AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00380_bsub_reg_300.orf -o00380_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 metS 300 methionyl-tRNA synthetase #2 yabD 78 similar to hypothetical proteins #3 yabE 155 similar to hypothetical proteins #4 yabF 144 similar to hypothetical proteins #5 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #6 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #7 ycbD 29 similar to aldehyde dehydrogenase #8 yclB 89 similar to phenylacrylic acid decarboxylase #9 yerQ 300 similar to hypothetical proteins #10 yefA 255 alternate gene name: yerS; similar to RNA methyltransferase #11 katA 300 vegetative catalase 1 #12 trpS 300 tryptophanyl-tRNA synthetase #13 odhA 227 2-oxoglutarate dehydrogenase (E1 subunit) #14 yojN 63 similar to nitric-oxide reductase #15 yojM 92 similar to superoxide dismutase #16 yojL 300 similar to cell wall-binding protein #17 gerCA 162 heptaprenyl diphosphate synthase component I #18 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #19 mtrA 187 GTP cyclohydrolase I #20 hbs 300 non-specific DNA-binding protein HBsu #21 mmgA 137 acetyl-CoA acetyltransferase #22 yqiK 78 similar to glycerophosphodiester phosphodiesterase #23 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #24 yqeT 24 similar to ribosomal protein L11 methyltransferase #25 dnaJ 199 heat-shock protein #26 dnaK 23 class I heat-shock protein (chaperonin) #27 grpE 71 heat-shock protein #28 hrcA 119 transcriptional regulator #29 hemN 52 coproporphyrinogen III oxidase #30 lepA 133 GTP-binding protein #31 spoIIP 62 spoIIP #32 gpr 203 spore protease #33 hemA 163 glutamyl-tRNA reductase #34 dhbE 28 2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E) #35 dhbC 25 isochorismate synthase #36 dhbA 193 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase #37 yuiI 138 yuiI #38 yuiH 100 similar to sulfite oxidase #39 ywpB 191 similar to hydroxymyristoyl-(acyl carrier protein) dehydratase #40 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #41 dltA 300 D-alanyl-D-alanine carrier protein ligase (Dcl) #42 katX 128 catalase #43 katB 200 catalase 2 #44 aldX 142 aldehyde dehydrogenase Motif number 1 TAAAGATTTTTAATTTTAATTATTCTTTTTCAGGGCGTAT 1 129 1 TTTTCTTTTT 0.75338 -172 TCAGAGGGTTTTGCGCCCTCTGTTTTTTTCGTTATAATAG 4 26 1 TGTTTTTTTC 0.890843 -119 ATAAAGATATTGACTTATTGTTTATTTGTCTTACAATTAA 6 100 1 TTTATTTGTC 0.440415 -127 GTTTTCGTTTTAGGATTTTGTCATCTTTTCAGCGTGATTG 10 60 1 TATTCTTTTC 0.722206 -196 TCCTTGTTTATCACTTACTCTGCTTGTTTCGCAAATAGAG 11 87 1 TTTTTGTTTC 0.775531 -214 GAGACTGCTCCGGCTGAGCCTACTTTTTTCCAGTTCGGTC 12 141 0 CTTTTTTTTC 0.643952 -160 AATCCTATGCTTTTTGGCGTTTGTTTTTTCGAATGATTAA 13 16 1 TTTTTTTTTC 0.962178 -212 ACTGTCTCCCCCTTGTTTTTTCTAACAGTGTG 15 71 0 TTTTTTTTTC 0.962178 -22 CAGTTTCTCCTCCTTTCTTGTCTATTTTTCTAATCAATTC 16 13 0 TTTATTTTTC 0.852836 -288 GGCACACAACTGTTTTATCGTCAATTTTTCAGCAAGTTAA 16 212 0 TTTATTTTTC 0.852836 -89 AGCGGGAGGATACAGCCAATTCTTTTTTTTATGCTATAAT 17 50 1 TGTTTTTTTT 0.598313 -113 TCTTAATCTATGTATGAGTTTTATCTTTTCATTCGCTTAC 17 99 0 TTTTCTTTTC 0.943623 -64 GCATCTAGCTTACATACACTTTATTTCTTCACAGAAAAGC 19 32 1 TTTTTTCTTC 0.775531 -156 CGAACGAATATTCCTTTTTTTCCTTTTTTCATCC 20 5 0 TTTTTTTTTC 0.962178 -296 TGTCTTTCTCTTACTTGCTCTCATTTTTTTCTGAGACAGG 20 196 1 TTTTTTTTTT 0.822791 -105 TACATTCAGTTCGTTTATTATCATTTCTTCACAGTTCAGT 20 247 0 TTTTTTCTTC 0.775531 -54 GGAGGCTGTTTGACGCAGCCTTCTTTTTTCATTCATTCAT 21 31 1 TGTTTTTTTC 0.890843 -107 TAAAGTTTTCTCCATTATACTTATTTTGTCGGCTCCACTC 22 32 0 TTTTTTTGTC 0.775531 -47 AAAAAGTTGCTTCTTTCCGCTAATTTTTTCTAATTGGCGC 23 93 1 TTTTTTTTTC 0.962178 -208 TTGAATCAGATTATGAAATGTGTTCTTTTCGGTCAGCTCC 25 38 0 TGTTCTTTTC 0.843002 -162 AAGTCAGGCATCTCTTGGCTTTGACTTTTTTTCTTGCCCG 25 92 1 TTTACTTTTT 0.410337 -108 AAAGTATTTTTCATTGAAGGTTCTCTTTTTAGCATGATTT 32 124 1 TTTTCTTTTT 0.75338 -80 AAAAAGAGATTAATTCATAATATACTTTTCAAATGTACAG 39 105 1 TTTACTTTTC 0.792222 -87 AAAACGCAGATATGAGTTTGTTATTTTTTCTGACAAACCT 40 68 1 TATTTTTTTC 0.798039 -100 GATCAGATGCTCAAAAAGTTTCATTTTTTCCCTAATCTCC 41 56 0 TATTTTTTTC 0.798039 -245 AGGCTTTTATTTGATGATACTGCTTGTTTTGTTTTTTATG 41 203 1 TTTTTGTTTT 0.386718 -98 TGGTTGGCCCTCCTTTTTTGAACGGTAACA 42 109 0 TTTTTTTTTG 0.58825 -20 AAAATCCCCCTCATTTGCTTTCTTCTTTTCTCGGACCTAT 44 110 0 TTTTCTTTTC 0.943623 -33 * * * ******* Masking position 11 Map Score: 22.1879 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 608 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 2 ATTATCCTACTAAAAATCCTTTTAAATCAAGACTT 1 20 1 TAACCTTTTA 0.786606 -281 TTGTTACACGTGAAACACCTTTTGTTTATCA 2 7 0 TAACCTTTTT 0.930174 -72 TAACAATTCGTCGAACACCTTTTGTGTTTCGACAA 2 36 1 TAACCTTTTT 0.931344 -43 GTTTCGACAAGAAAGGAGTTTTTCACTT 2 61 1 GAGGTTTTTA 0.530606 -18 TTCATGAATATACAAAAGTTTTTATTTTGTCTTGG 4 112 1 TAAGTTTTTT 0.873374 -33 CTGCTTATTTTCAAAATGTTTTTGTCGTATTTTGT 5 67 0 TAAGTTTTTT 0.872066 -234 GAGAAAACCTGCAAATTGCTTTTGACCCAGAACAT 5 121 0 GAAGCTTTTA 0.881076 -180 GGCCTCTATCTGTAAGCGCTTTTATTAATTTTTCT 6 173 0 TAAGCTTTTT 0.947364 -54 ATTCCGATATGTCAACTCTTTTTTAAATACGATTT 11 46 1 GAACTTTTTA 0.68334 -255 AAAACCTTGTTGTAACAGCTTTTTATGACACTTAA 11 154 0 TAAGCTTTTA 0.917648 -147 TTTTGTTTTTTATAAAGGTTTTTTACTATTTTGTG 13 59 1 TAAGTTTTTA 0.734144 -169 AAAATATCGTTGGAAGCGTTTTTATTACATAATTT 13 129 1 TAAGTTTTTT 0.874214 -99 TATCATCCAGGCCCTTTTGTATTGAGCATA 14 6 1 TAGCCTTTTT 0.84274 -58 GTATTGAGCATACAGGGGCTTTTTTAGTATACTCG 14 29 1 TAGGCTTTTT 0.876669 -35 AAAAAGCCTATAAAAGGCTTTTTGTCATACTCATT 15 12 0 TAACTTTTTT 0.836974 -81 TTTTCAGCAAGTTAAACCCTTTTCAAACATTTGGC 16 192 0 GAACCTTTTA 0.848147 -109 GGAGGATACAGCCAATTCTTTTTTTTATGCTATAA 17 54 1 GAACTTTTTT 0.775603 -109 AAGCCCCTTAGAAAGGGGCTTTTCTGTGAAGAAAT 19 54 0 GAGGCTTTTT 0.824224 -134 AGAAAGACAATTAAACGGCTTTTTAAGAAAAACTG 20 170 0 TAAGCTTTTA 0.828283 -131 ATTATGATTTTTCAATTCCTTTTATCCCGGGCAAG 25 124 0 TAACCTTTTT 0.931361 -76 ACCTCCCCTATTCAACAGCTTTTTTGGTAAGCGCT 43 17 1 TAAGCTTTTT 0.947351 -184 * ** ****** * Masking position 10 Map Score: 21.8739 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 338 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 3 CTCCTAATCAGAATGTCAAAAAGCTCCCGC 1 273 0 GAATGTCAAA 0.683229 -28 ATTTTGTCTTGGAGGAAATA 4 135 1 GGAGGAAATA 0.487393 -10 TAAAAAGCGAGGATGTGATCAACATAAAAC 5 170 1 GGATGTGATC 0.300663 -131 TTGTTTAATTGTAAGACAAATAAACAATAA 6 114 0 GTAAGACAAA 0.695794 -113 GGGAAGGAGCGGATGTGAAAGAAAAATTAA 6 154 1 GGATGTGAAA 0.814987 -73 AGAATGTTAAGGATGACAAAAGCTCAAAAC 9 143 1 GGATGACAAA 0.891412 -158 AGTTTTAAGCGAAAGAAAAACTTGGCCTAT 10 222 0 GAAAGAAAAA 0.646054 -34 CGCAAATAGAGAAGGAAAAATTATTTCTCC 11 116 1 GAAGGAAAAA 0.683199 -185 AAATGAGTATGACAAAAAGCCTTTTA 15 7 1 GTATGACAAA 0.653113 -86 AGACAAGAAAGGAGGAGAAACTGCTTCGTT 16 30 1 GGAGGAGAAA 0.906338 -271 ATTCATTGGTGGAGGACATAGAAC 19 174 1 GGAGGACATA 0.676267 -14 GGATGAAAAAAGGAAAAAAA 20 1 1 GGATGAAAAA 0.788871 -300 ATGAGAGCAAGTAAGAGAAAGACAATTAAA 20 190 0 GTAAGAGAAA 0.65259 -111 CCTTTTGGGAGGAGGTGAAAGGC 20 288 1 GGAGGTGAAA 0.863435 -13 GGGCATGAATGAATGAAAAAAGAAGGCTGC 21 45 0 GAATGAAAAA 0.600402 -93 TCAATGATTAGAAAGTCAAAGTCAGGCATC 25 74 1 GAAAGTCAAA 0.723772 -126 ACACTTTGAGGGAGGTGAACACA 27 59 1 GGAGGTGAAC 0.776811 -13 GTACGTGAAAGAGAAAAGCAACCCAG 30 7 1 GAAAGAGAAA 0.767088 -127 TGTAAAACAAGAAAGAGAAAAGTTCCCTAT 30 42 0 GAAAGAGAAA 0.767088 -92 TTGTATCTTAGGAGGTGAAACAC 32 4 0 GGAGGTGAAA 0.863435 -200 CTATCAATATGGAAGTAAAAACCTAATAAA 37 41 0 GGAAGTAAAA 0.747842 -98 TTCTTCCAAAGAAAGTCAACTTTTTCCCGA 37 109 0 GAAAGTCAAC 0.590568 -30 GACTTTCTTTGGAAGAAAACCTATTAT 37 122 1 GGAAGAAAAC 0.714185 -17 CTATGATTGTGTATGTCAACCTAAGGGGGA 38 17 0 GTATGTCAAC 0.40377 -84 ATAAAATGCAGGAAGACAACATTTATTTTT 40 25 0 GGAAGACAAC 0.845914 -143 TGAAACAGCTGTATGAAAAACCCGCTGTCA 41 157 1 GTATGAAAAA 0.461487 -144 GTTGAATAGGGGAGGTCATATC 43 3 0 GGAGGTCATA 0.577147 -198 TTTTCTGTAAGAAAGACAACGGTGAACCAT 44 66 0 GAAAGACAAC 0.688241 -77 ********** Masking position 3 Map Score: 20.097 Number of sites scoring better than the average of aligned sites = 1064 Number in coding regions = 847 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 4 GACGGATATATACTGGCCCTCATGCTGATT 5 220 1 TACTGGCCCT 0.790316 -81 TCCGCTCCAATGCTCCCCCTTCCTAGACTA 9 90 1 TGCTCCCCCT 0.991492 -211 TGTGCTCCGATGCTCGCCCTTCCTAGACTT 10 110 0 TGCTCGCCCT 0.961609 -146 TAACGGAGACTGCTCCGGCTGAGCCTACTT 12 156 0 TGCTCCGGCT 0.973125 -145 ATGCTGAAAATGCTGCGCCAAATGTTTGAA 16 176 1 TGCTGCGCCA 0.867573 -125 ATTGGCTGTATCCTCCCGCTGTTTGCGAGC 17 40 0 TCCTCCCGCT 0.848406 -123 TCAAACGATTTGCTCACCCTATTCTCAAAT 23 49 1 TGCTCACCCT 0.941839 -252 GAAGGACAGGTGCTGCCCTTCGATAAAATT 27 24 0 TGCTGCCCTT 0.84282 -48 AGTACAAGACTGCGGCGGCTT 29 2 0 TGCGGCGGCT 0.798303 -51 CGCAGTCTTGTACTGCGGCTTCTTTCTGTA 29 18 1 TACTGCGGCT 0.844964 -35 GACATACTCAGCCTTGCCTTTAAA 36 5 1 TACTCAGCCT 0.70902 -189 CGAAAAAGACTGCTGCGCCTTGAAAAACGC 36 129 0 TGCTGCGCCT 0.985202 -65 CGTTGTTCCCCCTTAGGTTGACA 38 4 1 TGTTCCCCCT 0.876462 -97 GTCTGCTCCCCCTTTTTAAAACG 43 188 0 TGCTCCCCCT 0.991492 -13 ********** Masking position 1 Map Score: 12.5095 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 461 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 5 ACACGAACAGACTTTTTTTATTTTCATTAAAG 1 102 1 ACTTTTTTTT 0.724913 -199 AATATACAAAAGTTTTTATTTTGTCTTGGAGG 4 118 1 AGTTTTATTT 0.275301 -27 TCACATCCTCGCTTTTTATTTTGGGGAATCGG 5 156 0 GCTTTTATTT 0.869209 -145 GGCTGACCAGGCTGTTTTTTTGCTGCGCAGAA 6 22 1 GCGTTTTTTG 0.875551 -205 TTCATAGCAAGCTTTTCTTTTGATTGCTTCAT 12 20 0 GCTTTCTTTG 0.663696 -281 GGAAGAATGAGCCTTTTTTATTATGTTTTAAG 12 260 1 GCTTTTTTTT 0.932971 -41 ATGCTTTTTGGCGTTTGTTTTTTCGAATGATT 13 22 1 GCTTTGTTTT 0.58325 -206 TATCGTTGGAAGCGTTTTTATTACATAATTTT 13 133 1 AGGTTTTTTT 0.344196 -95 GCCTTTTATAGGCTTTTTTGTTTATACCAGAC 15 29 1 GGTTTTTTTT 0.807781 -64 AACCTCCTAAACTGTTTTTTTGCAAAAACAGC 16 273 0 ACGTTTTTTG 0.571182 -28 TTTCTAAGGGGCTTTTCATATTTCAAGAGCAT 19 75 1 GCTTTCATTT 0.55152 -113 GCTTGATATGGCTTTTTATATGTGTTACTCTA 20 93 1 GCTTTTATTG 0.835857 -208 TCCTCAGAGTGCAGTTTTTCTTAAAAAGCCGT 20 159 1 GCGTTTTTTT 0.901786 -142 GTTTGACGCAGCCTTCTTTTTTCATTCATTCA 21 38 1 GCTTCTTTTT 0.559116 -100 CCTGATGTTTGGCTTTTATCTTTGACCAGAAT 23 266 0 GGTTTTATTT 0.667387 -35 CTTGGCTTTGACTTTTTTTCTTGCCCGGGATA 25 105 1 ACTTTTTTTT 0.724913 -95 GAAGTTTTTGGCGCTTTTTTTGGGTGAGTTAT 28 16 1 GCCTTTTTTG 0.574926 -104 TGATCAAGGTGCCTTTTTTATTCGGGAAAAAG 37 88 1 GCTTTTTTTT 0.932971 -51 ATGTCATACAGGCTTTTATTTGATGATACTGC 41 194 1 GGTTTTATTG 0.605904 -107 TGATGATACTGCTTGTTTTGTTTTTTATGTAT 41 214 1 GCTGTTTTTT 0.559116 -87 TTTTAAAACAGCCGTTTTTTTTGATCTGCTTC 42 57 0 GCGTTTTTTT 0.901786 -72 GAGCGGATTAGCAGTTTATATGAAGAACGCCA 43 131 1 GCGTTTATTG 0.770599 -70 ** ****** ** Masking position 9 Map Score: 11.7606 Number of sites scoring better than the average of aligned sites = 1223 Number in coding regions = 936 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 6 CTAATCAGAATGTCAAAAAGCTCCCGCCCA 1 270 0 TGTCAAAAAG 0.693421 -31 AAAGGATATATGGGAAGGAGCGGATGTGAA 6 143 1 TGGGAAGGAG 0.895259 -84 AAGGAGCGGATGTGAAAGAAAAATTAATAA 6 157 1 TGTGAAAGAA 0.803733 -70 AAAAGCTTGCTATGAAAAAGAGTAGTACAC 12 36 1 TATGAAAAAG 0.550494 -265 CTGACCGAACTGGAAAAAAGTAGGCTCAGC 12 139 1 TGGAAAAAAG 0.601247 -162 ATTCTTCCCCTGTAAAAAAGGGACGAATGA 12 238 0 TGTAAAAAAG 0.794066 -63 GGGGCTTTTCTGTGAAGAAATAAAGTGTAT 19 45 0 TGTGAAGAAA 0.873288 -143 CAGACTGAACTGTGAAGAAATGATAATAAA 20 244 1 TGTGAAGAAA 0.873288 -57 GGCTTCTTTCTGTAAAGAAGGTGAATCCG 29 34 1 TGTAAAGAAG 0.829312 -19 GTACGTGAAAGAGAAAAGCAACC 30 4 1 CGTGAAAGAG 0.812435 -130 TTTGTTCTATTGTGAAGAAGATTTAACCTT 32 52 0 TGTGAAGAAG 0.966881 -152 AGGTACTTAATGTGAAGGAGGCCCCTGT 32 186 1 TGTGAAGGAG 0.956252 -18 GTTCACATTTTGTGAAAGAAACTATGTTAT 33 69 1 TGTGAAAGAA 0.803733 -95 CTTTTTTATTCGGGAAAAAGTTGACTTTCT 37 100 1 CGGGAAAAAG 0.693466 -39 TGATTTATTATGTGAAAAATCTCTTCTGCT 40 121 0 TGTGAAAAAT 0.624404 -47 CCTTTCTTTCTGTGAAGAAGGCTTATTTCA 43 57 1 TGTGAAGAAG 0.966881 -144 ********** Masking position 5 Map Score: 10.0043 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 427 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 7 CTGAGGCTTTCAGCTTGTTGAAAAACCCTCGCATT 9 10 1 TCAGTGTAAA 0.977232 -291 TAACATTCTTTCAGCTTGATTGAAAACCCTTGTAGT 9 116 0 TCAGTGTAAA 0.977232 -185 TAAGCCAAGCTCAGAATGTTGACAAAATCCTAAAAC 10 23 1 TCAGTGTAAA 0.977232 -233 TGTCATCTTTTCAGCGTGATTGAAAACCTTTGAAGT 10 78 1 TCAGTGTAAA 0.977232 -178 AAGCCAAGTTTCAGCGTGTAGGCAAACCTTCGCATT 10 184 0 TCAGTGAAAA 0.932339 -72 TGAAAAGGGTTTAACTTGCTGAAAAATTGACGATAA 16 202 1 TTAATGTAAA 0.830583 -99 TCTTCACAGTTCAGTCTGATTCTAAACCTGTCTCAG 20 226 0 TCAGTGTAAA 0.977232 -75 CTCAAATTTTTTAAAATGAATAAAAAGTTGCTTCTT 23 72 1 TTAATGAAAA 0.611496 -229 TTAGATTATATCAATAGGATTGTAAAGATTCAATGT 30 69 0 TCAAGGTAAA 0.745416 -65 GAGTTCTATGTTAGAATGATTATAAATTAAGATTGG 33 115 1 TTAGTGTAAA 0.925023 -49 CTGCAGACTATCAATATGGAAGTAAAAACCTAATAA 37 42 0 TCAATGAAAA 0.845578 -97 AAAAAGATTGTCAACATGATTTTAAATTAGGTTAAC 38 60 1 TCAATGTAAA 0.944617 -41 TGGTTACATTTTAGCGCGGTTGAAAAAGAGATTAAT 39 83 1 TTAGCGTAAA 0.679278 -109 **** ** * *** Masking position 3 Map Score: 11.1805 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 149 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 TGTAGAACTTTTATAGAAAAACGCTGTAAGGGACAA 3 40 0 TTGAAAACTG 0.949406 -116 CTGGAACGGTTTATTGAAAAAGACGGATATATACTG 5 199 1 TTGAAAAGGG 0.690899 -102 GGCTTTCAGCTTGTTGAAAAACCCTCGCATTCGTTG 9 15 1 TTGAAAACTC 0.885269 -286 CCGACGCGCAGACCTGACAACGAATGCGAGGGTTTT 9 32 0 GCGACAAGTG 0.743582 -269 TCTTTCAGCTTGATTGAAAACCCTTGTAGTCTAGGA 9 110 0 TTGAAAACTG 0.949406 -191 CTTTTCAGCGTGATTGAAAACCTTTGAAGTCTAGGA 10 84 1 TTGAAAACTG 0.949406 -172 CCGAAGCACAGGCCTGACAACGAATGCGAAGGTTTG 10 162 1 GCGACAAGTG 0.743582 -94 AGTATCGAAATTGTTGAAAAACCTTGTTGTAACAGC 11 170 0 TTGAAAACTG 0.949406 -131 TTTTTGTTTATACCAGACAATGATTGACCACACTGT 15 43 1 TCGACAAGTG 0.915269 -50 CTGCGCCAAATGTTTGAAAAGGGTTTAACTTGCTGA 16 188 1 TTGAAAAGTT 0.564846 -113 TTCTTCACTTTGTTGGACAAACATTCCTCAGAGTGC 20 135 1 TTGACAACTC 0.89328 -166 ATAGAGTAATTACTAGACAAGCGCTGGAGGGATTCA 31 37 1 TTGACAACTG 0.953176 -26 TCTTATGCTATATTAGAAAAAGCTTCAGGGAAAAGA 33 21 0 TTGAAAAGTC 0.871364 -143 TTTGTTATTTTTTCTGACAAACCTTGCGCGATTGAC 40 84 1 TCGACAACTG 0.924837 -84 TCGGCGTATGTTTTTGAAAATGAATCTTTAT 41 6 0 TTGAAAAGTC 0.871364 -295 * * ***** * ** Masking position 9 Map Score: 9.31106 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 121 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 9 GGGGAGCATTGGAGCGGAGCGAATGTAGAATTC 9 75 0 GAGCGACGAA 0.992291 -226 GGTTTTCAATCAAGCTGAAAGAATGTTAAGGAT 9 124 1 CAGCGAAGAA 0.874721 -177 GGCGAGCATCGGAGCACAGCGAATGTTGAATTC 10 122 1 GAGCCACGAA 0.955165 -134 GGACTTTGGAGCAGCTGACCGAACTGGAAAAAA 12 125 1 GAGCGACGAA 0.992291 -176 ATCCTAGAGTGGAGCCGACAAAATAAGTATAAT 22 26 1 GAGCGAAAAA 0.932552 -53 TTAGAAAAAATTAGCGGAAAGAAGCAACTTTTT 23 93 0 TAGCGAAGAA 0.824897 -208 CCCCGCTTCCGGAGCTGACCGAAAAGAACACAT 25 28 1 GAGCGACGAA 0.992291 -172 TTCATTAATTGCAGCATATCAAAAATTCCCTTC 41 128 0 GAGCTACAAA 0.824897 -173 TACCATTCCCGAAGCAGATCAAAAAAAACGGCT 42 47 1 GAGCGACAAA 0.976845 -82 * *** ** **** Masking position 8 Map Score: 7.10889 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 207 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 TCGAGCGTCTAATAAGCAGAAAATGCACTTTGT 4 66 0 AATAACAAAA 0.610125 -79 ATATTTTATAAAAAAGCGGTAAATCACTGTCCG 6 61 0 AAAAACTAAA 0.777357 -166 CTTTTTTATAAAATATCAGAAAATAAAGATATT 6 78 1 AAATACAAAA 0.610125 -149 CCAGAAAAAACACGAAAGGGGCAATGG 7 5 1 AAAAACGAAA 0.745847 -25 TTAAGGATGACAAAAGCTCAAAACAAGAATCAG 9 149 1 CAAAACAAAA 0.911761 -152 TGAAAACGCACAAAAGCTCAAAACTGATTCTTG 9 172 0 CAAAACAAAA 0.911761 -129 TATGAGTTAAAAAAATCGCAACAAAATGTACAT 9 216 0 AAAAACAACA 0.821083 -85 AGAATGTTGACAAAATCCTAAAACAGTTTTCGT 10 35 1 CAAAACAAAA 0.911761 -221 GAAAAGATGACAAAATCCTAAAACGAAAACTGT 10 57 0 CAAAACAAAA 0.911761 -199 AAACCTTTATAAAAAACAAAAAATTTAATCATT 13 47 0 AAAAACAAAA 0.944735 -181 GGTATAAACAAAAAAGCCTATAAAAGGCTTTTT 15 24 0 AAAAACATAA 0.747911 -69 ACTCACCCAAAAAAAGCGCCAAAAACTTCATTG 28 12 0 AAAAACCAAA 0.745847 -108 ATATGGAAGTAAAAACCTAATAAAGATGCGTAT 37 32 0 AAAAACATAA 0.747911 -107 AACCATACATAAAAAACAAAACAAGCAGTATCA 41 217 0 AAAAACAACA 0.821083 -84 TACAATGTACAAAAATCGGTAAAAGGAGAGGTC 42 16 0 AAAAACTAAA 0.777357 -113 ***** * **** Masking position 5 Map Score: 8.86371 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 265 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 CAATTTGCAGGTTTTCTCCCGATTCCCCAA 5 138 1 GTTTTCTCCC 0.567454 -163 GCTTTTGTGCGTTTTCACCTGTAAGATTAT 9 188 1 GTTTTCACCT 0.95312 -113 GTTATCACCTCTTGGAATTT 11 291 0 GTTATCACCT 0.867149 -10 GAGTAGTACACGTTTCACCTGTTTGAAGAG 12 55 1 CGTTTCACCT 0.969923 -246 AATGAACCGTGGTACCACCCTGATTATTCC 12 213 0 GGTACCACCC 0.668857 -88 GCCTTTCACCTCCTCCCAAAA 20 290 0 CCTTTCACCT 0.824118 -11 GGTTTCACCTCATTCAGAAG 21 128 0 GGTTTCACCT 0.984383 -10 CGTTTCACCTCAAACCCTAA 22 69 0 CGTTTCACCT 0.969923 -10 TGTGTTCACCTCCCTCAAAGT 27 61 0 GTGTTCACCT 0.777293 -11 CGGATTCACCTTCTTTACAGA 29 42 0 GGATTCACCT 0.879532 -11 GTGTTTCACCTCCTAAGATAC 32 2 1 TGTTTCACCT 0.860715 -202 TCCGTTTCTCCTTTTTGTAAGG 40 156 0 CGTTTCTCCT 0.868187 -12 TTACAGAAAAGGTACCACCTTATAATAGGT 44 86 1 GGTACCACCT 0.864745 -57 ********** Masking position 6 Map Score: 7.90213 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 189 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 12 GGTTTTGCGCCCTCTGTTTTTTTCGTTATA 4 32 1 CCTCTGTTTT 0.556575 -113 CCTGGTCAGCCGGCTGTTTGGT 6 3 0 CGGCTGTTTG 0.962 -224 CCGGCTGACCAGGCTGTTTTTTTGCTGCGC 6 20 1 AGGCTGTTTT 0.907479 -207 CAGTGATTTACCGCTTTTTTATAAAATATC 6 65 1 CCGCTTTTTT 0.777948 -162 CCTAAAACGAAAACTGTTTTAGGATTTTGT 10 44 0 AAACTGTTTT 0.626296 -212 GTACACGTTTCACCTGTTTGAAGAGAGTCT 12 60 1 CACCTGTTTG 0.660856 -241 CGATATTTTACCACTGTTTGCAATTTGATT 13 108 0 CCACTGTTTG 0.801796 -120 AGCCTATAAAAGGCTTTTTGTCATACTCAT 15 13 0 AGGCTTTTTG 0.658031 -80 AGCCTTTTATAGGCTTTTTTGTTTATACCA 15 28 1 AGGCTTTTTT 0.662658 -65 AAATGGCACACAACTGTTTTATCGTCAATT 16 226 0 CAACTGTTTT 0.815354 -75 AACAAAATACTAGCTGTTTTTGCAAAAAAA 16 261 1 TAGCTGTTTT 0.595773 -40 TCAACCTCCTAAACTGTTTTTTTGCAAAAA 16 277 0 AAACTGTTTT 0.626296 -24 CTGTATCCTCCCGCTGTTTGCGAGCATTTG 17 35 0 CCGCTGTTTG 0.944861 -128 TGTTAGAAGGAGGCTGTTTGACGCAGCCTT 21 23 1 AGGCTGTTTG 0.905732 -115 GTTTTTCATACAGCTGTTTCATTAATTGCA 41 148 0 CAGCTGTTTC 0.778888 -153 TCAAAAAAAACGGCTGTTTTAAAATCTTTC 42 65 1 CGGCTGTTTT 0.962747 -64 CCCTATTCAACAGCTTTTTTGGTAAGCGCT 43 22 1 CAGCTTTTTT 0.789305 -179 ********** Masking position 5 Map Score: 9.70307 Number of sites scoring better than the average of aligned sites = 1112 Number in coding regions = 1015 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 13 TTATCGCCGCTCTCGTCCTTTGGGCGGGAG 1 250 1 TCTCGTCCTT 0.820484 -51 AAGAAAGCGCCTCCTTATCATACCTT 8 7 1 GCGCCTCCTT 0.97393 -83 CCGCTCCAATGCTCCCCCTTCCTAGACTAC 9 91 1 GCTCCCCCTT 0.987661 -210 GTGCTCCGATGCTCGCCCTTCCTAGACTTC 10 109 0 GCTCGCCCTT 0.96526 -147 ACTGTCTCCCCCTTGTTTTTTCTA 15 79 0 TCTCCCCCTT 0.946438 -14 CGAAGCAGTTTCTCCTCCTTTCTTGTCTAT 16 28 0 TCTCCTCCTT 0.929414 -273 TTTCAGCATCGTTCGACCTTTAAACCTTCA 16 155 0 GTTCGACCTT 0.458407 -146 ACAGGGGCCTCCTTCACATTAAGT 32 190 0 GGGCCTCCTT 0.9431 -14 CGTTGTTCCCCCTTAGGTTGACAT 38 5 1 GTTCCCCCTT 0.940341 -96 ATGGGCCTCCTTTTTGTTAACC 38 89 0 GGGCCTCCTT 0.9431 -12 TGGTTGGCCCTCCTTTTTTGAACGG 42 114 0 GGCCCTCCTT 0.860783 -15 GTCTGCTCCCCCTTTTTAAAACGA 43 187 0 GCTCCCCCTT 0.987661 -14 ********** Masking position 9 Map Score: 14.9506 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 89 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 14 AGATAAAGGATAAATATAAATAATATTCATA 1 207 1 TAATATAAAT 0.762513 -94 GAACATGAGGTTTTTATAAATCTTACTGCTT 5 96 0 TTTTATAAAT 0.584581 -205 TTTTAGGTATTAATTATAGATTTAATAGATA 8 35 1 TATTATAGAT 0.834675 -55 TGATATTATGTTCTTATAAATTCCAAGAGGT 11 274 1 TCTTATAAAT 0.793316 -27 TTTGATTGCTTCATTATAAATCA 12 3 0 TATTATAAAT 0.909098 -298 TTGTGAATATAGATCGTGTATGCA 19 4 1 TAATATAGAT 0.618447 -184 TATGTTATAATTATTATAAATAATGAGTTCT 33 91 1 TATTATAAAT 0.909098 -73 TATGTTAGAATGATTATAAATTAAGATTGGG 33 121 1 TATTATAAAT 0.909098 -43 ATAATGATTATCATTATCAATTATAAAAATA 36 89 0 TATTATCAAT 0.75959 -105 ATAATGATAATCATTATCAATAGATTGCGTT 36 103 1 TATTATCAAT 0.75959 -91 TATGATATGATAATTATAGATTTTACCAATA 39 27 0 TATTATAGAT 0.834675 -165 CAATTAGAAATCGTTATAAATATATGAACCG 41 266 0 TGTTATAAAT 0.67592 -35 ATTTTTGGTCTACATATAAATATGCGGTCAT 43 94 0 TCATATAAAT 0.552028 -107 * ********* Masking position 6 Map Score: 4.59473 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 50 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 15 TTATCCCCTCAATGAAGAATTCCGGGTCAGCT 5 279 1 AAGAAAATTC 0.725518 -22 TGATTTATAATGAAGCAATCAAAAGAAAAG 12 9 1 AAGAACAATC 0.910039 -292 ATTTCAAGATAGTGAATCAATCACTTGATTAT 13 184 1 AGGAACAATC 0.795186 -44 CTCCTCCCAAAAGGATACATTCAGTTCGTTTA 20 270 0 AAGATCATTC 0.953245 -31 GCCCGTTTCAAAGCATACATTCATAGAAGACA 21 71 1 AACATCATTC 0.704227 -67 CATAATTCAAAATGATACAATCTAATTTATGT 25 153 1 AAGATCAATC 0.923201 -47 GCTTCAGGGAAAAGAAGCATTCCTA 33 4 0 AAGAACATTC 0.944925 -160 CGGTTGAAAAAGAGATTAATTCATAATATACT 39 99 1 AGGATAATTC 0.546591 -93 AGCAATCATCAAAGATCCAATCTGTACATTTG 39 134 0 AAGATCAATC 0.923201 -58 ATAAAGATTCATTTTCAAAAACAT 41 3 1 AAGATCATTT 0.616338 -298 CCCTTTTTAAAACGAAACATTCTACAGCACAT 43 170 0 AAGAACATTC 0.944925 -31 ** *** ***** Masking position 5 Map Score: 4.15161 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 138 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405