTTACATCAAT 65 234 1 GGAGGTTACA 0.80021 -15 TCTAATGATTGGAGGTGTCTTTT 79 4 0 GGAGGTGTCT 0.923157 -139 ********** Masking position 3 Map Score: 14.8667 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 208 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 7 GAAAAATAAATTTTTATTAAAAAAGATAAAATT 3 163 0 TTTTTATAAA 0.553031 -68 TGTTTTTTTCTTTCTCCGTAAAAGTTTTATCAT 4 43 1 TTTCTCCAAA 0.832661 -101 ACAGGAAAAATTTTTCTCCAATAAGCATGATAA 6 108 0 TTTTTCTAAA 0.923924 -88 ATTTACCGCTTTTTTATAAAATATCAGAAAATA 8 70 1 TTTTTATAAA 0.72061 -157 CTTTTATTAATTTTTCTTTCACATCCGCTCCTT 8 157 0 TTTTTCTCAA 0.891668 -70 AAACATCCCCTTTCTCAAGAAGAAAGAGGATGC 18 147 0 TTTCTCAAAA 0.707086 -154 GAGGTAAAGATTTTTCTGAAAAATGAATGCTTT 22 146 1 TTTTTCTAAA 0.552581 -155 ACTGGTGAATTTTTTCTGCCATATCGGAATGGT 23 144 0 TTTTTCTCAA 0.891662 -90 GCTTTTTCGGTAACATGCTATACTC 25 3 1 TTTTTCGAAA 0.59065 -68 ATATCAGCATTTTTTCTGCAATAAAAGAATAGG 30 20 0 TTTTTCTAAA 0.923558 -156 CCAGTCTAAGTTTCTCTATAACATAACGATAAC 33 88 0 TTTCTCTAAA 0.92245 -35 AGTCTTTCTATGTAATAATTTTAATAA 34 5 1 TTTCTATAAA 0.716628 -296 AAATTTTGCATTTTTCTTCAAAAAGTTTCAAAA 34 36 1 TTTTTCTAAA 0.917838 -265 GAATCATCTATTTCTCCACAAAAGGAAAAAAGA 36 24 1 TTTCTCCAAA 0.832933 -94 AAAAGAAAACTTTCTATACAAGAGGTGCGTATT 36 51 1 TTTCTATAAA 0.716633 -67 AGATCGCAGCTTTCTACCGAAAAATACAAATAT 39 198 1 TTTCTACAAA 0.514567 -54 ATATTACACATTTTTCTTGAAAAAAGGTGATAA 47 43 0 TTTTTCTAAA 0.917838 -59 CAAACCTTTTTTTCTCTTGCATAATAGAAAACG 48 98 1 TTTCTCTCAA 0.889639 -48 GTGTGCAAATTTTTTCATACAAAGGGGTATCGG 56 129 1 TTTTTCACAA 0.596733 -24 TTCCCCTTTATTTTTCCAACATAAATCACATCA 67 62 1 TTTTTCCCAA 0.775278 -156 AAACATTAAATTTTTATTTAACAAACTTTATTT 69 159 1 TTTTTATAAA 0.720785 -40 AACGCGGTCGTTTCTCTATCACAGAGCGTTTTC 71 109 0 TTTCTCTCAA 0.889639 -192 TCTGCCCGTATTTTTCACGAAGAATCTGGATCG 77 102 1 TTTTTCAAAA 0.71137 -141 AGTTTGTTATTTTTTCTGACAAACCTTGCGCGA 78 82 1 TTTTTCTCAA 0.851428 -86 ******* ** * Masking position 5 Map Score: 21.7781 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 271 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 8 AAGATTGGCATTCATTTTTCAAAAGGTAAC 6 24 1 TTCATTTTTC 0.818562 -172 GTGTTTTTGCTTCTTTTTAAGATCATGTGA 12 49 1 TTCTTTTTAA 0.587183 -230 TGTCATATCCTTCTTTTTTTGTCTTTTCAT 13 102 0 TTCTTTTTTT 0.857896 -115 CGAATAAGCCTTCTTTTTTTTGGCTTTTTA 14 22 1 TTCTTTTTTT 0.857896 -141 ATGTAAAGCATTCATTTTTCAGAAAAATCT 22 153 0 TTCATTTTTC 0.818562 -148 TACGCTGAGTGTCTTTTTTTAGTTATACGC 23 100 1 GTCTTTTTTT 0.831824 -134 AGTTCAGGGTTTCTTTTTATGGGTAAACAG 26 36 1 TTCTTTTTAT 0.718267 -90 GCTCCACAACTTCATTTTACACTGTTTACC 26 57 0 TTCATTTTAC 0.65579 -69 TATGCAGGCTTTCTTTTTTTATGCCTTCAG 29 26 1 TTCTTTTTTT 0.857896 -91 TTAGGCTTGTTTCATTTTATGCCTGAATTT 29 78 0 TTCATTTTAT 0.647493 -39 TTCTAATTCGTTCTTTTTATCATTGAAGTC 30 137 0 TTCTTTTTAT 0.718267 -39 TTCTTTTTTCCCCCAGTCTA 33 113 0 TTCTTTTTTC 0.862294 -10 ATAGAAAGTTTTCTTTTTTCCTTTTGTGGA 36 38 0 TTCTTTTTTC 0.862294 -80 TATAGGTTTCGTCTTTTTTCAGCGTTCCTT 50 68 0 GTCTTTTTTC 0.836875 -233 GATCAGTTATGTCTTTTTTATAGGTTTCGT 50 86 0 GTCTTTTTTA 0.734008 -215 GGGAGCACCTGTCTTTTTTTGCAATGACCA 52 28 1 GTCTTTTTTT 0.831824 -273 TCCAGCCGCTTTCATTTTTACATAAATTTT 52 264 0 TTCATTTTTA 0.708173 -37 GGCAAAGCCATTCATTTTTAAAAGCATAAA 54 42 1 TTCATTTTTA 0.708173 -32 CCGTTATCGGGTCATTTTTATGATTGCTTA 57 30 1 GTCATTTTTA 0.665346 -49 TAAGAGAGATGTCTTTTTTTATACATAAAA 61 35 1 GTCTTTTTTT 0.831824 -96 TATCAAAGGTTTCATTTTTTTATGTATAAA 61 52 0 TTCATTTTTT 0.81307 -79 ATAAATCAGGTTCATTTTAAATGGTTTTTT 66 161 1 TTCATTTTAA 0.506121 -140 AGGACACTAAGTCATTTTTTATTTAGGTAA 73 20 1 GTCATTTTTT 0.780873 -121 AAATGGTTCAGTCTTTTTACATGGCAGCCA 74 74 1 GTCTTTTTAC 0.684195 -106 ********** Masking position 5 Map Score: 22.8419 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 712 Number in noncoding regions = 243 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 9 CGAAAAACAAAAAGAGCCAGAAAACACCCCT 2 222 0 AAAGGCCAGA 0.711742 -75 ACCAAACAGCCGGCTGACCAGGCT 8 4 1 AAACGCCGGC 0.935653 -223 TTCCGCTGTCGAAGCGCCGCAGCCTCAATTC 10 122 0 GAAGGCCGCA 0.644331 -179 AAAATAGGCCGAATGGGCGGCTTGCAAACGA 12 82 1 GAATGGCGGC 0.896783 -197 CAAGAATAATGAACTGGCACCCTTAAATAAT 16 183 0 GAACGGCACC 0.878388 -118 CTGTTTTGCGAAACAGCCAGACACGGAGGAT 17 14 0 AAACGCCAGA 0.80905 -259 TGCAATAAAAGAATAGGCAGCCCGAA 30 6 0 GAATGGCAGC 0.877284 -170 GTCTTGAAGTAAATCGGCAGCCCTAATGACT 32 17 1 AAATGGCAGC 0.771471 -44 TAACCCGTTTGAACGGGCAGCCCTTTACACT 39 60 1 GAACGGCAGC 0.96203 -192 TTTTTGTACAGAACTGCCGCCTGCAGCACCC 46 78 0 GAACGCCGCC 0.897732 -66 AGTGCGCGATGAAGTGGCAGCTCTTTAAAAG 50 37 1 GAAGGGCAGC 0.936568 -264 GCCTTAGGCGAAAGCGCCGGCAAAGCTGCTT 71 144 0 AAAGGCCGGC 0.894444 -157 GTATCATTCGGAACCGGCGGAATTGCCCGGG 74 22 0 GAACGGCGGA 0.916 -158 AATAGATCGTAAACAGCCAGACCTACAAGTT 75 71 1 AAACGCCAGA 0.80905 -230 **** ****** Masking position 3 Map Score: 6.90639 Number of sites scoring better than the average of aligned sites = 735 Number in coding regions = 689 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 10 TAATAATTATCCCCCTTTGCTGTTT 2 282 0 ATTATCCCCC 0.796978 -15 CATCATACAAGAAATCCCCCAAAATCATGC 3 52 0 GAAATCCCCC 0.88069 -179 AATATCCTCCTTTTTTTGTA 14 153 0 AATATCCTCC 0.838703 -10 CTGGATAACCTCCTAAATATAGA 16 288 0 GATAACCTCC 0.863378 -13 GTTAACCCCCGGTCATTCCA 35 36 0 GTTAACCCCC 0.826717 -10 TGTTATCCCCCTAATACCTTA 44 12 0 GTTATCCCCC 0.826717 -11 GATAACCTCCAAGTGTAAAC 48 136 0 GATAACCTCC 0.863378 -10 GTATTAACAAAAAAACCCCCTGTAAACATG 49 52 0 AAAAACCCCC 0.85863 -79 AAGAACCTCCTCTTGAAACA 57 69 0 AAGAACCTCC 0.829433 -10 AGTGTTAGAACCTCCTTTCAAATCA 58 6 1 TAGAACCTCC 0.574785 -51 ACAAAAAGAACCCCCTTTCATCTCA 58 42 0 AAGAACCCCC 0.886614 -15 AAAAACCTCCTTGACTATAC 63 1 1 AAAAACCTCC 0.790668 -116 GCCTAGGAGATCCTCCTTCAAAATGG 71 285 0 GAGATCCTCC 0.855281 -16 CAGAGTCCAGTTTATCCCCCGGCTTCAATT 75 195 0 TTTATCCCCC 0.521812 -106 ATAATCCTCCCCCTTTATTT 77 1 1 ATAATCCTCC 0.639423 -242 TGTAAAATCCCCCTCATTTGCTT 79 130 0 AAAATCCCCC 0.85863 -13 ********** Masking position 4 Map Score: 11.1925 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 98 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 11 CACTACCTGTCTTTCATAATAAAAAACGGAT 1 55 0 CTTCATAATA 0.883317 -44 TTCTTATTATCTCACATAATAAATTTCCAGT 5 71 0 CTCCATAATA 0.733574 -95 ACGCTTTCATAATAGCGGAAGGTA 7 4 1 CTTCATAATA 0.883317 -297 CTTCTAAAACTTCTCATAAAAGAATAACCAT 16 154 1 TTCCATAAAA 0.428212 -147 TTAAATTTAATTTTCAGAAAAAATAGTAACG 17 191 1 TTTCAGAAAA 0.572247 -82 AAGCATTCATTTTTCAGAAAAATCTTTACCT 22 147 0 TTTCAGAAAA 0.572247 -154 CTTTTTTTCTCTTGCATAATAGAAAACGGCA 48 103 1 CTTCATAATA 0.883317 -43 TATAGGTATATTTTCATAATATTCAAACTTT 51 16 0 TTTCATAATA 0.786805 -285 GAAGGGTTTCTTTTCATAAAAGTGAATGAAA 52 214 1 TTTCATAAAA 0.672913 -87 TTTGCAGAATAAACGCAAACA 55 1 1 TTTCAGAATA 0.717407 -124 TGGCATGGAACTTGCATAATAAAAGGCGGAG 55 80 1 CTTCATAATA 0.883317 -45 CAACCCCTTTCTTTCATTATATAGACAGGCA 62 11 1 CTTCATTATA 0.533191 -153 TTTTCGAAATATTCCATAATATTTACTAAAT 67 105 0 ATTCATAATA 0.398093 -113 CCCTTGTCCGCTTTCATTATAGCGCTTCTAT 71 32 0 CTTCATTATA 0.533191 -269 TGAAGACCGGCTTTCAGAAAACGCTCTGTGA 71 93 1 CTTCAGAAAA 0.7436 -208 GAAGAGATTTTTCACATAATAAATCACCATA 78 125 1 TTCCATAATA 0.573075 -43 CGTTGTCTTTCTTACAGAAAAGGTACCACCT 79 75 1 CTTCAGAAAA 0.743887 -68 *** ******* Masking position 6 Map Score: 7.84807 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 128 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 12 GGAAGTGAATATTATCCTTTTACTAAATGCA 2 62 0 ATATCCTTTT 0.407109 -235 ATACAACATTTGTTACCTTTTGAAAAATGAA 6 34 0 TTTACCTTTT 0.557523 -162 CTCCTTCCCATATATCCTTTTGTTTAATTGT 8 132 0 TTATCCTTTT 0.819849 -95 ATGTCACATCTCCTTTTCAATGCCATT 15 7 1 CTCTCCTTTT 0.873906 -168 ATTGTGTTGGTCCCACCTTTTATCAGGATGA 27 49 0 TCCACCTTTT 0.528784 -21 ATTAGCTGGATGTATCCTTTTATTTACGCTA 30 61 1 TTATCCTTTT 0.819849 -115 ATTTCTGTTTTTTCTCCTTTCTTTTCGGCAT 34 69 0 TTCTCCTTTC 0.597386 -232 AAAGTTTTCTTTTTTCCTTTTGTGGAGAAAT 36 33 0 TTTTCCTTTT 0.624909 -85 TATTGATCATTCTCACCTTTTGCAGGCTGAA 36 80 1 TTCACCTTTT 0.921498 -38 AATCTATCTCTCTCCTTGTGTTTCG 41 7 0 TTCTCCTTGT 0.597386 -19 GCTGTTTTTTCTCTCCTTTTAAATCGAAAA 42 13 0 TTCTCCTTTT 0.939471 -20 CAGTCCCTCTTATCACCTTTTGAATAGG 47 8 0 TTCACCTTTT 0.921498 -94 GACTGCCTTTTATCACCTTTTTTCAAGAAAA 47 34 1 TTCACCTTTT 0.921498 -68 CAGCAGGGAATGTAACCTTTTTGGGTGACGG 49 101 1 TTAACCTTTT 0.774868 -30 CGAAAAGCTCCATCTCCTTTTGGTCATTGCA 52 47 0 CTCTCCTTTT 0.873906 -254 ACCCTTTTTACCTATCCTTTTCGCTTGAAGC 63 71 0 CTATCCTTTT 0.670196 -46 ACTACATTCTCCTTTTTTCTTATCCC 64 153 0 ATCTCCTTTT 0.700764 -16 GAACAGACGGTTTCACGTTTTTCGTGCTGTA 71 248 1 TTCACGTTTT 0.408938 -53 TGATTGTCACCCTTTCGGTAGGAAT 73 126 0 TTCACCCTTT 0.528784 -15 CTCATGAGTACTTAACCTTTTTTAGGCGGTA 76 144 1 CTAACCTTTT 0.605813 -157 TCCGTTTCTCCTTTTTGTAAGGTAT 78 153 0 TTCTCCTTTT 0.939471 -15 * ********* Masking position 9 Map Score: 17.4746 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 345 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 13 AAAGAGCCCGGTTGTGTTCCCTTCCTCCCTT 17 97 0 GTTGTGTCCC 0.972999 -176 GTAAAGAGCTGCTGTGGTCTCCGAGTTCTCC 20 60 0 GCTGTGTCTC 0.95716 -119 ACACTTTGGTGCTGTGGTCTCTCCTCATCTC 21 56 0 GCTGTGTCTC 0.95716 -85 CACTTTGGCTGTTGTGGTCTCTTTTTCTATT 21 94 1 GTTGTGTCTC 0.933713 -47 GGGGACACATTTTGTGTTCCCTATTTTTAAA 48 57 1 TTTGTGTCCC 0.891802 -89 TTTAAGAATAGTTGTGATCCCAGTAAAAACT 52 153 1 GTTGTGTCCC 0.972999 -148 CTGTAATCATGCTGCGATCCCGGGATGAAAG 66 97 0 GCTGCGTCCC 0.946201 -204 ACGAGACAGATCTGGGTTCCCCTTTATTTTT 67 46 1 TCTGGGTCCC 0.800905 -172 ****** **** Masking position 8 Map Score: 4.55052 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 24 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 AATCTTAAAATTTCTTTAAAAATAAGCCAAA 14 71 1 TTTTTTAAAA 0.815406 -92 AACCCAATTATATTTTTAAACTGTTAAGCTA 16 243 0 TATTTTAAAC 0.675727 -58 CCGCAGTTTTTTTATTTAAACAAACATATCA 22 103 1 TTTTTTAAAC 0.818223 -198 TTGTAAACGCTTTATTTAAAAAATCCAAATA 24 43 1 TTTTTTAAAA 0.815406 -117 TGTGAGGACATTTTTTTACACGAACTTCATA 34 183 1 TTTTTTACAC 0.821006 -118 TTCCTCCTTATATGTTTAAACAAGAGTATGT 47 76 0 TATTTTAAAC 0.675727 -26 TTGTGTTCCCTATTTTTAAAACTATATTTAC 48 68 1 TATTTTAAAA 0.671588 -78 TTTTTAAAACTATATTTACAAACCTTTTTTT 48 80 1 TATTTTACAA 0.675727 -66 TTTCTTCCTTTTTATTTACAATCTTTATGGT 50 220 0 TTTTTTACAA 0.818223 -81 TTTTAAATGGTTTTTTTAAAAAACCCTTGCC 66 175 1 TTTTTTAAAA 0.815361 -126 AGTGCATGTTTTTATTTACAACACTTATGAT 66 261 1 TTTTTTACAA 0.818223 -40 AAGTAAATAGTTTGTTTACACATTTTCTCAG 73 66 1 TTTTTTACAC 0.821006 -75 TACGGGCAGATTTCTTTAAAACCAGCTTGCA 77 81 0 TTTTTTAAAA 0.815406 -162 *** ******* Masking position 8 Map Score: 6.15946 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 170 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 15 AATAATTATCCCCCTTTGCTGTTTGTGCTGGA 2 274 0 CCCCTTTTGT 0.963503 -23 TGTCATCTCCCTCCTTTAGTGTCAACCACCCG 4 120 0 CTCCTTTTGT 0.88619 -24 AAGGATAACGCCCCTTTTGTCTCGTAAGAAAA 5 111 0 CCCCTTTTCT 0.937142 -55 GCCCATTGCCCCTTTCGTGTTTTTTCTGG 9 10 0 CCCCTTTTGT 0.963503 -20 TCAAGATCCCCTCTCTCCTCATTGATCGT 12 260 0 CCCCTCTCCT 0.314763 -19 GCGAATAAGCCTTCTTTTTTTTGGCTTTTTAG 14 21 1 CTTCTTTTTT 0.412497 -142 GAAGCTGCATCCTCTTTCTTCTTGAGAAAGGG 18 141 1 CCTCTTTTCT 0.684057 -160 TACGTTTCCTCCTTGTTGTCACGGTAAAT 21 122 0 CCTCCTTTGT 0.250177 -19 GCCTCCTTTAATGTATTCCGTTTA 22 287 0 CTCCTTTTGT 0.88619 -14 GATCTCGCCTCCTTTTTTGCTATTATAAAG 23 9 1 CTCCTTTTGC 0.677291 -225 ACAAATCTCCCCCTTTGTTGTTTCTACATAT 24 10 1 CCCCTTTTGT 0.963503 -150 TCTGTTTTTTCTCCTTTCTTTTCGGCATTTTT 34 65 0 CTCCTTTTTT 0.828613 -236 TTGTATTCCTCCTTATATGTTTAAACAAGA 47 82 0 CTCCTTATGT 0.313759 -20 TTCAATCCAGCCGCTTTCATTTTTACATAAAT 52 267 0 CCGCTTTTTT 0.517456 -34 CTGTTACCACCTTTCTTGTTTCGACTCCG 55 106 0 CACCTTTTGT 0.582535 -19 CTTCAGAAAACCCCTTTATCTTTTCATTTCCT 56 11 1 CCCCTTTCTT 0.853009 -142 CAAAAAGAACCCCCTTTCATCTCATGTGTATG 58 34 0 CCCCTTTTCT 0.937142 -23 CAACCCCTTTCTTTCATTATATAGA 62 4 1 CCCCTTTTTC 0.815435 -160 CTGAATTCCCCTTTTACTCAATTGAACCC 63 98 0 CCCCTTTCTC 0.610007 -19 ACTACATTCTCCTTTTTTCTTATCCCGGTA 64 149 0 CTCCTTTTCT 0.814727 -20 GATCTGGGTTCCCCTTTATTTTTCCAACATAA 67 54 1 CCCCTTTTTT 0.942501 -164 ACTGACCCTCTTTTCCTTTAGAAAATTA 69 7 1 CCTCTTTCTT 0.457333 -192 ATAATCCTCCCCCTTTATTTGATGTTTCAAG 77 10 1 CCCCTTTTTG 0.622377 -233 ******* *** Masking position 4 Map Score: 18.4484 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 136 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559