AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_bsub_reg_300.orf -o00252_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 yccC 216 similar to asparaginase #2 ycnG 106 similar to 4-aminobutyrate aminotransferase #3 ydcB 94 similar to holo- acyl-carrier protein synthase #4 ydcC 60 ydcC #5 dal 114 D-alanine racemase #6 purE 300 phosphoribosylaminoimidazole carboxylase I #7 ykrV 94 similar to aspartate aminotransferase #8 ylaM 102 similar to glutaminase #9 ylaN 97 ylaN #10 ylaO 205 similar to cell-division protein #11 pycA 74 pyruvate carboxylase #12 ileS 300 isoleucyl-tRNA synthetase #13 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #14 lsp 102 signal peptidase II #15 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #16 pyrP 171 uracil permease #17 pyrB 145 aspartate carbamoyltransferase #18 yncD 300 similar to alanine racemase #19 asnS 143 asparaginyl-tRNA synthetase #20 aspB 22 aspartate aminotransferase #21 ypmA 142 ypmA #22 dinG 125 ATP-dependent helicase #23 panB 245 ketopantoate hydroxymethyltransferase #24 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #25 ypjD 300 alternate gene name: jojD #26 ansB 44 L-aspartase #27 ansA 181 L-asparaginase #28 alaS 300 alanyl-tRNA synthetase #29 hisS 300 histidyl-tRNA synthetase #30 nadB 102 L-aspartate oxidase #31 argG 169 argininosuccinate synthase #32 moaB 84 molybdopterin precursor biosynthesis protein B #33 ackA 300 acetate kinase #34 asnB 149 asparagine synthetase #35 metK 300 S-adenosylmethionine synthetase #36 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #37 ywfB 151 alternate gene name: ipa-80d #38 ywfA 209 alternate gene name: ipa-79d; similar to chloramphenicol resistance #39 rocB 73 alternate gene name: ipa-77d #40 rocA 226 pyrroline-5 carboxylate dehydrogenase #41 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #42 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis #43 yxbB 300 alternate gene name: yxaP; similar to hypothetical proteins #44 purA 205 adenylosuccinate synthetase #45 yycE 120 yycE #46 dnaC 169 replicative DNA helicase Motif number 1 TAGCGGTTATAAAAAAACCCAAACTGTTAA 10 30 0 AAAAAAACCC 0.747214 -176 TCAGAAAATAAAAAAAGCCCTCTCATCCCA 12 258 0 AAAAAAGCCC 0.963597 -43 TCTTGGCACAAAAAAAGCCCGGCTTTTACG 13 26 0 AAAAAAGCCC 0.963597 -52 TATTTCAGAAAAGAAACCCTCTGTCAACCG 15 95 0 AAGAAACCCT 0.861358 -179 CATATAGAAGAAAAAACCCCTCCTGCCAGA 15 235 0 AAAAAACCCC 0.985287 -39 TGACTGTATAAAAAAACCTCTTTGCTTTTT 16 107 0 AAAAAACCTC 0.968315 -65 TAAGGCTGAAAAAAAACCCCGGTCTAAGAT 17 102 0 AAAAAACCCC 0.985287 -44 AAGAAAAGCCCCCTTTATCGG 22 2 1 AGAAAAGCCC 0.866043 -124 AAATCTTAAAAGAAAACCCCCGATAAAGGG 22 21 0 AGAAAACCCC 0.942383 -105 TCTGCAAGCCAAAAAACCTTCCGTTACAAC 23 182 0 AAAAAACCTT 0.877074 -64 CAAGCATCACACAAAACCCCTTTTCCTTCC 25 165 1 ACAAAACCCC 0.918225 -136 TGAACGAAACCTCCTATCATCCT 25 288 0 ACGAAACCTC 0.67064 -13 CAGTGACAGCAAAAAAGCCCTCCCCCTATG 28 246 0 AAAAAAGCCC 0.963597 -55 CGCGTTCAGCAGGAAACCTCCGGAGTGTTG 29 84 0 AGGAAACCTC 0.747855 -217 ATGAAAATGAAAAAAACTCCCGCCCCTACT 29 231 0 AAAAAACTCC 0.854194 -70 CGTTCTCCATAAAAAACTCTTGAGTTTATT 30 27 1 AAAAAACTCT 0.577663 -76 CCTTTTATAAAAAAAACTTCACCTAAATTT 31 39 0 AAAAAACTTC 0.727779 -131 GATAAAAATCCCCTCTCAACCGT 31 157 0 AAAAATCCCC 0.776091 -13 TTATGAAATAAAAAAACCTTTTCCATCGAG 35 171 0 AAAAAACCTT 0.877074 -130 CATACAAACAAAAAAACCCTTTAAAAAGGG 37 41 0 AAAAAACCCT 0.939886 -111 GTAACACGTAAAAAAAGCTCTCCGGCCTCC 38 24 0 AAAAAAGCTC 0.923545 -186 ATGCTCAATGAAAAAAGCTTATAAGAAACC 43 55 1 AAAAAAGCTT 0.738238 -246 AAAAGCTTATAAGAAACCTCGCCTTTTTGA 43 67 1 AAGAAACCTC 0.923918 -234 ATGCTCAATGAAAAAAGCTTATAAGAAACC 43 173 1 AAAAAAGCTT 0.738238 -128 AAAAGCTTATAAGAAACCTCGCCTTTTTGA 43 185 1 AAGAAACCTC 0.923918 -116 TTTCGAATGAAAAAAACCCCAAGAGCAGCT 45 19 0 AAAAAACCCC 0.985287 -102 ********** Masking position 5 Map Score: 42.0647 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 268 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 2 TTTGTTGTCATATCCTTCTTTTTTTGTCTTTTCAT 1 102 0 TTCCTTTTTT 0.964003 -115 TCCGAGCCCCTTTTCTTCATTTTGG 3 1 1 TCGCCTTTTC 0.372928 -94 ACCCCAAATTTTTCTTTACTTTTTTCATTTAACCA 7 20 1 TTCATTTTTT 0.707906 -75 TGGACTATCATTTCAAGATTTTTTTAGAAGGTGAG 7 65 1 TTCATTTTTT 0.707906 -30 TGACTGTCCCTTTCAACCGTTTTTTCATCTGAATT 12 23 0 TTCCTTTTTT 0.964003 -278 TTTCATTCCTCCACTGCATTTTTTCAGAAAATAA 12 277 0 TCACTTTTTT 0.694553 -24 ATTTCTTTACTCCAGTGCTTTTTATTGATAAAATG 14 39 1 TCACTTTTAT 0.344427 -64 AGAAACCCTCTGTCAACCGTTTTTTCTGAGGTTTT 15 79 0 TTCCTTTTTT 0.964003 -195 CTTCTCAGCCTCTCTGGACTGTTTTAAAGAATCTA 15 140 0 TTCATGTTTT 0.429048 -134 GTTCTTTCCCCTCTCTTTTCAACTTAAGGC 17 126 0 TCCCCTTTTC 0.759011 -20 GATTATTTGTTTTGGGACATTTTTTTCTAAGGGTA 18 45 0 TTGCTTTTTT 0.834896 -256 GCGGCTTTTCTGTCAGCCGCTTTTTGATCTG 19 7 0 TTCCCTTTTT 0.922725 -137 AGCTTCCGAATGTCTTTCTTGTTTTGGAGGGAAAT 19 116 1 TTCCTGTTTT 0.892516 -28 CATCCCTCTGTCCCAGTCCTTTTTTGGATCAAGGC 23 110 0 TCCCTTTTTT 0.950251 -136 GAACTTCCGCTCCTTTTTCACCTTGAGCT 27 5 1 TCCCTTTTTC 0.875988 -177 TGAATAATAATGTCTTGCGTATTTTATTTTCCGTG 27 77 1 TTCCTATTTT 0.562286 -105 CGTTTCGTTTTTTCAAGCCTTTTATAAAAAAAACT 31 51 0 TTCCTTTTAT 0.860872 -119 AAAAATCCCCTCTCAACCGTGTTTCTATTTTGTAT 31 142 0 TTCCTGTTTC 0.754347 -28 CAACTTCGTTTTTCGTACTTTTTTCCCGGTGAATA 33 247 0 TTCCTTTTTC 0.908287 -54 TCTGTGTCACTCCCTTTTTTTGATGGTTG 36 5 1 TTCCCTTTTT 0.922725 -143 TAGCGGAAGTTTCTCCTCGTTTTTTCTTAGCATTC 36 65 1 TCTCTTTTTT 0.635874 -83 CTCATGACATTATATCACGTTTTTTGACGAATGCT 36 93 0 TTACTTTTTT 0.761227 -55 AACGCAAATTTATTTTGCGTTTTTTGCTCTTTACG 40 52 0 TTTCTTTTTT 0.710009 -175 ATGTAGTCCCCCTCGTGTTATGAAATATATC 40 206 0 TCCCTGTTAT 0.577777 -21 ACTGAGATGTTTTCAGTCTCTTTTTTTGTGGATTC 41 32 1 TTCCCTTTTT 0.922725 -145 TCTTCGACTTTTTTTGCCCTTTTTTAAAATAGGAT 42 22 1 TTTCTTTTTT 0.710009 -279 TAGTAACATCTGCCTGACATTTTATATCTTTTATC 42 54 0 TCCCTTTTAT 0.81527 -247 AAATGGACGATTTCCCTCTCTTTTTCTAGTAACAT 42 80 0 TTCCCTTTTT 0.922725 -221 AGGATGAAAGTTTCGCAAGCTTTTTATGACAAAGC 44 27 1 TTCACTTTTT 0.519371 -179 ATTCGTTCGCTTCCATTCGTTTTATAAGCGTTTTC 44 67 0 TCCCTTTTAT 0.81527 -139 CCATCTCCTTTTTGCACCATTTTATTAAAACGCTT 45 89 0 TTGCTTTTAT 0.538825 -32 TCCCTTATGTTTTATTGCATTTTTCCCGCCTTGTT 46 21 1 TTACTTTTTC 0.541069 -149 AGAAAAATTGTCTGTTTCCTGTTTTTTTCAGTTAG 46 79 0 TTGCTGTTTT 0.610582 -91 * ** * ****** Masking position 12 Map Score: 29.8459 Number of sites scoring better than the average of aligned sites = 1231 Number in coding regions = 964 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 283 Fraction of orfs with sites within 600 bp upstream = 0.0454545 Motif number 3 AAAGACAAAAAAAGAAGGATATGACAACAAA 1 106 1 AAGAAGGATA 0.87434 -111 TTTGATGGTATCAGAAGGAGAAACTACAAA 2 10 0 TAGAAGGAGA 0.836313 -97 GAAAATACCGACAGGGGGATATTCAC 2 91 1 AAGGGGGATA 0.937969 -16 CGCCTGGGGAACGGAGGGATACTT 9 84 1 AGGAGGGATA 0.867833 -14 TCCATTCGGGTAAGGGGGAGAAAAGT 11 59 1 TAGGGGGAGA 0.917378 -16 CCAGAGAGGCTGAGAAGGATAACGGATAGAC 15 158 1 TAGAAGGATA 0.87434 -116 AAGTCAACAATCAGGGGGAAATCATC 16 156 1 TAGGGGGAAA 0.937969 -16 AGGGTTATGAAGAGAAGGAAGCTTCAATGCT 17 43 1 AAGAAGGAAG 0.866619 -103 TTATAATCCATAAGAAGGAAGGAAGCGTTG 18 281 1 TAGAAGGAAG 0.866619 -20 CTTTCTTGTTTTGGAGGGAAATATG 19 129 1 TGGAGGGAAA 0.867833 -15 AAGGACTGGGACAGAGGGATGAAACTCGCCG 23 124 1 AAGAGGGATG 0.926112 -122 CCTCTAAACATGAGGAGGAGAAAAC 23 231 1 TAGGAGGAGA 0.851977 -15 ACGCTATCTAATGGAAGGAAAAGGGGTTTTG 25 176 0 AGGAAGGAAA 0.772922 -125 GTTGGTTTGCATAGGGGGAGGGCTTTTTTGC 28 237 1 AAGGGGGAGG 0.912036 -64 CGATTTTTATAGAGGAGGAAATACA 28 286 1 AAGGAGGAAA 0.886857 -15 GGTGTAAACAACAGGAGGATGGCAT 30 88 1 AAGGAGGATG 0.8798 -15 AACACAAAATACAGAGGGAAAAACCGCAAAT 33 65 1 AAGAGGGAAA 0.930664 -236 TACTAGAAAAAGAGAGGGAAATCGTCCATTT 42 84 1 AAGAGGGAAA 0.930664 -217 CAACAATCAATTAGGGGGAAATGTC 42 286 1 TAGGGGGAAA 0.937969 -15 TACTCTATTTTAGGAGGGATGCTCAATGAAA 43 37 1 TGGAGGGATG 0.859777 -264 TACTCTATTTTAGGAGGGATGCTCAATGAAA 43 155 1 TGGAGGGATG 0.859777 -146 GCCAACTTGATAAGGAGGATGCTGAAG 43 284 1 TAGGAGGATG 0.8798 -17 * ********* Masking position 9 Map Score: 25.2929 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 123 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 4 AAAATAAAAAATACCCGCTCTGCATTGCAC 6 247 0 ATACCCGCTC 0.950104 -54 GGCTTTTCTGTCAGCCGCTTTTTGATCTG 19 10 0 TCAGCCGCTT 0.779897 -134 GGCTGACAGAAAAGCCGCTTTTTATCTGCA 19 24 1 AAAGCCGCTT 0.830509 -120 TCACTTTATTATACCCGCTCTTAACTAACC 19 61 0 ATACCCGCTC 0.950104 -83 CCACACCGCAAAAGCCGCTTTATGCGGCTT 21 11 0 AAAGCCGCTT 0.830509 -132 TAAAAGCGGATTTCCCGCTCTGTGATACTA 21 61 1 TTTCCCGCTC 0.894636 -82 GTAAAACGGTTTTGCCGCTCCATTTCCGTA 22 56 1 TTTGCCGCTC 0.926503 -70 AAATGAAAAAATTGCCGCTCCGATTAAAAT 25 106 1 ATTGCCGCTC 0.972976 -195 GAACTTCCGCTCCTTTTTCACC 27 3 1 ACTTCCGCTC 0.697869 -179 GCAGTTAATCACTGCCGCTTATCCTGCGTT 28 129 1 ACTGCCGCTT 0.928001 -172 ATACGTTCATATTCCCGCTCGATCCTTTAA 29 150 0 ATTCCCGCTC 0.960398 -151 AATGAAAAAAACTCCCGCCCCTACTATACA 29 226 0 ACTCCCGCCC 0.816396 -75 GATTGACGCTCCTTTATACTC 33 290 0 ATTGACGCTC 0.655542 -11 TTTTATAGCCGCTTACTGGTTAAG 34 5 1 ATAGCCGCTT 0.932351 -145 TAAAAAAGGGAAAGCCGCTTAACCAGTAAG 34 22 0 AAAGCCGCTT 0.830509 -128 TTATTGCATTTTTCCCGCCTTGTTACTGTC 46 32 1 TTTCCCGCCT 0.508265 -138 ********** Masking position 6 Map Score: 16.4486 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 474 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 TTTTGATTGCAATTCAGTAAGGTGGGAATGTT 1 11 0 AATCATAAGG 0.835883 -206 TATATTTGATAGTGCATTAAGGGAGACAAGTT 4 37 1 AGTCATAAGG 0.890991 -24 TCATAAGTGCAATGCAGAGCGGGTATTTTTTA 6 241 1 AATCAAGCGG 0.800618 -60 ACCTACTGTGAGTTCAGCAAGGAAACTAAAGG 12 130 0 AGTCACAAGG 0.827421 -171 TTATTGATAAAATGCATAATGGATTAAAGTAA 14 60 1 AATCAAATGG 0.628011 -43 TCTTTAAAACAGTCCAGAGAGGCTGAGAAGGA 15 145 1 AGTCAAGAGG 0.976109 -129 CCCTCCTGCCAGAGCATAGAGGGGTTTTAGGA 15 216 0 AGACAAGAGG 0.922823 -58 CTTTTTAAGCAATCCAGAGAGGTTGCAAAGAG 16 19 1 AATCAAGAGG 0.962206 -153 TTTGCGTAAAAAAGCAAAGAGGTTTTTTTATA 16 99 1 AAACAAGAGG 0.881669 -73 TTTTAATGAAAGTCCAGAGAGGCTTGGAAGGG 17 15 1 AGTCAAGAGG 0.976109 -131 GCCGGCCAAAAAAACAATGAGGTGAAAAAG 41 157 1 AAACATGAGG 0.705197 -20 AGCACGGCGCAGTTCAAAAAGGCGAGGTTTCT 43 78 0 AGTCAAAAGG 0.962206 -223 AGCGCGGCGCAATTCAAAAAGGCGAGGTTTCT 43 196 0 AATCAAAAGG 0.940703 -105 TTAATAAAATGGTGCAAAAAGGAGATGGTAAC 45 96 1 GGTCAAAAGG 0.787858 -25 *** ** ***** Masking position 6 Map Score: 11.2007 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 51 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 GTTTGTATTGCTTCCTCATAAGTGCAATGCAGA 6 226 1 CTTCCTATAT 0.763426 -75 CTGTTCCCCACCTTCTAATGCTTTTGTTTTCAG 6 277 0 CCTTCTATGT 0.879846 -24 GATGATTTCCCCCTGATTGTTGACTTTCATT 16 151 0 CCCCCTATTT 0.913247 -21 ACGCTTCCTTCCTTCTTATGGATTATAAATACC 18 276 0 CCTTCTATGT 0.879846 -25 GGGCAATGAGCTTCCGAATGTCTTTCTTGTTTT 19 108 1 CTTCCGATGT 0.746468 -36 CTTGAACTCCCCCTAATTCGTC 20 2 0 CCCCCTATTT 0.913247 -21 GTTTTCTCCTCCTCATGTTTAGAGGAGATG 23 226 0 CCTCCTATGT 0.983015 -20 TTCGCGTACACTTCCTAATACCTATATGATATA 27 43 0 CTTCCTATAT 0.763426 -139 AGGTAGACCTCCTTATGTATTCCTTATAAA 29 281 0 CCTCCTATGT 0.983015 -20 ATGCCATCCTCCTGTTGTTTACACCTGTCT 30 83 0 CCTCCTTTGT 0.860315 -20 TTACGTGTTACATCCTCATGTATTTTTAGAATG 38 43 1 CATCCTATGT 0.850161 -167 GACATTTCCCCCTAATTGATTGTTGAAATT 42 281 0 CCCCCTATTT 0.913247 -20 CTTTCATTCCTCCCTTATGTTTTATTGCATTT 46 10 1 CTCCCTATGT 0.932007 -160 ****** *** * Masking position 9 Map Score: 9.39891 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 97 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 TCAAGAAAAATTCATTGTATGAAAAGACAAAAAA 1 84 1 TTATTGTGAA 0.656074 -133 GCCCCTTTTCTTCATTTTGGTATATCTATAGTAA 3 16 1 TTATTTTTAA 0.850627 -79 CCTTTAGCCTTTAATTTTAGTATGATATGTAAAT 5 61 1 TTATTTTTAG 0.835666 -54 GCGGGTATTTTTTATTTTCTGAAAACAAAAGCAT 6 259 1 TTATTTTGAA 0.890991 -42 ATTTATCTTTTTTATTTTACTACAATTTATCAAA 10 134 0 TTATTTTTAA 0.850626 -72 GAGGGCTTTTTTTATTTTCTGAAAAAATGCAGTG 12 266 1 TTATTTTGAA 0.890991 -35 ATTGTTGACTTTCATTTTAGGATGACTCAATGAC 16 133 0 TTATTTTGAG 0.879499 -39 AGAATAAATGTTAATTGTTGGATGATTCGATCTT 18 229 0 TTATTGTGAG 0.630099 -72 TTAGTCATACTCCATTTCAGGACACGCCATACTA 21 89 0 TCATTTCGAA 0.671589 -54 GTTTTGCCGCTCCATTTCCGTACAAAACGTGTTA 22 64 1 TCATTTCTAA 0.58759 -62 TACAAGCCCGTTGATTTTGGTATACTTCCATTGG 23 19 1 TTATTTTTAA 0.850627 -227 TTTGGCTTGGTTCATTTCAATATGCAGAACAATC 25 75 0 TTATTTCTAG 0.649066 -226 GAAGAGAATTTCGATTTTTATAGAGGAGGAAATA 28 275 1 TCATTTTTAA 0.796635 -26 TTAAATATAATTTATTTTTATACAAAATAGAAAC 31 123 1 TTATTTTTAA 0.850626 -47 TGTATTCATGTTTATTTTTTTACATAACTGTGAA 34 56 1 TTATTTTTAA 0.850627 -94 CATCTAGTACTCTATTTTAGGAGGGATGCTCAAT 43 30 1 TCATTTTGAG 0.833906 -271 CATCTAGTACTCTATTTTAGGAGGGATGCTCAAT 43 148 1 TCATTTTGAG 0.833906 -153 ** ***** ** * Masking position 6 Map Score: 9.31749 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 206 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 8 ACATGACTGTCCCTTTCAACCGTTTTTTCAT 12 30 0 CCTTTCAACC 0.910736 -271 GCGAGATAAGCTTTCTCGTCCCTTATGGGAT 12 233 1 CTTCTCGTCC 0.878396 -68 ATAAAAAAAGCCCTCTCATCCCATAAGGGAC 12 250 0 CCTCTCATCC 0.980307 -51 AAAAGAAACCCTCTGTCAACCGTTTTTTCTG 15 86 0 CCTGTCAACC 0.78861 -188 TATCCGTTATCCTTCTCAGCCTCTCTGGACT 15 155 0 CTTCTCAGCC 0.910618 -119 CCTGTAAAACCGCCCTCAGCCAGATTGTTCT 25 53 1 CCCCTCAGCC 0.848259 -248 TTGCTGTTTTCTTTTTCATCCACTATAATAT 25 209 0 CTTTTCATCC 0.866253 -92 ACCGCGAGACAGCTCTCGTCCCTGTGTAAAC 28 206 1 ACTCTCGTCC 0.878396 -95 CAATGGGATCCGCTTTCAGCCTGGGGCGGGT 29 39 0 CCTTTCAGCC 0.941325 -262 CCACGGGTATAACTCTCGTCCCTACTATCAT 29 196 1 ACTCTCGTCC 0.878396 -105 GATAAAAATCCCCTCTCAACCGTGTTTCTAT 31 149 0 CCTCTCAACC 0.95752 -21 AAGCTTGCGAAACTTTCATCCTTTAGCATAA 44 18 0 ACTTTCATCC 0.866253 -188 AACGCTTTCAATTTTTCATCCGCTGAGCGAA 45 65 0 ATTTTCATCC 0.65056 -56 * ********* Masking position 6 Map Score: 9.24892 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 204 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 TGATATGTAAATGATATTGAATAAAAGCTAGGAAGT 5 83 1 ATATGAATAA 0.928709 -32 CGTTGTTAAGATAAACATGAAATCAAAACACGACCT 6 53 1 ATATGAAAAA 0.908187 -248 ATGATTTCAAATAAAGTTGAATAAAATAAGATCGAA 18 202 1 ATATGAATAA 0.928709 -99 AATAAAAAATATGTTTTTTAATCTAATTTCTCCAAG 25 133 1 ATTTTAATAA 0.463219 -168 TAGCGTTTATATTATAGTGGATGAAAAAGAAAACAG 25 201 1 ATATGGATAA 0.655207 -100 ATCGTTAATGATGAAAATGAAAAAAACTCCCGCCCC 29 235 0 ATATGAAAAA 0.908187 -66 ATAAAAATAAATTATATTTAATAAAAATACATTTTG 31 108 0 ATATTAATAA 0.602072 -62 CCTATAGTGAATGTGTCTGAAAATAACGACTTCTTA 33 119 1 ATTTGAAAAA 0.849438 -182 ATGTAAAAAAATAAACATGAATACAACGATAAAAAA 34 45 0 ATATGAATAA 0.928709 -105 ATTTTTTTACATAACTGTGAAACCAAATACTATTCA 34 69 1 ATATGAAAAA 0.908187 -81 GTTAATTGGCATATTTATGAAATAAAAAAACCTTTT 35 179 0 ATTTGAAAAA 0.849438 -122 ATATAATGGGATTTAAATGAAAATAATAAAACTTAT 38 88 1 ATTTGAAAAA 0.849438 -122 TTGCATGATGATAAGGGTGAATCCAATGAAGAAAGG 41 84 1 ATATGAATAA 0.928709 -93 GATAAACTTGATTTGTTTGAATAGAATCGTTTTGAA 44 158 1 ATTTGAATAA 0.881376 -48 ** * ***** ** Masking position 11 Map Score: 9.85474 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 128 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 AGAAGAATTAGGTACTCGCCTGGGGAACGGA 9 68 1 GGTACCGCCT 0.980116 -30 CTTATCTCGCGGTACCACCCTTTTAGAAAAA 12 212 0 GGTACACCCT 0.974546 -89 TTTAGGACAAGGTGCGCGCCTATACACGCAT 15 192 0 GGTGCCGCCT 0.979722 -82 TGTGTTGGTACAAGCCCGTTGATTTTG 23 7 1 GGTACAGCCC 0.966075 -239 GCTGTCTCGCGGTACCACCCTGATTACGGGC 28 188 0 GGTACACCCT 0.974546 -113 TGATTAGAGAGGAACCCGCCCCAGGCTGAAA 29 26 1 GGAACCGCCC 0.83339 -275 TTATACCCGTGGTGCCACCCTAGTTGGAATA 29 177 0 GGTGCACCCT 0.974044 -124 AGACAACCAAGGTGCTAACCTGTTGCAAGGT 35 88 1 GGTGCAACCT 0.904264 -213 ***** ***** Masking position 5 Map Score: 5.16379 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 19 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 AAGTATCCCTCCGTTCCCCAGGCGAGTAC 9 79 0 CCTCCGTTCC 0.984736 -19 TGAACGAAACCTCCTATCATCCTCTTACATG 25 280 0 CCTCCTATCC 0.942479 -21 TTCTGATAAAGCTCCTTTCAGCTTATGGAGCT 28 73 0 GCTCCTTTCC 0.941509 -228 GGATTAGCTTCCTCCGATCTTCTGATAAAGCT 28 92 0 CCTCCGATCC 0.971298 -209 GGTCTTCCTCCATCCGTTCTCCATAAAAAACT 30 13 1 CATCCGTTCC 0.927025 -90 GATTGACGCTCCTTTATACTCTGTATCAA 33 282 0 GCTCCTTTAC 0.760177 -19 GTCCGTGCACCTCCGTTAACCTTTCAAAACG 44 185 0 CCTCCGTTAC 0.927025 -21 TGTCCGAAACGATCCAATCTGCTAACTGAAAA 46 58 1 GATCCAATCC 0.537123 -112 AAATCTCCAACCTCCATTCTACCATTTCTACA 46 124 0 CCTCCATTCC 0.956138 -46 ********* * Masking position 8 Map Score: 3.65157 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 86 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 CCGGTTTGTATTGCTTCCTCATAAGTGCAAT 6 223 1 TTCTTCCTCA 0.852257 -78 TGTCATATGCTTAAATCCTCTTGCATTTTCT 9 15 1 TTAATCCTCT 0.560132 -83 TTTCATTCCTCCACTGCATTTT 12 289 0 TTATTCCTCC 0.880472 -12 CAACGCTTCCTTCCTTCTTATGGATTA 18 284 0 TTCTTCCTTC 0.705387 -17 TTTTTCATCCTCCAGTTTGAACA 21 130 0 TTCATCCTCC 0.970904 -13 CGAAACCTCCTATCATCCTCTTACATGTTAG 25 276 0 TACATCCTCT 0.696757 -25 CACTCAGGATTAGCTTCCTCCGATCTTCTGA 28 99 0 TACTTCCTCC 0.930028 -202 ATGCCATCCTCCTGTTGTTTAC 30 91 0 TGCATCCTCC 0.886318 -12 GATTTGCTTCCTCCTGCACAAGGC 35 287 0 TTCTTCCTCC 0.970904 -14 TTTTTACGTGTTACATCCTCATGTATTTTTA 38 40 1 TTCATCCTCA 0.852257 -170 CTTCAGCATCCTCCTTATCAAGTT 43 287 0 CACATCCTCC 0.695282 -14 CTTTCATTCCTCCCTTATGTTTT 46 3 1 TTATTCCTCC 0.880472 -167 ** ******** Masking position 6 Map Score: 7.40649 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 136 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 13 TCCATTAGATAGCGTTTATATTATAGTGGA 25 192 1 AGCGTTTATA 0.574053 -109 TATGCAAACCAACGTTTACACAGGGACGAG 28 220 0 AACGTTTACA 0.844164 -81 TGTATTGATGAACGCTTACAATTTGCGGTT 33 86 0 AACGCTTACA 0.964924 -215 GCGTATTGATAACGCTTACAATAAGAAGTC 33 146 0 AACGCTTACA 0.964924 -155 GATTTTTTAAAGCGCTTACATTACAGCCGG 41 132 1 AGCGCTTACA 0.930781 -45 CTCAATGAAAAAAGCTTATAAGAAACCTCG 43 58 1 AAAGCTTATA 0.733841 -243 CTCAATGAAAAAAGCTTATAAGAAACCTCG 43 176 1 AAAGCTTATA 0.733841 -125 GCAGTGAGAAAACGCTTATAAAACGAATGG 44 60 1 AACGCTTATA 0.933342 -146 ATTTTATTAAAACGCTTTCAATTTTTCATC 45 76 0 AACGCTTTCA 0.812617 -45 ********** Masking position 6 Map Score: 5.1915 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 44 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 14 CATAGTCCGGCAATTTACGGTTGCCGGGTA 6 122 0 CAATTTACGG 0.639889 -179 AACGTTCCTCCAGTTTACGGTTACTTTAAT 14 82 0 CAGTTTACGG 0.771669 -21 GATGATAAAAGAGTTCGCGGGGCAATGAGC 19 89 1 GAGTTCGCGG 0.911648 -55 ATAATAGGTGCAGTTCGCAGGCGATACTGC 23 53 0 CAGTTCGCAG 0.676095 -193 CATTATTATTCAATTCGCGTACACTTCCTA 27 59 0 CAATTCGCGT 0.682116 -123 TGAACGCTTACAATTTGCGGTTTTTCCCTC 33 78 0 CAATTTGCGG 0.920217 -223 CTTTTCAAGTCAACTTGCGTATTGATAACG 33 162 0 CAACTTGCGT 0.624311 -139 TCCCGAGCTGGCGGAGGGACAGGC 35 5 1 GAGCTGGCGG 0.926872 -296 ATGAAGAAAGGAATTGGCGGGCTGATTTTT 41 109 1 GAATTGGCGG 0.876934 -68 CGTGCTGTAGCAGCTGGCGGCCATTAATCT 43 104 1 CAGCTGGCGG 0.970166 -197 CGCGCTGTAGCAGCTGGCGGTCATTAATCT 43 222 1 CAGCTGGCGG 0.970166 -79 ********** Masking position 2 Map Score: 4.00588 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 443 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 15 TCAACAGAAAATGCAAGAGGATTTAAGCAT 9 21 0 ATGCAAGAGG 0.864179 -77 AGTTAGAAGCAGGGAAGAGGATGTT 10 191 1 AGGGAAGAGG 0.955366 -15 AGGGGCTGATGTGGAAAAGGGCATAAAGCA 25 12 1 GTGGAAAAGG 0.851336 -289 TATCTAATGGAAGGAAAAGGGGTTTTGTGT 25 173 0 AAGGAAAAGG 0.831107 -128 ATTAGCTAACATGTAAGAGGATGATAGGAG 25 271 1 ATGTAAGAGG 0.811068 -30 CTTTAGATACAGTGAAGAGGTGCATGGT 27 164 1 AGTGAAGAGG 0.651575 -18 CAATGTTTAAATGGAAAAGTCAGATATTTT 33 201 1 ATGGAAAAGT 0.7058 -100 CCTTTCCTCGATGGAAAAGGTTTTTTTATT 35 165 1 ATGGAAAAGG 0.964862 -136 TAAGAAGATTATGGAAGAGGTGTTTGAGAA 38 187 1 ATGGAAGAGG 0.977673 -23 ATTTACTTCCATGGAAAATGATGATAGATT 42 178 1 ATGGAAAATG 0.7058 -123 ********** Masking position 5 Map Score: 3.44053 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 283 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392