AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_bsub_reg_300.orf -o00330_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 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 amhX 300 amidohydrolase #5 yclB 89 similar to phenylacrylic acid decarboxylase #6 yitV 120 similar to hypothetical proteins #7 yitW 63 similar to hypothetical proteins #8 yitX 54 yitX #9 yitY 57 similar to L-gulonolactone oxydase #10 yitZ 44 similar to multidrug resistance protein #11 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #12 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #13 ykrV 94 similar to aspartate aminotransferase #14 flgB 300 flagellar basal-body rod protein #15 fliF 45 flagellar basal-body M-ring protein #16 fliH 117 flagellar assembly protein #17 fliK 160 fliK #18 flgE 21 flagellar hook protein #19 fliL 251 flagellar protein #20 fliM 33 flagellar motor switch protein #21 cheY 25 two-component response regulator #22 flhA 32 flagella-associated protein #23 cheW 21 cheW #24 sigD 22 RNA polymerase sigma-28 factor (sigma-D) #25 ylxL 28 ylxL #26 rpsB 143 ribosomal protein S2 #27 tsf 101 elongation factor Ts #28 smbA 145 uridylate kinase #29 yluA 130 similar to hypothetical proteins #30 yluB 61 similar to hypothetical proteins #31 proS 32 prolyl-tRNA synthetase #32 ynaD 300 similar to hypothetical proteins #33 kdgK 37 2-keto-3-deoxygluconate kinase #34 kdgR 221 transcriptional regulator (LacI family) #35 aspB 22 aspartate aminotransferase #36 ypmA 142 ypmA #37 dinG 125 ATP-dependent helicase #38 panB 245 ketopantoate hydroxymethyltransferase #39 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #40 ypjD 300 alternate gene name: jojD #41 argG 169 argininosuccinate synthase #42 moaB 84 molybdopterin precursor biosynthesis protein B #43 ackA 300 acetate kinase #44 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #45 ywiB 300 ywiB #46 ywhG 60 similar to agmatinase #47 ywhF 201 similar to spermidine synthase #48 ywfB 151 alternate gene name: ipa-80d #49 ywfA 209 alternate gene name: ipa-79d; similar to chloramphenicol resistance #50 rocB 73 alternate gene name: ipa-77d #51 rocA 226 pyrroline-5 carboxylate dehydrogenase #52 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #53 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis #54 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #55 aldX 142 aldehyde dehydrogenase #56 rocF 73 arginase #57 rocE 222 amino acid permease #58 rocD 240 ornithine aminotransferase Motif number 1 GCTGACCAGGCTGTTTTTTTGCTGCGCAGA 2 23 1 CTGTTTTTTT 0.867747 -204 CAGTGATTTACCGCTTTTTTATAAAATATC 2 65 1 CCGCTTTTTT 0.946558 -162 GTTCCCTCACTCCTTTTTTCTACAGTATA 7 45 0 CTCCTTTTTT 0.946102 -19 ATGTCAGGCTGTCCTTTTTTGTT 8 4 0 GTCCTTTTTT 0.912323 -51 ATGTGAGGCTGTCCTTTTTTACAGCTGAAA 8 32 1 GTCCTTTTTT 0.912323 -23 AGTGCTCTCCCTGCTGTTTTTATGACCA 9 9 0 CTGCTGTTTT 0.777449 -49 CGCGGTCAGCCTGTTTTTTTATGCGGCTGA 11 11 1 CTGTTTTTTT 0.867747 -196 TGGAGTCGTGCTGATTTTTTTTGAGCGGAA 11 70 1 CTGATTTTTT 0.752321 -137 TAATTGTGAGGACATTTTTTTACACGAACT 14 179 1 GACATTTTTT 0.534948 -122 ACCTCCATTTCAGTTTTTTTCACCCTCAAT 14 273 0 CAGTTTTTTT 0.795762 -28 AATCGCTTCTCCGCTGTTTTATGATTAAAG 19 30 1 CCGCTGTTTT 0.791322 -222 TGCCTTTTATCACCTTTTTTCAAGAAAAAT 27 37 1 CACCTTTTTT 0.912463 -65 AATTTGGGAAGAGTTTTTTTAATAATATGT 34 128 0 GAGTTTTTTT 0.697853 -94 CTCTGTCCCAGTCCTTTTTTGGATCAAGGC 38 110 0 GTCCTTTTTT 0.912323 -136 TCTCTTGAATGTGCTTTTTTGTTGATGCAT 42 28 1 GTGCTTTTTT 0.906299 -57 CTGTGTCACTCCCTTTTTTTGATGGTTGTA 44 12 1 CCCTTTTTTT 0.884557 -136 ATTTCCTTTTCACATTTTTTTCAAAATATA 45 83 0 CACATTTTTT 0.659921 -218 AGCGAATCTTGCGCTTTTTTACAGGAAAGC 46 28 1 GCGCTTTTTT 0.913038 -33 AACGGGTTCCCCCTTTTTTTATGTTTCTA 47 10 1 CCCCTTTTTT 0.950136 -192 GGAGGCCGGAGAGCTTTTTTTACGTGTTAC 49 24 1 GAGCTTTTTT 0.851712 -186 TGTTTTCAGTCTCTTTTTTTGTGGATTCAA 52 39 1 CTCTTTTTTT 0.87591 -138 AATTGGCGGGCTGATTTTTTAAAGCGCTTA 52 120 1 CTGATTTTTT 0.752321 -57 AGGCATCTTCGACTTTTTTTGCCCTTTTTT 53 17 1 GACTTTTTTT 0.713035 -284 GACTTTTTTTGCCCTTTTTTAAAATAGGAT 53 27 1 GCCCTTTTTT 0.918668 -274 TCCGTTTCTCCTTTTTGTAAGGTATGG 54 151 0 CTCCTTTTTG 0.564344 -17 CATATCCTCTCCGTTTTTTTATAAAATAGA 58 48 0 CCGTTTTTTT 0.876882 -193 TTTGAATTCCCCCTTGTTTTCTGTTTCAAC 58 220 0 CCCTTGTTTT 0.621282 -21 ********** Masking position 5 Map Score: 29.604 Number of sites scoring better than the average of aligned sites = 1336 Number in coding regions = 968 Number in noncoding regions = 368 Number of orfs with sites within 600 bp upstream = 356 Fraction of orfs with sites within 600 bp upstream = 0.0571796 Motif number 2 TCAGGCTTATATCAGGGCGAGAAATGTAGTTC 14 110 1 ATAGGGCGAA 0.864383 -191 AAACATCTGGGGGAATATATT 18 5 1 ATTGGGGGAT 0.892269 -17 TTAAGGTATTAGGGGGATAACA 24 8 1 ATAGGGGGAA 0.987013 -15 AAACCATTATATTAGGAGGAAATAAC 26 128 1 ATAGGAGGAA 0.956719 -16 TCAAAAGGTGATAAGAGGGACTGCCTTTTATC 27 16 1 ATAGAGGGAT 0.906172 -86 GTTTAAACATATAAGGAGGAATACAA 27 86 1 ATAGGAGGAT 0.965697 -16 GAAATCCTAACCAAGGGGGAAATATA 34 5 0 CCAGGGGGAA 0.842586 -217 GACGAATTAGGGGGAGTTCAAG 35 6 1 ATAGGGGGAT 0.989775 -17 TTCCGTTACAACGAGAAGGATTCTTCACTTTC 38 162 0 ACAGAAGGAT 0.609362 -84 TCCTCTAAACATGAGGAGGAGAAAAC 38 230 1 ATAGGAGGAA 0.956719 -16 CAACTTTTTGATCAGGAGGACAATTT 50 58 1 ATAGGAGGAA 0.956719 -16 ATTTCATAACACGAGGGGGACTACAT 51 211 1 ACAGGGGGAT 0.981737 -16 TTGCATGATGATAAGGGTGAATCCAATGAAGA 52 84 1 ATAGGGTGAT 0.845607 -93 TCAACAATCAATTAGGGGGAAATGTC 53 285 1 ATAGGGGGAA 0.987013 -16 AAGAAAGCAAATGAGGGGGATTTTACA 55 126 1 ATAGGGGGAT 0.989775 -17 GAAACAGAAAACAAGGGGGAATTCAAAT 58 223 1 ACAGGGGGAT 0.981737 -18 ** ******* * Masking position 10 Map Score: 26.3204 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 44 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 ACTGGAACGGTTTATTGAAAAAGACGGATATATACTGGCCCT 1 198 1 TTTAAAAATA 0.91461 -103 TTTACCGCTTTTTTATAAAATATCAGAAAATAAAGATATTGA 2 71 1 TTTATAAATA 0.648101 -156 CTTTACTTTATTTATATTGAAACAGGAAGATAGGCTGTATAT 4 228 0 TTTAAAAATA 0.91461 -73 TTTTTTTTCGATATAAAGGCATAAAAATTCATTTTTA 12 6 1 TTTAAAAAAA 0.942504 -65 ATTTTGCATTTTTCTTCAAAAAGTTTCAAAAATGCCGAAAAG 14 38 1 TTTAAAAAAA 0.94218 -263 GAATCATCTATTTCTCCACAAAAGGAAAAAAGAAAACTTTCT 16 24 1 TTTAAAAAAG 0.856224 -94 TGGTAAGAAGTTTGTAGTAAAAGAAGATGAAGAAGCTGTTCT 19 151 1 TTTAAATAAG 0.671364 -101 AGATCGCAGCTTTCTACCGAAAAATACAAATATTTGCAATGG 19 198 1 TTTAAAAATA 0.91461 -54 ATTTTTCGATTTAAAAGGAGAGAAAAAACAGC 22 4 1 TTTAAAAAAA 0.942504 -29 ATTACACATTTTTCTTGAAAAAAGGTGATAAAAGGCAGTCCC 27 32 0 TTTAAAAAAA 0.94218 -70 GAAAAAAAGGTTTGTAAATATAGTTTTAAAAATAGGGAACAC 28 70 0 TTTATAAAAA 0.721982 -76 TATCCTAAAATTTTCTTTGAAACCGTTACCAAAATATTTTCA 34 50 0 TTTAAAACAA 0.821753 -172 TCAAAGAAAATTTTAGGATAAATAGTGAAAAGAGTCAACGAA 34 72 1 TTTAAAAAAG 0.856125 -150 GGAAATCCGCTTTTAAATAAAACACCATCCTACTCCCACACC 36 34 0 TTTAAATCTA 0.508184 -109 GCAAAACCGTTTTACTCTCAAAATCTTAAAAGAAAACCCCCG 37 29 0 TTTAAAAAAG 0.856228 -97 TAGGTGAAGTTTTTTTTATAAAAGGCTTGAAAAAACGAAACG 41 44 1 TTTAAATAAA 0.848729 -126 CGTGTTTCTATTTTGTATAAAAATAAATTATATTTAATAAAA 41 118 0 TTTAAATATA 0.786066 -52 ATATCTGACTTTTCCATTTAAACATTGTCATGTCGGCTTTTC 43 186 0 TTTAAATATG 0.571696 -115 ATTTGATAGTTTTAAGATAAAAGTACAACATAGATCTGCTAG 45 26 0 TTTAAAAATA 0.914612 -275 GCTCATCAGATTTGAAGATAAACCTCATAAAAAGCATTTCCT 45 179 0 TTTAAATAAA 0.848923 -122 AAAACGATCTTTTTTTCTCATAATAGTAGAAACATAAAAAAA 47 24 0 TTTATAAAAA 0.721982 -178 CTCATGTATTTTTAGAATGAAATATAGAAATATATAATGGGA 49 57 1 TTTAAAAATA 0.914609 -153 AGTTTTATTATTTTCATTTAAATCCCATTATATATTTCTATA 49 79 0 TTTAAATATA 0.786063 -131 TTGCATTTGTTTTTTGCGTAAAGAGCAAAAAACGCAAAATAA 51 36 1 TTTAAAAAAA 0.94218 -191 TTCAACAAGTTTTTTCAGCAAAAGACAAGAAAATGGCATGAT 51 139 1 TTTAAAAAAA 0.94218 -88 GATTCTTGCATTTTTATTCATATGCGAAGATATATTTCATAA 51 178 1 TTTATAAATA 0.635764 -49 ATCCTCTCCGTTTTTTTATAAAATAGAAGCAATATTAAGAAA 58 33 0 TTTAAAACAA 0.82175 -208 CATTCTGATATTTCGAGCGAAAATTTCAGCAAGTGCAAAATT 58 84 0 TTTAAAACAA 0.821753 -157 *** *** * *** Masking position 12 Map Score: 31.9532 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 139 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 4 GCCCCTTTCGTGTTTTTTCTGG 3 3 0 TGTTTTTTCT 0.945157 -27 AAATGTCATACGTTTTTTCTTAGGCTGTGT 4 111 1 CGTTTTTTCT 0.951016 -190 TTCCCTCACTCCTTTTTTCTACAGTATAAC 7 43 0 CCTTTTTTCT 0.65461 -21 TGCAAGCAATTTCTTTTTCATAGTGCTCTC 9 30 0 TTCTTTTTCA 0.527882 -28 GCAGAATTTCTGTTTTTTCTCCTTTCTTTT 14 75 0 TGTTTTTTCT 0.945157 -226 ACTTTATGCCTGTTATTTCTTACAATAAGC 14 215 1 TGTTATTTCT 0.662178 -86 GCTGTTTTTTCTCTCCTTTTAA 22 21 0 TGTTTTTTCT 0.945157 -12 ATTTACAAACCTTTTTTTCTCTTGCATAAT 28 93 1 CTTTTTTTCT 0.890253 -53 GTTTGCTGTTTTCTTTTTCATCCACTATAA 40 212 0 TTCTTTTTCA 0.527882 -89 AAGTACGTTTCGTTTTTTCAAGCCTTTTAT 41 61 0 CGTTTTTTCA 0.820468 -109 AGTTTCTCCTCGTTTTTTCTTAGCATTCGT 44 72 1 CGTTTTTTCT 0.951016 -76 TAAAAACGATCTTTTTTTCTCATAATAGTA 47 38 0 CTTTTTTTCT 0.890253 -164 AGTTTAGCATTGTTTTTTCTCTATTTACAA 49 140 0 TGTTTTTTCT 0.945157 -70 AATCGCACGATTTTATTTCTCTCAAA 50 7 0 TTTTATTTCT 0.450243 -67 CGATTTCCCTCTCTTTTTCTAGTAACATCT 53 78 0 CTCTTTTTCT 0.842547 -223 GAATTACCAGTTCTTTTTCTTAAAAATTAA 53 206 0 TTCTTTTTCT 0.826088 -95 TATGAAAAAGCGCTTTTTCTGCAGAGGACG 53 242 1 CGCTTTTTCT 0.927574 -59 AACTCATATCTGCGTTTTCAGCAGGAATTT 54 56 0 TGCGTTTTCA 0.419042 -112 ATGAGTTTGTTATTTTTTCTGACAAACCTT 54 79 1 TATTTTTTCT 0.531643 -89 TAGGGAGTGCTGATTTTTCTGTTGTAAATT 57 48 0 TGATTTTTCT 0.595898 -175 CAAGAATTCGTGTGTTTTCTACAATTTTCG 58 143 0 TGTGTTTTCT 0.822857 -98 TGAATTCCCCCTTGTTTTCTGTTTCAACAT 58 218 0 CTTGTTTTCT 0.686169 -23 ********** Masking position 6 Map Score: 20.0796 Number of sites scoring better than the average of aligned sites = 828 Number in coding regions = 689 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 5 CAACATAACCTCCTGTTATTTGTGTATA 2 209 0 TAACTCCTTA 0.804079 -18 GAAAAGCTCCTTTAACCTTAGATTT 6 3 1 AAACTCCTTA 0.952597 -118 GTTAACCCCCGGTCATTCCACTCTT 15 31 0 TAACCCCGTA 0.770858 -15 ATAATAGTGAAAAGACCCTCTCATGTTTACAGG 29 31 1 AAAACCCTTA 0.911408 -100 ATTAACAAAAAAACCCCCTGTAAACATGAGAGG 29 47 0 AAACCCCTTA 0.982683 -84 AGAATTAAACAAACATCCTCTTACAA 32 4 0 AAAATCCTTA 0.784633 -297 TAAAGCAACTCCCCTCTAATATACTTAAT 32 282 0 AACCCCCTTA 0.892214 -19 CTCTTCCCAACCTCCTCTTAGTTGAGGGCA 33 18 0 CAACTCCTTA 0.77527 -20 ACAGAGCGGGAAATCCGCTTTTAAATAAAACAC 36 51 0 AAACCGCTTA 0.836586 -92 TCTTAAAAGAAAACCCCCGATAAAGGGGGCTTT 37 15 0 AAACCCCGTA 0.942763 -111 AGCATCACACAAAACCCCTTTTCCTTCCATTAG 40 167 1 AAACCCCTTC 0.892214 -134 TGAACGAAACCTCCTATCATCCTCTTACA 40 282 0 AAACTCCTTA 0.952597 -19 GATAAAAATCCCCTCTCAACCGTGTTTC 41 152 0 AAACCCCTTA 0.982683 -18 ATACAAACAAAAAAACCCTTTAAAAAGGGTTTT 48 37 0 AAAACCCTTA 0.911408 -115 *** ***** * * Masking position 2 Map Score: 12.8429 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 72 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 6 GGAATCGGGAGAAAACCTGCAAATTGCTTTTGACCCAG 1 126 0 GAAAAAATGT 0.888767 -175 TAAAATATCAGAAAATAAAGATATTGACTTATTGTTTA 2 86 1 GAAAAATTGC 0.706034 -141 CCCTCTGTTTGAAAATATTAATTATTCTGAATAGTAGC 4 175 1 GAAAAATTTT 0.906769 -126 AGTAAAGAAGGTAAAAATTCATTCTGATAGAAGGAGGT 4 263 1 GTAAAATTGT 0.502001 -38 TGGTCTTTGTGAAATTATTTAACATTATAACATGAATA 11 163 0 GAAATAATTT 0.719508 -44 ACTTTTTGAAGAAAAATGCAAAATTTATTAAAATTATT 14 24 0 GAAAAAATTT 0.906833 -277 GTCGAGAATTGTAAAACTATATGCTTATTGTAAGAAAT 14 229 0 GTAAAATTTT 0.551301 -72 CTTTTGTGGAGAAATAGATGATTCTTGTTTAATGATA 16 10 0 GAAATATTTT 0.720168 -108 TCCACAAAAGGAAAAAAGAAAACTTTCTATACAAGAGG 16 38 1 GAAAAAATTT 0.906875 -80 GTAGTATCCGGAAAACATTCAATCTGTTCAATAAATAG 19 98 0 GAAAAAATGT 0.88876 -154 CTAAGCGGAGGAAAAAAACCATTATATTAGGAGGAAAT 26 113 1 GAAAAATTAT 0.646334 -31 TTGCATAATAGAAAACGGCAATGTTTACACTTGGAGGT 28 114 1 GAAAAATTTC 0.74531 -32 GGATGAAAAAGAAAACAGCAAACGTGCTTAAACATTTG 40 219 1 GAAAAAATGT 0.888767 -82 TAAAAGGCTTGAAAAAACGAAACGTACTTGTTAAAGTG 41 62 1 GAAAAAATAT 0.646335 -108 TGTTTAAATGGAAAAGTCAGATATTTTTCGGAGAAGAT 43 204 1 GAAAAATTTT 0.9065 -97 TTACCTTTAGGAAATGTTACATTTTTCCGAAATCTATC 45 113 0 GAAATATTTC 0.41765 -188 AATGTTTTTTGAAAATATTGATAATTATTCCCATACAA 48 64 0 GAAAAATTTT 0.90605 -88 GGATTTAAATGAAAATAATAAAACTTATAAATATTTCG 49 96 1 GAAAAAATTT 0.90688 -114 TTCAAGATCGGAAAAAGAGAAAGGTGATCACCTGTTAG 51 85 1 GAAAAAATGT 0.888767 -142 ATTTTCGCTCGAAATATCAGAATGTTTTTGCACCTTGT 58 102 1 GAAATAATTT 0.720162 -139 ***** ** ** * Masking position 15 Map Score: 15.1898 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 214 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 TCAAAAGCAATTTGCAGGTTTTCTCCCGATTC 1 131 1 TTTGCGTTTT 0.759383 -170 ATACAGCCTATCTTCCTGTTTCAATATAAATA 4 230 1 TCTTCGTTTC 0.538831 -71 AACCTTAGATTTTGCTTGTTTTGCCTTACTTA 6 24 1 TTTGCGTTTT 0.759383 -97 CAAATTTTTCTTTACTTTTTTCATTTAACCAT 13 24 1 TTTACTTTTC 0.761261 -71 TTTAATAAATTTTGCATTTTTCTTCAAAAAGT 14 30 1 TTTGCTTTTC 0.9598 -271 AAACAGAAATTCTGCTATTTTCAGGCTTATAT 14 90 1 TCTGCTTTTC 0.943979 -211 GTATAGAAAGTTTTCTTTTTTCCTTTTGTGGA 16 38 0 TTTTCTTTTC 0.761261 -80 TCCTGGCTACTTTTCATGTTTTTAGCGGCAGA 17 46 0 TTTTCGTTTT 0.296517 -115 ATTGCAAATATTTGTATTTTTCGGTAGAAAGC 19 206 0 TTTGTTTTTC 0.487037 -46 CGCGGCTAAGTCGGCTCTTTTCAGGCAGTATA 28 25 1 TCGGCTTTTC 0.827283 -121 AAGTGTAAACATTGCCGTTTTCTATTATGCAA 28 114 0 ATTGCTTTTC 0.606294 -32 TATTTTTTCGTTGACTCTTTTCACTATTTATC 34 88 0 TTGACTTTTC 0.475452 -134 TTTCTAAAGTTCGGCGAGTTTCATCCCTCTGT 38 134 0 TCGGCGTTTC 0.713204 -112 GAGGAGATGATCTGCCGTTTTCTTCTGCAAGC 38 203 0 TCTGCTTTTC 0.943979 -43 ACTTTTGCTTTATGCCCTTTTCCACATCAGCC 40 15 0 TATGCTTTTC 0.686092 -286 TTTAAGCACGTTTGCTGTTTTCTTTTTCATCC 40 219 0 TTTGCTTTTC 0.9598 -82 ACGCTTACAATTTGCGGTTTTTCCCTCTGTAT 43 73 0 TTTGCTTTTT 0.858732 -228 GCAAATTTATTTTGCGTTTTTTGCTCTTTACG 51 52 0 TTTGCTTTTT 0.858732 -175 TTCGACTTTTTTTGCCCTTTTTTAAAATAGGA 53 24 1 TTTGCTTTTT 0.858732 -277 ATCCCCCTCATTTGCTTTCTTCTTTTCTCGGA 55 115 0 TTTGCTCTTC 0.695346 -28 TCGTGTGTTTTCTACAATTTTCGAGGACAAGG 58 134 0 TCTACTTTTC 0.692351 -107 ***** ***** Masking position 10 Map Score: 17.8657 Number of sites scoring better than the average of aligned sites = 850 Number in coding regions = 738 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 8 GATGGATCGAAATATGAGTATGCCAGCAGCCG 4 143 0 ATAGAGTATG 0.677326 -158 ATATGGATATATCAGGAGTATGATTGAA 5 72 1 ACAGAGTATG 0.890077 -18 TTTCACAAAGACCAAGAGGGTGAACTTGTT 11 187 1 ACAGAGGGTG 0.948763 -20 TTAATTATTCATCAAGAGGTGGGCTGTTAG 12 51 1 ACAGAGGTGG 0.809128 -20 TATATGTTTAAACAAGAGTATGTATATTACAC 27 67 0 ACAGAGTATG 0.890077 -35 ACCCCCTGTAAACATGAGAGGGTCTTTTCACT 29 36 0 ACAGAGAGGG 0.721814 -95 TTGTAAGAGGATGTTTGTTTAAT 32 2 1 TTAGAGGATG 0.798999 -299 GGTGCCCTCAACTAAGAGGAGGTTGGGAAGAG 33 16 1 ATAGAGGAGG 0.89636 -22 TATTTGTTCAAACTGGAGGATGAAAAA 36 126 1 ACTGAGGATG 0.783089 -17 ATCTCCTCTAAACATGAGGAGGAGAAAAC 38 227 1 ACAGAGGAGG 0.970899 -19 TTAGCTAACATGTAAGAGGATGATAGGAGGTT 40 272 1 TTAGAGGATG 0.798999 -29 AAAAAGCACATTCAAGAGAATGTGCTTTCATG 42 15 0 TCAGAGAATG 0.702588 -70 ATTCTAAAAATACATGAGGATGTAACACGTAA 49 43 0 TCAGAGGATG 0.938778 -167 TATATTTCATAACACGAGGGGGACTACAT 51 208 1 ACAGAGGGGG 0.943953 -19 * ** ******* Masking position 7 Map Score: 11.3445 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 164 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 AAGCGCTTTTATTAATTTTTCTTTCACATC 2 165 0 ATTAATTTTT 0.868162 -62 TTCTATCAGAATGAATTTTTACCTTCTTTA 4 265 0 ATGAATTTTT 0.860303 -36 AGCCATTTTAATTTGTTTTTCCCCA 10 6 0 ATTTGTTTTT 0.750214 -39 ATACGATTGAATTAATTTTTATTCATGTTA 11 144 1 ATTAATTTTT 0.868162 -63 AATTATAAAAATGAATTTTTATGCCTTTAT 12 23 0 ATGAATTTTT 0.860303 -48 TACATACAAAATGTATTTTTATTAAATATA 41 102 1 ATGTATTTTT 0.879785 -68 ATTAAATATAATTTATTTTTATACAAAATA 41 122 1 ATTTATTTTT 0.886692 -48 TTACATCCTCATGTATTTTTAGAATGAAAT 49 50 1 ATGTATTTTT 0.879785 -160 ATAATTTTGCATTTGTTTTTTGCGTAAAGA 51 30 1 ATTTGTTTTT 0.750214 -197 ATGATGATAGATTAATTTTTAAGAAAAAGA 53 195 1 ATTAATTTTT 0.868162 -106 GGAAGACAACATTTATTTTTTTGGAGGGTG 54 15 0 ATTTATTTTT 0.886692 -153 ********** Masking position 1 Map Score: 8.39199 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 171 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 10 GCTTTTATTAATTTTTCTTTCACATCCGCTC 2 160 0 ATTTTTCTTC 0.597324 -67 TCTTTACTTTATTTATATTGAAACAGGAAGA 4 240 0 ATTTATATTA 0.457868 -61 AGTCGTGCTGATTTTTTTTGAGCGGAATTCC 11 73 1 ATTTTTTTTA 0.682305 -134 TATATTTAATATTTTTATTCATTTATAAATT 11 116 0 ATTTTTATTA 0.913158 -91 GATTGAATTAATTTTTATTCATGTTATAATG 11 148 1 ATTTTTATTA 0.913158 -59 AACACCCCAAATTTTTCTTTACTTTTTTCAT 13 17 1 ATTTTTCTTA 0.864055 -78 TAAATTTTGCATTTTTCTTCAAAAAGTTTCA 14 35 1 ATTTTTCTTA 0.864055 -266 TATATTACACATTTTTCTTGAAAAAAGGTGA 27 46 0 ATTTTTCTTA 0.864055 -56 CACTACTCCTATTCTTATTGCTGCATGATCA 30 35 0 ATTCTTATTC 0.471625 -27 CTTTAAAACTATTCTTATTCAACAATATTGC 32 220 0 ATTCTTATTA 0.792726 -81 TTACCAAAATATTTTCATTCAAGTGATGCTG 34 36 0 ATTTTCATTA 0.843771 -186 TTATCCTAAAATTTTCTTTGAAACCGTTACC 34 62 0 ATTTTCTTTA 0.52451 -160 TACAAAATGTATTTTTATTAAATATAATTTA 41 106 1 ATTTTTATTA 0.913158 -64 AATATAATTTATTTTTATACAAAATAGAAAC 41 126 1 ATTTTTATAA 0.457868 -44 AAGTTTTATTATTTTCATTTAAATCCCATTA 49 91 0 ATTTTCATTA 0.843771 -119 TGATTCTTGCATTTTTATTCATATGCGAAGA 51 177 1 ATTTTTATTA 0.913158 -50 ACAGGAAGGAATTCTCATTGAATTCCAAGTG 53 128 1 ATTCTCATTA 0.662659 -173 ********* * Masking position 8 Map Score: 9.6839 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 171 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 11 GGAATTCTTCATTGAGGGGATAAAATTTCA 1 272 0 ATTGAGGGGA 0.867455 -29 ATATTTTCAAACAGAGGGGATGGATCGAAA 4 163 0 ACAGAGGGGA 0.977827 -138 AGAAAAAAGGAGTGAGGGAAC 7 53 1 AGTGAGGGAA 0.855685 -11 GGAGGGAGGGGAGGCGAGTAAT 19 3 1 AGGGAGGGGA 0.971894 -249 TTGACAGAATACGGAGGTGAGGAAA 20 19 1 ACGGAGGTGA 0.715143 -15 CCTATCCTTCTCTGAGGGGTAATATGGGGA 32 119 0 TCTGAGGGGT 0.523051 -182 ATTAAGTATATTAGAGGGGAGTTGCTTTA 32 282 1 TTAGAGGGGA 0.808794 -19 CTAGTATCACAGAGCGGGAAATCCGCTTTT 36 62 0 AGAGCGGGAA 0.791705 -81 AAGGACTGGGACAGAGGGATGAAACTCGCC 38 124 1 ACAGAGGGAT 0.745591 -122 GAAACACGGTTGAGAGGGGATTTTTATC 41 152 1 TGAGAGGGGA 0.915408 -18 AACACAAAATACAGAGGGAAAAACCGCAAA 43 65 1 ACAGAGGGAA 0.939823 -236 AGTATAGAGGATGGCGGGGAAAAAGTAAAG 47 90 0 ATGGCGGGGA 0.796891 -112 TACTAGAAAAAGAGAGGGAAATCGTCCATT 53 84 1 AGAGAGGGAA 0.929051 -217 TTATAAAAAAACGGAGAGGATATGCAAAAG 58 54 1 ACGGAGAGGA 0.715143 -187 ********** Masking position 6 Map Score: 6.55758 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 159 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 12 GTGAGACACCTCCTCGAATGG 23 7 0 AGACCTCCTC 0.953123 -15 TGCCGCCTGCAGCACCCTCTGCATAAATCGTT 26 63 0 AGCCCTCTGC 0.946974 -81 GAGATTCCTCCGTCACCCAAAAA 29 118 0 AGACCTCCGT 0.908483 -13 TAGAAAGTGAAGAATCCTTCTCGTTGTAACGG 38 160 1 AGACCTTCTC 0.63982 -86 AAAAACGAGGAGAAACTTCCGCTAGAATTGAC 44 57 0 AGACTTCCGC 0.88593 -91 TTTGAGAAGCCTCCGCAAAATAATTT 51 5 1 AGACCTCCGC 0.988876 -222 AAAAAGTCGAAGATGCCTCTGCTC 53 3 0 AGACCTCTGC 0.96166 -298 ATTTGGCCAGAGCGTCCTCTGCAGAAAAAGCG 53 252 0 AGCCCTCTGC 0.946974 -49 GAAGCACCCTCCAAAAAAATAAAT 54 3 1 AGCCCTCCAA 0.740305 -165 AAAAGACACCTCCAATCATTAGACA 55 4 1 AGACCTCCAA 0.80015 -139 *** ******* Masking position 8 Map Score: 5.40678 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 107 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 ACCAAACAGCCGGCTGACCAGGCTGTTTTTT 2 10 1 CCGGCTGCAG 0.886122 -217 GCGCAGAATCCCGGCCGGACAGTGATTTACCG 2 46 1 CCGGCCGAAG 0.968273 -181 CTTACAGATAGAGGCCGTATACACAAATAACA 2 192 1 GAGGCCGAAC 0.883671 -35 GTTTTTTTATGCGGCTGAAATGCGGCACCGCA 11 23 1 GCGGCTGATG 0.962245 -184 TCACCTTTTGCAGGCTGAAGAGAACCCGGAGC 16 92 1 CAGGCTGAAG 0.971784 -26 GCTTATGTCTGAGGCTGGATTGAAGGAACTTT 17 91 1 GAGGCTGATG 0.959218 -70 CGGCTCTTTTCAGGCAGTATAGGGGACACATT 28 36 1 CAGGCAGAAG 0.877303 -110 TCTCCCTTTCGAGGCTGTATTCATTTATTGTA 47 174 0 GAGGCTGATC 0.862834 -28 AGCTCTCCGGGAGGCCGGAGAGCTTTTTTTAC 49 15 1 GAGGCCGAAG 0.965978 -195 GTTTTTTTGGCCGGCTGTAATGTAAGCGCTTT 52 140 0 CCGGCTGATG 0.962245 -37 ******* * ** Masking position 5 Map Score: 5.68897 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 182 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 AATTAATAAAAGCGCTTACAGATAGAGGCC 2 178 1 AGCGCTTACA 0.972343 -49 TGTATTGATGAACGCTTACAATTTGCGGTT 43 86 0 AACGCTTACA 0.97021 -215 GCGTATTGATAACGCTTACAATAAGAAGTC 43 146 0 AACGCTTACA 0.97021 -155 AAGCTGATAAGACGCTTACAATAAATGAAT 47 158 1 GACGCTTACA 0.936189 -44 GATTTTTTAAAGCGCTTACATTACAGCCGG 52 132 1 AGCGCTTACA 0.972343 -45 ********** Masking position 6 Map Score: 3.85829 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 12 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 15 TTTCTTTCACATCCGCTCCTTCCCATATAT 2 148 0 ATCCGCTCCT 0.633877 -79 CTATTCTCACCTTCTAAAAAAA 13 83 0 ATTCTCACCT 0.944382 -12 GAATTTCTGTTTTTTCTCCTTTCTTTTCGG 14 72 0 TTTTTCTCCT 0.615185 -229 AGAATGATCAATACGCACCTCTTGTATAGA 16 63 0 ATACGCACCT 0.644497 -55 CGTATTGATCATTCTCACCTTTTGCAGGCT 16 78 1 ATTCTCACCT 0.944382 -40 TTTCCTCACCTCCGTATTCTG 20 23 0 TTCCTCACCT 0.77585 -11 GCTGTTTTTTCTCTCCTTTTAAATCGA 22 16 0 TTTCTCTCCT 0.818651 -17 GGCAGTCCCTCTTATCACCTTTTGAATAGG 27 11 0 CTTATCACCT 0.529368 -91 GGGACTGCCTTTTATCACCTTTTTTCAAGA 27 32 1 TTTATCACCT 0.665141 -70 TTCTTCGCACCTCTGATTGATT 31 21 0 CTTCGCACCT 0.887895 -12 TTGATTCACACCTTTGCAATGTC 44 135 0 ATTCACACCT 0.704948 -13 AAAGCGCAAGATTCGCTCCTGCGCCATACC 46 15 0 ATTCGCTCCT 0.865757 -46 TTGAAATCTCATTTTCACCTAAGGAAAAAG 47 118 0 ATTTTCACCT 0.857412 -84 CTTTTTCACCTCATTGTTTTT 52 166 0 TTTTTCACCT 0.820338 -11 GAAATCGTCCATTTGAACCTTGTATAAACA 53 101 1 ATTTGAACCT 0.256392 -200 ATCAGAATGTTTTTGCACCTTGTCCTCGAA 58 117 1 TTTTGCACCT 0.832023 -124 ********** Masking position 2 Map Score: 8.25526 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 176 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613