AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_bsub_reg_300.orf -o00360_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 yckG 231 similar to D-arabino 3-hexulose 6-phosphate formaldehyde lyase #2 yclB 89 similar to phenylacrylic acid decarboxylase #3 yflL 66 similar to hypothetical proteins #4 yjlC 300 yjlC #5 yjlD 39 similar to NADH dehydrogenase #6 yjmA 197 similar to glucuronate isomerase #7 yjmB 67 similar to Na+:galactoside symporter #8 yjmC 104 similar to malate dehydrogenase #9 ykrV 94 similar to aspartate aminotransferase #10 pksF 300 pksF #11 yocC 170 yocC #12 yocD 63 similar to immunity to bacteriotoxins #13 yocE 161 similar to fatty-acid desaturase #14 aspB 22 aspartate aminotransferase #15 ypmA 142 ypmA #16 dinG 125 ATP-dependent helicase #17 panB 245 ketopantoate hydroxymethyltransferase #18 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #19 ypjD 300 alternate gene name: jojD #20 trpE 215 anthranilate synthase #21 aroB 61 3-dehydroquinate synthase #22 aroF 69 chorismate synthase #23 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #24 ndk 115 nucleoside diphosphate kinase #25 gerCA 162 heptaprenyl diphosphate synthase component I #26 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #27 mtrA 187 GTP cyclohydrolase I #28 hbs 300 non-specific DNA-binding protein HBsu #29 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #30 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #31 yqiS 124 similar to phosphate butyryltransferase #32 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #33 mmgC 27 acyl-CoA dehydrogenase #34 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #35 mmgA 137 acetyl-CoA acetyltransferase #36 yqiK 78 similar to glycerophosphodiester phosphodiesterase #37 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #38 blt 116 multidrug-efflux transporter #39 bltD 168 spermine/spermidine acetyltransferase #40 hemA 163 glutamyl-tRNA reductase #41 ribR 46 transcriptional regulator #42 ytmM 29 similar to amino acid ABC transporter (permease) #43 ytmL 21 similar to amino acid ABC transporter (permease) #44 ytmI 152 similar to hypothetical proteins from B. subtilis #45 yugK 103 similar to NADH-dependent butanol dehydrogenase #46 yugJ 229 similar to NADH-dependent butanol dehydrogenase #47 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #48 yurR 300 similar to opine catabolism #49 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #50 yusM 300 similar to proline dehydrogenase #51 ywpB 191 similar to hydroxymyristoyl-(acyl carrier protein) dehydratase #52 ywjF 154 similar to hypothetical proteins #53 ywfB 151 alternate gene name: ipa-80d #54 ywfA 209 alternate gene name: ipa-79d; similar to chloramphenicol resistance #55 rocB 73 alternate gene name: ipa-77d #56 rocA 226 pyrroline-5 carboxylate dehydrogenase #57 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #58 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis #59 yxjD 78 similar to 3-oxoadipate CoA-transferase #60 yxjC 153 similar to hypothetical proteins from B. subtilis #61 yxjB 300 similar to hypothetical proteins Motif number 1 AAAGGTTACTAAGGGGGGATTCTAT 1 5 0 AAGGGGGATT 0.942734 -227 TACAACCTGTAAAGGGGATGTGTTTGT 3 7 0 AAAGGGGTGT 0.853879 -60 CATAAAAAGAAAAGGTGGTTTTTAC 3 52 1 AAAGGTGTTT 0.826572 -15 TGCTTATAGTAAAGGAGAATTGGAT 4 286 1 AAAGGAGATT 0.635024 -15 AAGCCGCATAAAGCGGCTTTTGCGGTGTGG 15 10 1 AAAGCGGTTT 0.794279 -133 GTTTTATTTAAAAGCGGATTTCCCGCTCTGT 15 53 1 AAAGCGGTTT 0.970584 -90 ACCCCCGATAAAGGGGGCTTTTCTT 16 5 0 AAGGGGGTTT 0.977949 -121 TTTTGAGAGTAAAACGGTTTTGCCGCTCCAT 16 48 1 AAAACGGTTT 0.656584 -78 AATGGAAGGAAAAGGGGTTTTGTGTGATGCT 19 167 0 AAAGGGGTTT 0.985101 -134 AATCAGCTGAAAAGCTGATTTTTTTATTGAA 23 149 1 AAAGCTGTTT 0.674402 -88 AGCCCCTTAGAAAGGGGCTTTTCTGTGAAGA 27 57 0 AAAGGGGTTT 0.947632 -131 GCCCCTTTCTAAGGGGCTTTTCATATTTCAA 27 70 1 AAGGGGCTTT 0.873115 -118 ATGAAAAGATAAAGGGGTTTTCTGAAG 32 7 0 AAAGGGGTTT 0.985101 -146 TTTTTCATACAAAGGGGTATCGGG 32 139 1 AAAGGGGATC 0.800944 -14 ACATGATGAAAAAGGGGATTTGAATGGAAAT 34 12 1 AAAGGGGTTT 0.987202 -138 CCGTATAGTCAAGGAGGTTTTT 38 2 0 AAGGAGGTTT 0.668744 -115 CAATTGAGTAAAAGGGGAATTCAG 38 103 1 AAAGGGGATT 0.966098 -14 ACTGCCGCTGAAGACGGATTTTTTTTCTCTC 49 144 1 AAGACGGTTT 0.536478 -124 CGCGATGAAAAAAGCGCATTTCATGGCGCAG 50 94 0 AAAGCGCTTT 0.838871 -207 GAAATAACGGAAGGCGGCATTTGAGATTGCT 50 173 1 AAGGCGGATT 0.881065 -128 TATCAGTAAAAAGGGGGAATTGGA 52 141 1 AAGGGGGATT 0.942734 -14 AACCCTTTAAAAAGGGTTTTTAATTATAGGA 53 26 0 AAAGGGTTTT 0.840838 -126 AACCCTTTTTAAAGGGTTTTTTTGTTTGTAT 53 39 1 AAAGGGTTTT 0.840838 -113 CTCTGCAGAAAAAGCGCTTTTTCATAATTCG 58 237 0 AAAGCGCTTT 0.814483 -64 GAAGAAAACGAAAGGGGCATCAAT 59 65 1 AAAGGGGATC 0.800938 -14 AGCTCCGAAAAAAGGAGCTTTCCTTTTTTAA 60 23 1 AAAGGAGTTT 0.671032 -131 CATACAGCAGAAAGGGAGTTTTTTTCATGAT 61 143 1 AAAGGGATTT 0.750025 -158 ******* *** Masking position 2 Map Score: 37.7491 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 246 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 2 TACTTTTTTGCAGACTCTTTTTTCATTATACT 1 66 1 CACTCTTTTT 0.723497 -166 TGTTGATCCACTCCCTTTTCGAATTATTGT 1 212 0 CTCCCTTTTC 0.924111 -20 GTAAAAACCACCTTTTCTTTTTATGATAATCA 3 45 0 CTTTCTTTTT 0.858864 -22 TGCTTTCTGGCAATGTCTTTTTTTATGTTTAT 6 55 1 CTGTCTTTTT 0.939643 -143 CCTTTGGGATCAATCTCTTTTTTGAAAATGAA 6 101 0 CTCTCTTTTT 0.977046 -97 CCCTCTGTCCCAGTCCTTTTTTGGATCAAGGC 17 110 0 CTCCTTTTTT 0.886245 -136 CTCCCAGTCTCGCTGTCTTTTTGTCCTAGTAT 23 208 0 CTGTCTTTTT 0.939643 -29 AGGATACAGCCAATTCTTTTTTTTATGCTATA 25 56 1 CTTCTTTTTT 0.526927 -107 TTTGACGCAGCCTTCTTTTTTCATTCATTCAT 35 39 1 CTCTTTTTTC 0.791504 -99 ACTACATTCTCCTTTTTTCTTATCCC 39 153 0 CTCTCCTTTT 0.882193 -16 CACTGCTCCCTCTCTTTTTAC 43 3 0 CTCTCTTTTT 0.977046 -19 GGCTGCTTCCCTTTTTCTTTTTTGTCAACTTA 45 32 1 CTTTCTTTTT 0.858864 -72 TCTGTGTCACTCCCTTTTTTTGATGGTTG 47 8 1 CTCCCTTTTT 0.970251 -140 TATTATGAATTAATCTCTTTTTCAACCGCGCT 51 95 0 TTCTCTTTTT 0.617269 -97 TATAGTTTAGCATTGTTTTTTCTCTATTTACA 54 141 0 CTGTTTTTTC 0.581325 -69 AGGTGATCACCTTTCTCTTTTTCCGATCTTGA 56 86 0 CTCTCTTTTT 0.977046 -141 GAGATGTTTTCAGTCTCTTTTTTTGTGGATTC 57 35 1 CTCTCTTTTT 0.977046 -142 TTTTTCACCTCATTGTTTTTTTGGCCGGCTGT 57 154 0 CTGTTTTTTT 0.788084 -23 TGGACGATTTCCCTCTCTTTTTCTAGTAACAT 58 80 0 CTCTCTTTTT 0.977046 -221 AAAAAAGGAGCTTTCCTTTTTTAATCGGAATA 60 30 1 CTCCTTTTTT 0.886245 -124 TCGGCTGTTTCCGTCCCCTTTCCATATGTACG 60 78 0 CTCCCCTTTC 0.681765 -76 GTTTATTTGTCTATGCCTTTTTCATTTATCTA 61 251 1 CTGCCTTTTT 0.922653 -50 * ********* Masking position 9 Map Score: 27.7016 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 415 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 3 ATGATAAGGAGGCGCTTTCTT 2 1 0 GGGCTTTCTT 0.943692 -89 TAATCGAATTGGAGTTTTTTGTGTTTGCTAT 4 55 1 GGGTTTTTTG 0.871533 -246 TAAGCAGTTTGCTGATTTTTTTGGAAAGGGT 4 261 0 GCGATTTTTT 0.753882 -40 GTGTTTCTAAGCTGTTTTTTGAAAGGAGTTT 11 146 1 GCGTTTTTTG 0.820079 -25 CACCGCAAAAGCCGCTTTATGCGGCTT 15 7 0 GCGCTTTATG 0.514388 -136 GGAGTAGGATGGTGTTTTATTTAAAAGCGGA 15 40 1 GGGTTTTATT 0.743617 -103 CCCGATAAAGGGGGCTTTTCTT 16 2 0 GGGCTTTTCT 0.919379 -124 CCCTTTATCGGGGGTTTTCTTTTAAGATTTT 16 21 1 GGGTTTTCTT 0.936425 -105 GAGATGATCTGCCGTTTTCTTCTGCAAGCCA 17 201 0 GCGTTTTCTT 0.908224 -45 AAGCACGTTTGCTGTTTTCTTTTTCATCCAC 19 217 0 GCGTTTTCTT 0.908224 -84 CAGCTGAAAAGCTGATTTTTTTATTGAAACA 23 152 1 GCGATTTTTT 0.753882 -85 CCCTTAGAAAGGGGCTTTTCTGTGAAGAAAT 27 54 0 GGGCTTTTCT 0.919379 -134 CCCTTTCTAAGGGGCTTTTCATATTTCAAGA 27 72 1 GGGCTTTTCA 0.647994 -116 TCCTCAGAGTGCAGTTTTTCTTAAAAAGCCG 28 159 1 GCGTTTTTCT 0.870695 -142 AAAAGATAAAGGGGTTTTCTGAAG 32 4 0 GGGTTTTCTG 0.875571 -149 GAATTGGCGGGCTGATTTTTTAAAGCGCTTA 57 119 1 GCGATTTTTT 0.753882 -58 TCCTTTTTTCGGAGCTTTCCTCTACCAT 60 8 0 GGGCTTTCCT 0.922047 -146 TCCGAAAAAAGGAGCTTTCCTTTTTTAATCG 60 26 1 GGGCTTTCCT 0.922047 -128 CAGCAGAAAGGGAGTTTTTTTCATGATTATC 61 147 1 GGGTTTTTTT 0.934214 -154 GAATGAATGGGGTGTTTTTTATC 61 288 1 GGGTTTTTTA 0.696267 -13 ** ******** Masking position 6 Map Score: 16.9647 Number of sites scoring better than the average of aligned sites = 806 Number in coding regions = 588 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 4 AAATCTGATTGTCTCTCCTCACAGTATCCT 1 120 1 GTCTCTCCTC 0.970276 -112 GTTCCACCTCTGTGTCTTAA 7 58 0 GTTCCACCTC 0.937234 -10 CCATAATGCGCTCTCTCCTCAAGGGATTAT 10 59 0 CTCTCTCCTC 0.918902 -242 GTTTTCTCCTCCTCATGTTTA 17 235 0 TTTTCTCCTC 0.846838 -11 TAAACATAATGTCTCAGCTCAACTAAACTC 20 96 0 GTCTCAGCTC 0.924558 -120 GCCTTTCACCTCCTCCCAAAAG 28 289 0 CTTTCACCTC 0.942549 -12 GGTTTCACCTCATTCAGAAGA 35 127 0 GTTTCACCTC 0.979281 -11 CGTTTCACCTCAAACCCTAAA 36 68 0 GTTTCACCTC 0.979281 -11 TTTTGTCACTCCTCTTCACAAAAT 44 139 0 GTCACTCCTC 0.790834 -14 TCTAGCGGAAGTTTCTCCTCGTTTTTTCTT 47 63 1 GTTTCTCCTC 0.972892 -85 CGTACCATTCCCTTCACCTCCGGGCTTAAG 49 174 1 CCTTCACCTC 0.826453 -94 CTTTTTCACCTCATTGTTTTTT 57 165 0 TTTTCACCTC 0.879249 -12 AGTCGAAGATGCCTCTGCTC 58 1 0 GCCTCTGCTC 0.72981 -300 TCACTATAAGGTTCCAGCTCCTGGATATTT 61 88 1 GTTCCAGCTC 0.80977 -213 ********** Masking position 9 Map Score: 14.0814 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 96 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 TGAGTGAGTATAATGAAAAAAGAGTCTGCAA 1 73 0 TAATGAAAAA 0.439256 -159 TGATATATCCATATGAAAAATATCTATTAAA 2 55 0 ATATGAAAAT 0.296294 -35 GATTGATCCCAAAGGAATATAAAGGTAAAAT 6 118 1 AAAGGAAATA 0.215986 -80 ATATATGGTTAAATGAAAAAAGTAAAGAAAA 9 29 0 AAATGAAAAA 0.923924 -66 GAACTTTAGAAAGTGAAGAATCCTTCTCGTT 17 154 1 AAGTGAAAAT 0.477104 -92 CTGCATATTGAAATGAACCAAGCCAAATGAA 19 82 1 AAATGAACAA 0.513839 -219 GAACCAAGCCAAATGAAAAAATTGCCGCTCC 19 96 1 AAATGAAAAA 0.923924 -205 GTTTACATTAAAGTGAATAAAGGGTTGAATG 23 79 1 AAGTGAAAAA 0.803456 -158 CTGCGTAAGCGAATGAAAAGATAAAACTCAT 25 95 1 GAATGAAAGA 0.569533 -68 GGATGAAAAAAGGAAAAAAAGGAATATTC 28 9 1 AAAGGAAAAA 0.660454 -292 TTGTCCAACAAAGTGAAGAATTTCTGTATGT 28 124 0 AAGTGAAAAT 0.477104 -177 ACAATAAAGGAAATGAAAAGATAAAGGGGTT 32 19 0 AAATGAAAGA 0.882633 -134 AAAATGAATAGTTGTTAGAAGG 35 2 1 AAATGAAAGT 0.626662 -136 GGGCATGAATGAATGAAAAAAGAAGGCTGCG 35 44 0 GAATGAAAAA 0.681189 -94 AAATTTTTTAAAATGAATAAAAAGTTGCTTC 37 75 1 AAATGAAAAA 0.923924 -226 CTTTCACAAAATGTGAACAGATTTTAAAATT 40 56 0 ATGTGAAAGA 0.282218 -108 ATCGTCATGAAAATGAAGAAAACAGACGCGA 48 112 0 AAATGAAAAA 0.923924 -189 TGATTTGGTAAAATGAATAGACATTATAATA 48 264 1 AAATGAAAGA 0.882633 -37 GGAAACTATAAAATGAACAGAAACCAAAGGA 50 225 0 AAATGAAAGA 0.882633 -76 AATGGGATTTAAATGAAAATAATAAAACTTA 54 92 1 AAATGAAATA 0.632364 -118 ATATCTTCGCATATGAATAAAAATGCAAGAA 56 180 0 ATATGAAAAA 0.653549 -47 AGGGTGAATCCAATGAAGAAAGGAATTGGCG 57 97 1 CAATGAAAAA 0.537254 -80 ATTTTTAGATAAATGAAAAAGGCATAGACAA 61 257 0 AAATGAAAAG 0.54978 -44 ATTTATCTAAAAATGAATGAATGGGGTGTTT 61 274 1 AAATGAAGAA 0.513839 -27 ******* *** Masking position 6 Map Score: 12.0555 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 404 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 6 TGCAGACTCTTTTTTCATTATACTCACTCA 1 74 1 TTTTTCATTA 0.599164 -158 TTAATAGATATTTTTCATATGGATATATCA 2 56 1 TTTTTCATAT 0.501397 -34 TACTACCCAGTTTTTCATCTTGCCATATTC 4 148 0 TTTTTCATCT 0.814282 -153 TTCACCGATGTTTTTCACCCCGGATAGCTC 10 265 0 TTTTTCACCC 0.77295 -36 TTTTTCATCCTCCAGTTTGA 15 133 0 TTTTTCATCC 0.939538 -10 TGCTGTTTTCTTTTTCATCCACTATAATAT 19 209 0 TTTTTCATCC 0.939538 -92 CTATAACATATTTTTCAGCAAAAAG 22 6 0 TTTTTCAGCA 0.827014 -64 TTTTTTTCCTTTTTTCATCC 28 1 0 TTTTTCATCC 0.939538 -300 CAGAGTGCAGTTTTTCTTAAAAAGCCGTTT 28 163 1 TTTTTCTTAA 0.447152 -138 GTGTGCAAATTTTTTCATACAAAGGGGTAT 32 129 1 TTTTTCATAC 0.780893 -24 TCAAATCCCCTTTTTCATCATGTT 34 5 0 TTTTTCATCA 0.937428 -145 GCAGCCTTCTTTTTTCATTCATTCATGCCC 35 45 1 TTTTTCATTC 0.60791 -93 CTCCCTCCTGTTTTTCATCATTAAAATTAC 44 15 1 TTTTTCATCA 0.937428 -138 GAAATGCGCTTTTTTCATCGCGAGCAAATT 50 103 1 TTTTTCATCG 0.720035 -198 AATTAATCTCTTTTTCAACCGCGCTAAAAT 51 90 0 TTTTTCAACC 0.555179 -102 TTCAACAAGTTTTTTCAGCAAAAGACAAGA 56 139 1 TTTTTCAGCA 0.827014 -88 CTTTTTCACCTCATTGTTTTT 57 166 0 TTTTTCACCT 0.489939 -11 TTACCAGTTCTTTTTCTTAAAAATTAATCT 58 203 0 TTTTTCTTAA 0.447152 -98 GAAAAAGCGCTTTTTCATAATTCGCGAATT 58 231 0 TTTTTCATAA 0.774574 -70 GAAAAAGCGCTTTTTCTGCAGAGGACGCTC 58 245 1 TTTTTCTGCA 0.529491 -56 TCAGTACTGATTTTTCTTCACTATAAGGTT 61 71 1 TTTTTCTTCA 0.77908 -230 AAAGGGAGTTTTTTTCATGATTATCCAATT 61 153 1 TTTTTCATGA 0.556812 -148 ********** Masking position 5 Map Score: 18.1023 Number of sites scoring better than the average of aligned sites = 947 Number in coding regions = 827 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 7 CAATTCCATTATTACTAGAAATTAGCGGAAAGTCAGGTTT 11 66 0 AAAATAGCGA 0.910354 -105 GCCTTTCCCAACGATCTAAAATCAGCTGAAAAGCTGATTT 23 130 1 AAAACAGCGA 0.98246 -107 GTTAAAAGCAAATGCTCGCAAACAGCGGGAGGATACAGCC 25 27 1 AGAACAGCGA 0.976264 -136 TTTGCAGAATAAACGCAAACATCTGCACGAATGTTTC 31 8 1 AAAACATCGA 0.866767 -117 TGAGGCGCCAATTAGAAAAAATTAGCGGAAAGAAGCAACT 37 97 0 AAAATAGCGA 0.910354 -204 CTGGTCAAAGATAAAAGCCAAACATCAGGAAGAGGTGGTC 37 269 1 AAAACATCGA 0.866767 -32 ACCTTTTCTTATTGTGCCTAACCAGGGGCATTCCCTGCAT 39 40 0 AGAACAGGGA 0.787721 -129 AAAAAGGGGAAATAGCCGTTTGGCTGCTTC 45 1 1 AAAATAGCGT 0.655838 -103 CGGCAGTGGCAAAAGTCCAAAACAGCGGTAATGCAAAAGT 48 70 0 AAAACAGCGA 0.98246 -231 AAGCAGCCGTGGGAAGCAGCTGCATTATGATTGT 49 5 1 ACAACAGCGA 0.921144 -263 CGGAAAACGGACAAGTCAAAATCAGCAGTATAAAAAACAT 49 53 0 AAAACAGCGA 0.98246 -215 AAGGAGGATCACAATGGATAATCAGCAGCAATCTCAAATG 50 190 0 AAAACAGCGA 0.98246 -111 TAGTAAAGGTAGTGTGCCCGAACAGCAGGAATTTAATTAT 52 28 1 AGGACAGCGA 0.85714 -127 ACATATGGAAAGGGGACGGAAACAGCCGATGCGGACAGGT 60 81 1 AGAACAGCGT 0.885297 -73 * * ** **** * * Masking position 11 Map Score: 12.8816 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 231 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 TTACTTGGAGGATACTGTGAGGAGAGACAATC 1 126 0 GAATGTGAGG 0.724853 -106 AAAAGCGTGAGACAGGGAGAGGCACTACCCTT 4 235 1 GAAGGAGAGG 0.981393 -66 TCCGCTCAGCGATACTGAGCGGACACTTTG 7 9 0 GAATGAGCGG 0.957559 -59 AACCGAGACACACAATGAGAGGATACTTACT 13 141 1 CAATGAGAGG 0.706817 -21 GTTTTGTACGGAAATGGAGCGGCAAAACCGTT 16 60 0 GAAGGAGCGG 0.973176 -66 TAACATGTAAGAGGATGATAGGAGGTTTCGTT 19 277 1 GAGTGATAGG 0.618726 -24 TTATGGCAAGGAGAATGAGAAGATGGCATGAG 20 182 0 GAATGAGAAG 0.765949 -34 AGATCGTTGGGAAAGGCAGAGGTCTGATGCAC 23 115 0 GAAGCAGAGG 0.794942 -122 GCGCAGGTCAGATGGGGAGCGGAATTGCTCAA 34 63 1 GAGGGAGCGG 0.934155 -87 AGCTTCAAGCGAAAAGGATAGGTAAAAAGGGT 38 70 1 GAAGGATAGG 0.869676 -47 GTAAAAAGAGAGGGAGCAGTG 43 8 1 GAAGGAGCAG 0.783545 -14 TTTCTCTATTGATAGTGACAGGATATTCGATA 48 163 1 GAATGACAGG 0.924707 -138 CCGTAATGCTGAGTCGGACCGGCATCTCCCTT 49 96 1 GATGGACCGG 0.572113 -172 TTTGTAGTCAGAGACTGAGATGTTTTCAGTCT 57 19 1 GAATGAGATG 0.649844 -158 GATGTTACTAGAAAAAGAGAGGGAAATCGTCC 58 79 1 GAAAGAGAGG 0.83794 -222 GGAAACAGCCGATGCGGACAGGTTTTTGTAAA 60 98 1 GAGGGACAGG 0.885355 -56 ATTCGTTATAGATAATGACAGGTGTAGACAAA 61 184 1 GAATGACAGG 0.924707 -117 ** * ******* Masking position 2 Map Score: 12.8062 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 253 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 CAACCTGTAAAGGGGATGTGTTTGT 3 6 0 AGGGGATGTG 0.907892 -61 CTTATAGTAAAGGAGAATTGGAT 4 288 1 AGGAGAATTG 0.690259 -13 GACGAATTAGGGGGAGTTCAAG 14 10 1 GGGGGAGTTC 0.574414 -13 TTTATTTAAAAGCGGATTTCCCGCTCTGTG 15 55 1 AGCGGATTTC 0.774871 -88 CCCCTTTATCGGGGGTTTTCTTTTAAGATT 16 20 1 GGGGGTTTTC 0.697058 -106 TGGAAGGAAAAGGGGTTTTGTGTGATGCTT 19 166 0 AGGGGTTTTG 0.787952 -135 CCCCTTAGAAAGGGGCTTTTCTGTGAAGAA 27 56 0 AGGGGCTTTT 0.611697 -132 CCCCTTTCTAAGGGGCTTTTCATATTTCAA 27 71 1 AGGGGCTTTT 0.611697 -117 GAAAAGATAAAGGGGTTTTCTGAAG 32 6 0 AGGGGTTTTC 0.787952 -147 ATGATGAAAAAGGGGATTTGAATGGAAATC 34 14 1 AGGGGATTTG 0.937274 -136 TCAGATGGGGAGCGGAATTGCTCAAACAGC 34 70 1 AGCGGAATTG 0.682431 -80 AAAGATAACGAGCAGATTTGTCTATGAGGA 37 147 0 AGCAGATTTG 0.451209 -154 ATTGAGTAAAAGGGGAATTCAG 38 105 1 AGGGGAATTC 0.903186 -12 GTGCCTAACCAGGGGCATTCCCTGCATCCA 39 37 0 AGGGGCATTC 0.876219 -132 TAAAAAGAGAGGGAGCAGTG 43 12 1 GGGAGCAGTG 0.408536 -10 AAATCTAAGGAGGAGATGTC 46 220 1 AGGAGATGTC 0.7019 -10 ATCCGTCTTCAGCGGCAGTCAGCGCGGCGA 49 133 0 AGCGGCAGTC 0.518219 -135 ATGCAGATGAAGGAGATGTCAAGACA 51 176 1 AGGAGATGTC 0.7019 -16 TCAGTAAAAAGGGGGAATTGGA 52 143 1 GGGGGAATTG 0.852437 -12 CAATCAATTAGGGGGAAATGTC 58 289 1 GGGGGAAATG 0.330785 -12 CTCCGAAAAAAGGAGCTTTCCTTTTTTAAT 60 25 1 AGGAGCTTTC 0.730341 -129 TCGCGGAAACGGGGGATGTGTGT 60 141 1 GGGGGATGTG 0.859226 -13 ********** Masking position 9 Map Score: 11.7751 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 332 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 10 GATACTGTGAGGAGAGACAATCAGATTTCTT 1 117 0 GGAGGACAAT 0.952944 -115 CGTGAGACAGGGAGAGGCACTACCCTTTCCA 4 240 1 GGAGGGCACT 0.965689 -61 GTACGGAAATGGAGCGGCAAAACCGTTTTAC 16 56 0 GGAGGGCAAA 0.981969 -70 TATTTTAATCGGAGCGGCAATTTTTTCATTT 19 106 0 GGAGGGCAAT 0.976649 -195 TTTGTGAAGAGGAGTGACAAAA 44 141 1 GGAGGACAAA 0.963463 -12 TCAAAAAAAGGGAGTGACACAGA 47 3 0 GGAGGACACA 0.946649 -145 ACGCGATGCGGCAGTGGCAAAAGTCCAAAAC 48 87 0 GCAGGGCAAA 0.912816 -214 **** ****** Masking position 3 Map Score: 4.3326 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 38 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 ATTGTGAATTCATGCACAATCATTTACAAAAATAAATGTTT 4 177 0 CCATATTAAA 0.939132 -124 CCGCAGATGGCAAAGCCATTCATTTTTAAAAGCATAAAGGA 30 34 1 CCATATTAAA 0.939132 -40 CCTATTTATTCCGTTGCAATAATTTGCACAACCCTATGTTA 32 89 0 CCATATTAAA 0.939132 -64 TGCAGGCGAGCAAGTTCCATGATTTTCAAAAGGGCTATACG 37 200 0 CCCTATTAAA 0.961082 -101 GTTTTGCAACCTCCTCCATGAATTATTAAAACAGTTATAGA 46 11 1 CCAGATAAAA 0.499767 -219 GAGGGCAGGCCAGCTTCCCTCATATGGAGAATGCATGTATA 46 72 0 CCCTATTAAA 0.961082 -158 TTCCTTCGACCTTTTGCCCTAATGTGGAAAAACCGCGAAGT 48 217 0 CCCTATTAAA 0.961082 -84 TCTCAAATGCCGCCTTCCGTTATTTCGACAAAGGATCATTT 50 158 0 CCCTATTAAA 0.961082 -143 CCGACTCCCTCCCGCCGTCATCTTCAAAACACCTGTATA 50 272 0 CCCTATTAAA 0.961082 -29 ACCGCGATCCCCTACCCCCGAATCTGTATAAGATTATCTTT 52 97 0 CCCGATTAAA 0.932458 -58 TTACGTGTTACATCCTCATGTATTTTTAGAATGAAATATAG 54 43 1 CCAGATTAAA 0.89611 -167 TTGTCTATGCCTTTTTCATTTATCTAAAAATGAATGAATGG 61 257 1 CCATATTAAT 0.641203 -44 * ** * ** * * ** Masking position 12 Map Score: 10.3242 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 47 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 12 GTTTTTCATCTTGCCATATTCAGTATTATTT 4 138 0 TTGCCATTTC 0.74054 -163 GCTTTTGGCAATGCCAGATTCATTAAAAGGA 6 11 0 ATGCCAGTTC 0.979109 -187 CTTTTGCTTTATGCCCTTTTCCACATCAGCC 19 15 0 ATGCCCTTTC 0.939149 -286 TTATCCTCTCATGCCATCTTCTCATTCTCCT 20 175 1 ATGCCATTTC 0.961001 -41 TGCAAGTTCCATGCCAGCTCTTAAGGGTGCT 31 65 0 ATGCCAGTCT 0.652777 -60 GCCTTTTATTATGCAAGTTCCATGCCAGCTC 31 76 0 ATGCAAGTCC 0.784503 -49 TCATTCATTCATGCCCGTTTCAAAGCATACA 35 59 1 ATGCCCGTTC 0.967056 -79 AAGCGAGGGCAGGCCAGCTTCCCTCATATGG 46 86 0 AGGCCAGTTC 0.889451 -144 TGCAAGAATCATGCCATTTTCTTGTCTTTTG 56 157 0 ATGCCATTTC 0.961001 -70 CCTTATCATCATGCAAGATCCGTACCAGCTT 57 69 0 ATGCAAGTCC 0.784503 -108 ATTGATGCCCCTTTCGTTTTCTTCT 59 64 0 ATGCCCCTTC 0.849471 -15 TTATTTGTCTATGCCTTTTTCATTTATCTAA 61 253 1 ATGCCTTTTC 0.795273 -48 ******* *** Masking position 9 Map Score: 5.55567 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 174 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 TTATCATAAAAAGAAAAGGTGGTTTTTAC 3 48 1 AAGAAAAGTG 0.436648 -19 TCCTCATGTTTAGAGGAGATGATCTGCCGTT 17 216 0 TAGAGGAGTG 0.91071 -30 AGAGAAAATGTGGAGAATATGAGAAAACTGT 21 28 1 TGGAGAATTG 0.845826 -34 GTATCCTTTTGGGAGGAGGTGAAAGGC 28 284 1 GGGAGGAGTG 0.914414 -17 AGCAATTGGAGAAGCTGCGCTTGCCGC 30 7 1 TGGAGAAGTG 0.964982 -67 TTGACCAGAATGGAGAATTTGTAAAGACAAC 37 246 0 TGGAGAATTG 0.845826 -55 GCCAAACATCAGGAAGAGGTGGTCAT 37 285 1 AGGAAGAGTG 0.87861 -16 TATGTTACAATGGAAAATCTGTTTTTTACCA 45 62 1 TGGAAAATTG 0.685543 -42 TAATAATTCATGGAGGAGGTTGCAAAAC 46 8 0 TGGAGGAGTT 0.771395 -222 AAAAAATCTAAGGAGGAGATGTC 46 217 1 AGGAGGAGTG 0.947955 -13 GACATTATAATAGAAAAGGTGTTTGCAT 48 283 1 TAGAAAAGTG 0.685543 -18 CTAATGCAGATGAAGGAGATGTCAAGACA 51 173 1 TGAAGGAGTG 0.771395 -19 AAGAAGATTATGGAAGAGGTGTTTGAGAAAG 54 188 1 TGGAAGAGTG 0.953179 -22 ******** ** Masking position 7 Map Score: 5.72128 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 355 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 14 TACCTTCTATATGATAACACTTTTTGAACAAAATT 4 22 0 AGTACACTTT 0.85299 -279 ATACGACAAAAGTGTAACACGTTTTGTACGGAAAT 16 77 0 ATTACACTTT 0.912117 -49 AAGTAAGACTACTATAACATATTTTTCAGCAAAAA 22 12 0 ATTACATTTT 0.926557 -58 TTTTTGTCCTAGTATAGCTTGTTTTATCAGGAAAT 23 188 0 ATTACTTTTT 0.593709 -49 GCACAACCCTATGTTACCACGTTTTCTTCTCTTGA 32 70 0 AGTACACTTT 0.85299 -83 ATTTATAATAATTATAACATAGTTTCTTTCACAAA 40 77 0 ATTACATTTT 0.926557 -87 CAGATTTTCCATTGTAACATAAGTTGACAAAAAAG 45 48 0 ATTACATGTT 0.684124 -56 ATCTCATGACATTATATCACGTTTTTTGACGAATG 47 95 0 ATTACACTTT 0.912117 -53 ATTTTCGCTCATGGTATCATCCTTTCTCTATTGAT 48 141 1 AGTACATTTT 0.875823 -160 GTTGTATTATAGTTTAGCATTGTTTTTTCTCTATT 54 145 0 ATTACATTTT 0.926558 -65 CTTAAAAATTAATCTATCATCATTTTCCATGGAAG 58 183 0 ATTACATTTT 0.926553 -118 TCAGCATAGCAATCCAGCATGTTTTTCCTTTATT 61 10 0 ATCACATTTT 0.684124 -291 * * ** *** *** Masking position 6 Map Score: 4.97407 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 27 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 15 ATTCTATAGGTTCCTTCTTTTGTTGAGAAGT 1 179 0 TTCCTCTTTT 0.927413 -53 CGTATATCCTCCGTCCTTTATATCAATTT 5 21 0 CTCCTCCTTT 0.949108 -19 GCAAGTGCCTCCTTCCTTTTCAGTTTTTT 8 86 0 CTCCTCCTTT 0.949108 -19 TCCGATTCCTCCTTTTTCACAGGTTA 11 6 1 TTCCCCTTTT 0.854644 -165 AAAACCCCTTTTCCTTCCATTAGATAGCGTT 19 177 1 TTCCTCCATT 0.573746 -124 CGAACGAATATTCCTTTTTTTCCTTTTTTCA 28 14 0 TTCCTTTTTT 0.597414 -287 CTTGTTTCGACTCCGCCTTTTATTATGCAAG 31 90 0 CTCCCCTTTT 0.904175 -35 CACTGCTCCCTCTCTTTTTAC 43 6 0 CTCCTCTCTT 0.86627 -16 TGTGCTCCCTCCTGTTTTTCATCAT 44 5 1 CTCCTCCTGT 0.89564 -148 TCTGTGTCACTCCCTTTTTTTGATGGTTGT 47 10 1 CTCCTTTTTT 0.704266 -138 CTTCTCCGTCTTGTGACTGCGCCT 48 4 1 CTCCTCTTGT 0.904175 -297 TCCAATTCCCCCTTTTTACTGATAAA 52 139 0 TTCCCCTTTT 0.854644 -16 AATGGACGATTTCCCTCTCTTTTTCTAGTAA 58 83 0 TTCCTCTCTT 0.80145 -218 TCAATGAGAATTCCTTCCTGTTTATACAAGG 58 118 0 TTCCTCCTGT 0.842466 -183 **** ****** Masking position 2 Map Score: 10.4165 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 218 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949