AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_bsub_reg_300.orf -o00310_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 ybxI 172 alternate gene name: ybdS; similar to beta-lactamase #2 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #3 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #4 ycbD 29 similar to aldehyde dehydrogenase #5 yckG 231 similar to D-arabino 3-hexulose 6-phosphate formaldehyde lyase #6 yhfI 151 similar to hypothetical proteins #7 yjlC 300 yjlC #8 yjlD 39 similar to NADH dehydrogenase #9 yjmA 197 similar to glucuronate isomerase #10 yjmB 67 similar to Na+:galactoside symporter #11 yjmC 104 similar to malate dehydrogenase #12 cad 184 lysine decarboxylase #13 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #14 nusA 34 nusA #15 truB 81 tRNA pseudouridine 55 synthase #16 rpsO 156 ribosomal protein S15 (BS18) #17 pnpA 172 polynucleotide phosphorylase (PNPase) #18 ylxY 117 alternate gene name: ymxI; similar to deacetylase #19 ymxG 39 similar to processing protease #20 pksF 300 pksF #21 penP 225 beta-lactamase precursor #22 odhB 29 2-oxoglutarate dehydrogenase complex (dihydrolipoamide transsuccinylase, E2 subunit) #23 odhA 227 2-oxoglutarate dehydrogenase (E1 subunit) #24 yojN 63 similar to nitric-oxide reductase #25 yojM 92 similar to superoxide dismutase #26 yojL 300 similar to cell wall-binding protein #27 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #28 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #29 yqiS 124 similar to phosphate butyryltransferase #30 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #31 mmgA 137 acetyl-CoA acetyltransferase #32 yqiK 78 similar to glycerophosphodiester phosphodiesterase #33 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #34 yqhS 86 similar to 3-dehydroquinate dehydratase #35 yqhR 226 yqhR #36 blt 116 multidrug-efflux transporter #37 bltD 168 spermine/spermidine acetyltransferase #38 yteI 185 similar to protease IV #39 yugK 103 similar to NADH-dependent butanol dehydrogenase #40 yugJ 229 similar to NADH-dependent butanol dehydrogenase #41 dhbE 28 2,3-dihydroxybenzoate-AMP ligase (enterobactin synthetase component E) #42 dhbC 25 isochorismate synthase #43 dhbA 193 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase #44 yuiI 138 yuiI #45 yuiH 100 similar to sulfite oxidase #46 glyA 206 serine hydroxymethyltransferase #47 ywlF 156 alternate gene name: ipc-32d; similar to ribose 5-phosphate epimerase (pentose phosphate) #48 ywlE 75 alternate gene name: ipc-31d; similar to protein-tyrosine-phosphatase #49 ywlD 78 alternate gene name: ipc-30d; similar to hypothetical proteins #50 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #51 ywlB 66 alternate gene name: ipc-28d #52 spoIIR 140 alternate gene name: ipc-27d, csfX #53 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #54 dltA 300 D-alanyl-D-alanine carrier protein ligase (Dcl) #55 aldX 142 aldehyde dehydrogenase Motif number 1 CTTACCCTGCCTTCCTTTTTACCCTCTATT 1 14 1 CTTCCTTTTT 0.787363 -159 TGATCACATCCTCGCTTTTTATTTTGGGGA 2 161 0 CTCGCTTTTT 0.814495 -140 CCAGTATATATCCGTCTTTTTCAATAAACC 2 206 0 TCCGTCTTTT 0.728102 -95 ATTCTATAGGTTCCTTCTTTTGTTGAGAAG 5 180 0 TTCCTTCTTT 0.707028 -52 TCCCTCTTTCCCCTTTGTAGTGATTT 6 7 1 TTTCCCCTTT 0.611433 -145 CGTATATCCTCCGTCCTTTATATCAATTT 8 21 0 TCCGTCCTTT 0.718334 -19 TTGGGATCAATCTCTTTTTTGAAAATGAAA 9 100 0 TCTCTTTTTT 0.79362 -98 AGTGGGGAAACCCGCTCTTTTGTATTGAAC 13 163 1 CCCGCTCTTT 0.893069 -138 CTTTTTAGCCCCTGCTCTTTTGAAGCAGGG 13 226 1 CCTGCTCTTT 0.863866 -75 ATACGCCTATCCTCTCTTTTT 15 2 0 CCTCTCTTTT 0.748255 -80 TTGCCTTTCACTCCTTCTTTTGAGTTTTTT 15 62 0 CTCCTTCTTT 0.760549 -20 CGGGAATCCTCCCGCTTTTTACGA 17 5 0 CCCGCTTTTT 0.897641 -168 CGGGAGGATTCCCGCTTTTTTATCGTATTA 17 21 1 CCCGCTTTTT 0.897641 -152 CTTTTTGGCGTTTGTTTTTTCGAATGATTA 23 25 1 TTTGTTTTTT 0.634317 -203 GATTAAATTTTTTGTTTTTTATAAAGGTTT 23 50 1 TTTGTTTTTT 0.634317 -178 CTGTCTCCCCCTTGTTTTTTCTAACAGTGT 25 72 0 CTTGTTTTTT 0.695398 -21 GAAGCAGTTTCTCCTCCTTTCTTGTCTATT 26 27 0 CTCCTCCTTT 0.650999 -274 TCAAGCCCCTCCTTTATGCTTTTAA 28 59 0 CCCCTCCTTT 0.788386 -15 TTGTTTCGACTCCGCCTTTTATTATGCAAG 29 90 0 TCCGCCTTTT 0.796461 -35 TTGACGCAGCCTTCTTTTTTCATTCATTCA 31 40 1 CTTCTTTTTT 0.717034 -98 ACAATCTCTCCTTTTCGCGAGGGT 34 73 0 TCTCTCCTTT 0.682617 -14 CTGAATTCCCCTTTTACTCAATTGA 36 102 0 TTCCCCTTTT 0.684999 -15 ACTACATTCTCCTTTTTTCTTATCCCG 37 152 0 TCTCCTTTTT 0.848925 -17 ATCCCATTTCCCCTTTGCTGTCATAT 38 7 1 TTTCCCCTTT 0.611433 -179 TTTTTCTCCTCCTTTTTCCTAAACTCT 38 169 0 CCTCCTTTTT 0.880891 -17 AACGGCTATTTCCCCTTTTT 39 1 0 TCCCCTTTTT 0.880891 -103 GTTTGGCTGCTTCCCTTTTTCTTTTTTGTC 39 28 1 TTCCCTTTTT 0.787363 -76 CAATGGAAAATCTGTTTTTTACCAGCATCA 39 69 1 TCTGTTTTTT 0.776012 -35 TGACAATCTTTTTGTTCTTTATTACTCTAT 45 43 0 TTTGTTCTTT 0.622924 -58 ATGGGCCTCCTTTTTGTTAACCTAA 45 86 0 CCTCCTTTTT 0.880891 -15 CTATCCGTATCCTGTTCTTTGTTTTTACCA 46 172 0 CCTGTTCTTT 0.812825 -35 GCGCAGCCTGTCCGCTCTTTGATTCACACC 47 88 0 TCCGCTCTTT 0.863866 -69 GAAGTCGCCGTTTCTTTTTTCTTCATATAT 48 29 1 TTTCTTTTTT 0.658158 -47 TTGGACACGCCCCGCTTTTTTAGCCTATGC 49 44 0 CCCGCTTTTT 0.897641 -35 TCCGTTTCTCCTTTTTGTAAGGTATG 53 152 0 TCTCCTTTTT 0.848925 -16 AAATTCCCTTCCCGTTTTTTCGACAATCAC 54 109 0 CCCGTTTTTT 0.857169 -192 TACTGCTTGTTTTGTTTTTTATGTATGGTT 54 220 1 TTTGTTTTTT 0.634317 -81 CCTCATTTGCTTTCTTCTTTTCTCGGACCT 55 112 0 TTTCTTCTTT 0.647095 -31 ********** Masking position 8 Map Score: 40.0048 Number of sites scoring better than the average of aligned sites = 2022 Number in coding regions = 1468 Number in noncoding regions = 554 Number of orfs with sites within 600 bp upstream = 519 Fraction of orfs with sites within 600 bp upstream = 0.0833601 Motif number 2 TTTGTTCTCCCCTTCGTTTTGATT 1 159 0 TTCTCCCCTT 0.872814 -14 AAATCTGATTGTCTCTCCTCACAGTATCCT 5 120 1 GTCTCTCCTC 0.881828 -112 TCCCTCTTTCCCCTTTGTAGTGATT 6 6 1 CTTTCCCCTT 0.733744 -146 GTTCCACCTCTGTGTCTTAA 10 58 0 GTTCCACCTC 0.895569 -10 TTGTTTTCCCACCTTTGTAATCATA 12 170 0 TTCCCACCTT 0.58789 -15 AAAAGAGCGGGTTTCCCCACTCTTTGCCTC 13 154 0 GTTTCCCCAC 0.768169 -147 TTAACGGTCTCCCCCCTTAAAACATT 14 19 0 GTCTCCCCCC 0.942567 -16 CCTGTTTCACCTCCAAATCATAT 16 144 0 GTTTCACCTC 0.942915 -13 GTTCTGTCCCCCCCTCACCTCACAT 18 103 0 GTCCCCCCCT 0.863179 -15 TCACCGATGTTTTTCACCCCGGATAGCTCA 20 264 0 TTTTCACCCC 0.715462 -37 TTTTTCATTTCCCCCTTAGTTTTTGCG 22 13 0 TTTCCCCCTT 0.823005 -17 ACTGTCTCCCCCTTGTTTTTTCT 25 80 0 GTCTCCCCCT 0.923963 -13 GAACGAAGCAGTTTCTCCTCCTTTCTTGTC 26 31 0 GTTTCTCCTC 0.90688 -270 GGTTTCACCTCATTCAGAAGA 31 127 0 GTTTCACCTC 0.942915 -11 CGTTTCACCTCAAACCCTAAA 32 68 0 GTTTCACCTC 0.942915 -11 ATCCCATTTCCCCTTTGCTGTCATA 38 6 1 ATTTCCCCTT 0.766285 -180 TTTTTCTCCTCCTTTTTCCTA 38 175 0 TTTTCTCCTC 0.740631 -11 CCAAACGGCTATTTCCCCTTTTT 39 4 0 ATTTCCCCTT 0.766285 -100 CGTTGTTCCCCCTTAGGTTGACAT 45 5 1 GTTCCCCCTT 0.940683 -96 GTCAGTCACCCCTTATTTTTCTCT 48 62 0 GTCACCCCTT 0.65276 -14 TGCTAGATTTTTTTCACCCTGCACGTTTAT 52 58 1 TTTTCACCCT 0.650563 -83 TCCGTTTCTCCTTTTTGTAAGGT 53 155 0 GTTTCTCCTT 0.878209 -13 ********** Masking position 2 Map Score: 21.0589 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 261 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 CGCTTTTTGATTATTTTTTAAAGGAAGAACAAAC 1 105 1 TTATTTAAAG 0.813858 -68 ATCTTACTGCTTATTTTCAAAATGTTTTTGTCGT 2 74 0 TTATTTAAAG 0.813852 -227 AACTGGAACGGTTTATTGAAAAAGACGGATATAT 2 197 1 GTTTTTAAAG 0.751757 -104 ATATACCCATTTTTCTTGAAAAAAGCATGTTTTA 6 88 0 TTTTTTAAAA 0.865617 -64 GGAGGACCAATTTTTTTGAAAAGATAGGAGGACA 6 126 1 TTTTTTAAAA 0.865369 -26 CACGTTCAAATTTTGTTCAAAAAGTGTTATCATA 7 14 1 TTTTTTAAAG 0.953647 -287 TTCAGTATTATTTTTATCTAAAAATAAACAATTG 7 117 0 TTTTATAAAA 0.369253 -184 AGTAAACATTTATTTTTGTAAATGATTGTGCATG 7 174 1 TATTTTAAAG 0.700857 -127 AGTTTGCTGATTTTTTTGGAAAGGGTAGTGCCTC 7 253 0 TTTTTTAAAG 0.95371 -48 GGATCAATCTCTTTTTTGAAAATGAAATGTTAAC 9 93 0 CTTTTTAAAG 0.620691 -105 CCGTCTTTCATTCTATTTCAAAATGTTAACGTTA 9 167 0 TTCTTTAAAT 0.398173 -31 ATAACCATATTTTTATTGCAAATGGATATACGCT 13 87 0 TTTTTTAAAG 0.953711 -214 TATGGTATAGTTTTATTGGAAATGCTAACGATTA 13 118 1 TTTTTTAAAG 0.953711 -183 TTTTGAGTTTTTTTCTTATAAACGAAGAAAGAGG 15 41 0 TTTTTTAAAG 0.953498 -41 CGCACGCAAATTTTATTCTAAAATATTTGCATAT 16 18 1 TTTTTTAAAT 0.720805 -139 TAAATTTTTTGTTTTTTATAAAGGTTTTTTACTA 23 53 1 GTTTTTAAAG 0.751739 -175 AAGCACGATATGTTTTTCGAAAGTCTAAGGAACT 26 98 0 TGTTTTAAAT 0.518399 -203 TCCTAAACTGTTTTTTTGCAAAAACAGCTAGTAT 26 267 0 TTTTTTAAAA 0.86556 -34 CCCTCCTTTATGCTTTTAAAAATGAATGGCTTTG 28 44 0 TGCTTTAAAG 0.687175 -30 TGTGCAAATTTTTTCATACAAAGGGGTATCGGG 30 130 1 TTTTATAAAG 0.652829 -23 GATCATTTCCTGTTGTTAGAAAGATAACGAGCAG 33 162 0 TGTTTTAAAA 0.729895 -139 GCAAGTTCCATGATTTTCAAAAGGGCTATACGAC 33 198 0 TGATTTAAAG 0.645758 -103 CAGTGACAAATATTTTTTTAAAGGCAAGGCTGAG 43 17 0 TATTTTAAAG 0.700894 -177 GGTTCTATTTCAAATAGGACAATACG 44 3 1 TTCTTTAAAA 0.624203 -136 ATAATAGGTTTTCTTCCAAAGAAAGTCAACTT 44 117 0 TTTTTTAAAA 0.866339 -22 ATGTAAAAGATTATTTTTAAAAAATCTAAATTTT 46 110 0 TTATTTAAAA 0.578548 -97 TATCGGCGTATGTTTTTGAAAATGAATCTTTAT 54 10 0 TGTTTTAAAG 0.895129 -291 **** ** *** * Masking position 7 Map Score: 23.6143 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 346 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 4 TTCGTTTGTTCTTCCTTTAAAAAATAATCAAA 1 110 0 CTTCCTTTAA 0.499802 -63 ATAGAATCCCCCCTTAGTAACCTTTTTGT 5 8 1 CCCCCCTTAA 0.967084 -224 AAAAATTGGTCCTCCTTCAATATACCCATTTT 6 109 0 CCTCCTTCAA 0.8515 -43 ATCCAATTCTCCTTTACTATAAGCAGTTT 7 282 0 TCTCCTTTAA 0.689186 -19 TGTAGATTTACTTCCCTTAAGAGAAAGCATCT 12 24 1 CTTCCCTTAA 0.801965 -161 TTAACGGTCTCCCCCCTTAAAACATTTGTATT 14 13 0 CCCCCCTTAA 0.967084 -22 ACCTTGTCCTTCTCCTTCATAATGTGAGGTGA 18 82 1 TCTCCTTCAA 0.645287 -36 GTTCTGTCCCCCCCTCACCTCACATTATGA 18 98 0 CCCCCCTCAT 0.973886 -20 TTTTTCATTTCCCCCTTAGTTTTTGCGAG 22 9 0 TCCCCCTTAT 0.935156 -21 TCATTTTTACCCTCGCTTAAATAGTTCCTTAG 26 76 1 CCTCGCTTAT 0.855661 -225 GATTGTATCCTCCCTTACGTCT 27 3 0 CCTCCCTTAT 0.977691 -20 GGCAGGCCAGCTTCCCTCATATGGAGAATGCA 40 78 0 CTTCCCTCAT 0.837145 -152 GCTGGCCTGCCCTCGCTTATATCAGCTTCTTT 40 99 1 CCTCGCTTAT 0.855661 -131 TCTCATGAACCTCCTTTAAATTCAG 42 5 0 CCTCCTTTAT 0.915351 -21 CGTTGTTCCCCCTTAGGTTGACATACAC 45 7 1 TCCCCCTTAT 0.935156 -94 GTCAGTCACCCCTTATTTTTCTCTATTA 48 58 0 CACCCCTTAT 0.720047 -18 TTTTCCCTAATCTCCCTCAAATTAATATATCG 54 39 0 TCTCCCTCAT 0.919402 -262 TGTAAAATCCCCCTCATTTGCTTTCTTCT 55 124 0 TCCCCCTCAT 0.922069 -19 ********* * Masking position 7 Map Score: 14.9693 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 157 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 5 TCCCCCCTTAGTAACCTTTTTGTATGTTAGA 5 17 1 GTACCTTTTT 0.872834 -215 AAACTGGGTAGTAAACATTTATTTTTGTAAA 7 165 1 GTAACATTTA 0.821058 -136 TTATGACAGCGTTAACATTTCATTTTCAAAA 9 83 1 GTAACATTTC 0.876504 -115 AAATGTTAACGTTAACATTTTGATTTGTTTT 9 150 0 GTAACATTTT 0.948699 -48 AAATGTTAACGTTAACATTTTGAAATAGAAT 9 161 1 GTAACATTTT 0.948699 -37 CTCGGTAATCGTTAGCATTTCCAATAAAACT 13 126 0 GTAGCATTTC 0.816355 -175 CATGTTCATCGTTTACTTTTTAGCCCCTGCT 13 211 1 GTTACTTTTT 0.629455 -90 GACAGTCATTGTCAGCTTTTTTGTTGATTCT 21 63 1 GTAGCTTTTT 0.909074 -163 TCAGCCAAGCGTAACCTTTTAAAGGATATT 33 10 0 GTACCTTTTA 0.630046 -291 TTCACTTCTCGTGAACATTTTATCATACTGG 34 25 0 GTAACATTTT 0.948699 -62 TTCACGAGAAGTGAACATTTTTTACATGAGA 34 41 1 GTAACATTTT 0.948699 -46 GCCAAAAAGTGTGAGCTTTTTTATTGACATT 35 173 1 GTAGCTTTTT 0.909074 -54 TCCAAAGAAAGTCAACTTTTTCCCGAATAAA 44 104 0 GTAACTTTTT 0.941048 -35 ** ******** Masking position 8 Map Score: 10.1863 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 64 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 CAAAAGCAATTTGCAGGTTTTCTCCCGATTCC 2 132 1 TTGAGTTTTC 0.947064 -169 GGTAATCGAATTGGAGTTTTTTGTGTTTGCTA 7 53 1 TTGAGTTTTT 0.930224 -248 TATAAGCAGTTTGCTGATTTTTTTGGAAAGGG 7 262 0 TTGTGTTTTT 0.795985 -39 CCTCCTTCCTTTTCAGTTTTTTGGGCACTCTC 11 76 0 TTTAGTTTTT 0.825211 -29 TCTTCACTCCTTGTAGATTTACTTCCCTTAAG 12 13 1 TTGAGTTTAC 0.770495 -172 CACTCCTTCTTTTGAGTTTTTTTCTTATAAAC 15 52 0 TTTAGTTTTT 0.825211 -30 CTTCTTTATTTTGAAGCTTTTCAAAAGCAGGC 18 43 1 TTGAGTTTTC 0.947063 -75 ATGATTAAATTTTTTGTTTTTTATAAAGGTTT 23 48 1 TTTTGTTTTT 0.580132 -180 AGATGTTTATTTGAAGGTTTAAAGGTCGAACG 26 144 1 TTGAGTTTAA 0.567525 -157 AAGCCCCTCCTTTATGCTTTTAAAAATGAATG 28 50 0 TTTTGTTTTA 0.42022 -24 TCCTTTTCGCTTGAAGCTTTTTTCAAGTACAA 36 56 0 TTGAGTTTTT 0.930223 -61 TGCTGTCATATTTAAGTTTTTCTGCCATCCAG 38 26 1 TTTAGTTTTC 0.863681 -160 CCAGCATCATTTGGAGGTTTTACT 39 90 1 TTGAGTTTTA 0.874894 -14 AATGACCTGTTTGCAGATTTTCTGACAAC 47 8 0 TTGAGTTTTC 0.947064 -149 *** ** ***** Masking position 8 Map Score: 10.332 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 161 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 GTATAATGAAAAAAGAGTCTGCAAAAAAGTAAGTAA 5 61 0 AAAGAGTGAA 0.964283 -171 CAATAATTCGAAAAGGGAGTGGATCAACA 5 213 1 AAAGGGTGTA 0.948852 -19 ATTTTTCTTGAAAAAAGCATGTTTTAAACATTGTAT 6 78 0 AAAAAGTGTA 0.780924 -74 CAGAGAGAGTAAAGGATTTTGACTTATTCAATTGTT 7 89 1 AAAGATTGTA 0.888346 -212 TTATTTTTGTAAATGATTGTGCATGAATTCACAATC 7 183 1 AAAGATTGTA 0.888346 -118 TAAACATAAAAAAAGACATTGCCAGAAAGCACTCGG 9 50 0 AAAGACTGAA 0.759202 -148 TATCAATGTCAAAGTAGTATGTAAAAGGATTTCAAT 17 75 0 AAATAGTGAA 0.64006 -98 TGAAAACATAAAAGGAGCCTGGGAGACCCGGCTTCT 18 12 1 AAAGAGTGAA 0.964283 -106 TTACTAGCGCAAAGGGGTTTGTTACACTAACTGTCA 21 151 1 AAAGGGTGAA 0.94226 -75 CTCCTCATTCAAATGATTTTGTATTACCTTTGAAAT 21 195 0 AAAGATTGTA 0.888346 -31 TGCTCAATACAAAAGGGCCTGGATGATA 24 3 0 AAAGGGTGTA 0.948852 -61 AAATGAGTATGACAAAAAGCCTTTTA 25 1 1 AAAGAGTGAA 0.964283 -92 ATGAATGAAAAAAGAAGGCTGCGTCAAACAGCCTCC 31 31 0 AAAAAGTGTA 0.780924 -107 GTATGCTTTGAAACGGGCATGAATGAATGAAAAAAG 31 53 0 AAAGGGTGTA 0.948852 -85 TAAAACCTCCAAATGATGCTGGTAAAAAACAGATTT 39 76 0 AAAGATTGAA 0.874982 -28 *** *** ** * * Masking position 3 Map Score: 13.2242 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 139 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 AAAACCAAATTTAAGCGCTTTTTGATTATTTT 1 90 1 TAACGCTTTT 0.657813 -83 CGGACAGTGATTTACCGCTTTTTTATAAAATA 3 61 1 TTACGCTTTT 0.867881 -166 CCTCCTTCAATATACCCATTTTTCTTGAAAAA 6 99 0 TTACCATTTT 0.855613 -53 ATTTTACCTTTATATTCCTTTGGGATCAATCT 9 117 0 TTATCCTTTG 0.739304 -81 AAGGTAAGCGTATATCCATTTGCAATAAAAAT 13 81 1 TTACCATTTG 0.614022 -220 AACAAATCATTGAAATCCTTTTACATACTACT 17 67 1 TAATCCTTTT 0.755595 -106 AAGGGATTATTTTAATGATTTTTATAGGTATA 20 37 0 TTATGATTTT 0.394889 -264 TTTCAGCAAGTTAAACCCTTTTCAAACATTTG 26 194 0 TAACCCTTTT 0.880188 -107 GAAGCAACTTTTTATTCATTTTAAAAAATTTG 33 74 0 TTATCATTTT 0.713775 -227 GATCGGGTCGTATAGCCCTTTTGAAAATCATG 33 192 1 TTACCCTTTT 0.961687 -109 TGTATAATCCTTTTCCAGTATGAT 34 3 1 TTATCCTTTT 0.913522 -84 TTTTACTCAATTGAACCCTTTTTACCTATCCT 36 84 0 TGACCCTTTT 0.811649 -33 AGTCAGATGTTCTAACCCTTTTTGGACACGCA 49 15 1 TTACCCTTTT 0.961689 -64 GTTTTACGCGTGTAATCCTTTTGAAAGTATAA 50 97 0 TTATCCTTTT 0.913522 -60 GTGCTTTGTTTCTAGCCCTATTATGGACAAGG 52 98 0 TTACCCTATT 0.696781 -43 * ** ******* Masking position 4 Map Score: 7.95887 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 203 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 TTCCTTTAAAAAATAATCAAAAAGCGCTTA 1 101 0 AAATAATCAA 0.87651 -72 AAATATCAGAAAATAAAGATATTGACTTAT 3 88 1 AAATAAAGAT 0.52134 -139 ATTGTAAGACAAATAAACAATAAGTCAATA 3 107 0 AAATAAACAA 0.90716 -120 TTTGTCTTACAATTAAACAAAAGGATATAT 3 124 1 AATTAAACAA 0.530905 -103 TTTTATCTAAAAATAAACAATTGAATAAGT 7 110 0 AAATAAACAA 0.90716 -191 TCGTTGTGTGAAATAATCAATTACTCCTAT 17 133 0 AAATAATCAA 0.87651 -40 AAAAGCTTCAAAATAAAGAAGCCGGGTCTC 18 34 0 AAATAAAGAA 0.677419 -84 CCCCCAACTTAAATAATCAAGTGATTGATT 23 198 0 AAATAATCAA 0.87651 -30 TTGATTAGAAAAATAGACAAGAAAGGAGGA 26 16 1 AAATAGACAA 0.626505 -285 TTAAACCTTCAAATAAACATCTAACATTTT 26 136 0 AAATAAACAT 0.835197 -165 TCAATTATAAAAATAATCATATCCAAATGT 43 74 0 AAATAATCAT 0.786384 -120 TCTGATCGTCAAATAATCATGTGATTGTCG 54 89 1 AAATAATCAT 0.786384 -212 ********** Masking position 5 Map Score: 7.09508 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 126 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 GTTGACTTCAAAGTGCCTACTTCTCAACAAAAG 5 161 1 ATGCCTCTTC 0.981314 -71 AATGTTTAAAACATGCTTTTTTCAAGAAAAATG 6 82 1 ATGCTTTTTC 0.927464 -70 GCAAGTGCCTCCTTCCTTTTCAGTT 11 90 0 ATGCCTCTTC 0.981314 -15 ACTCTGCATAAAAACCCTGCTTCAAAAGAGCAG 13 237 0 AACCCTCTTC 0.767426 -64 TTCAAAGACAAGCTGCCTTCATCTG 19 3 0 ATGCCTCATC 0.848224 -37 AAGGAGGAGAAACTGCTTCGTTCATCAATAGAA 26 38 1 ATGCTTGTTC 0.823796 -263 GGCTGCGTCAAACAGCCTCCTTCTAACAACTAT 31 18 0 AAGCCTCTTC 0.94401 -120 ATGAATAAAAAGTTGCTTCTTTCCGCTAATTTT 33 87 1 ATGCTTTTTC 0.927464 -214 ATTATCAACCTGCCTATTTCTTTAGGATTG 35 8 1 ATGCCTTTTC 0.95963 -219 CCTCGCTTATATCAGCTTCTTTCCCAGCACCTT 40 109 1 AAGCTTTTTC 0.804113 -121 ATCATCAATTCCTTTCTTCGCTCTAAATG 43 175 0 ATCCTTCTTC 0.846823 -19 TATTTGATCAAGGTGCCTTTTTTATTCGGGAAA 44 84 1 ATGCCTTTTT 0.610244 -55 AATCCCCCTCATTTGCTTTCTTCTTTTCTCGGA 55 115 0 ATGCTTCTTC 0.965809 -28 * ***** **** Masking position 1 Map Score: 10.5592 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 202 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 11 GCCTTCCTTTTTACCCTCTATTTTCACGTTATCTT 1 22 1 TTCCTTTTTC 0.916998 -151 GGGCCAGTATATATCCGTCTTTTTCAATAAACCGT 2 204 0 ATCCCTTTTC 0.839569 -97 AATGTCCTCCTATCTTTTCAAAAAAATTG 6 133 0 TCCCTTTTTC 0.919738 -19 ATAAATGTTTACTACCCAGTTTTTCATCTTGCCAT 7 152 0 ACCCGTTTTC 0.844432 -149 AAGAGCGGGTTTCCCCACTCTTTGCCTCGGTAATC 13 147 0 TTCCTTTTGC 0.919738 -154 TGAAGTATTAATCACCAATATTTGCGAGGTGCTTC 20 105 1 ATCCTTTTGC 0.927736 -196 CCAACGATATTTTACCACTGTTTGCAATTTGATTC 23 107 0 TTCCTTTTGC 0.919738 -121 AAGCAGTTTCTCCTCCTTTCTTGTCTATTTTTCTA 26 21 0 TCCCTTTGTC 0.715137 -280 GAAACAAAATACTAGCTGTTTTTGCAAAAAAACAG 26 259 1 ACGCTTTTGC 0.643017 -42 TTATCTTTTCATTTCCTTTATTGTCCAGCGGAAAA 30 26 1 ATCCTTTGTC 0.730575 -127 AAAAATTGCCATAGCCTTGCTTTTCCTACATGCAT 35 105 1 ATCCGTTTTC 0.839569 -122 TACATGCATTATACCCGTTATTTTCAAATTTTACT 35 131 1 ATCCTTTTTC 0.925247 -96 TTTTTCTCCTCCTTTTTCCTAAACTCTC 38 168 0 TTCCCTTTTC 0.823668 -18 AAGGACTGCATAGCCAGTCTTTTCTTTTATTTTA 46 10 1 ATCCTTTTTC 0.925247 -197 TTCTACTCCTTCACGCAGGATTTGCAAATGACCTG 47 31 0 TCGCGTTTGC 0.404683 -126 CCGTTCACCCCGTTTTTGCGTTCTTTCTT 51 48 0 TCCCTTTTGC 0.922395 -19 TCAAAAATTCCCTTCCCGTTTTTTCGACAATCACA 54 108 0 CCCCTTTTTC 0.728067 -193 TGTAAAATCCCCCTCATTTGCTTTCTTCTTT 55 122 0 ATCCCTTTGC 0.844432 -21 ** ** * ***** Masking position 11 Map Score: 13.8934 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 349 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 12 CTTTCATAATAGCGGAAGGTATAATTACTGT 2 14 1 AGCGGAAGGA 0.909001 -287 CATAAAATCAAGCGAAAGAAATCTGATTGTC 5 102 1 AGCGAAAGAA 0.914114 -130 TACCTAAGCAAGTGACAGAAACTCTAATATT 13 48 0 AGTGACAGAA 0.603496 -253 CAAAAGAAGGAGTGAAAGGCAA 15 70 1 AGTGAAAGGA 0.899564 -12 TTTATTGTCCAGCGGAAAAAATATTTTGTCA 30 42 1 AGCGGAAAAA 0.840583 -111 AGAAAAAATTAGCGGAAAGAAGCAACTTTTT 33 93 0 AGCGGAAAGA 0.907432 -208 GAGAAACCCTCGCGAAAAGGAGAGATTGT 34 68 1 CGCGAAAAGA 0.753861 -19 TGTACAATAGAGTGAAAGGAAATGGTTAGCA 35 39 0 AGTGAAAGGA 0.899564 -188 AAAAGCTTCAAGCGAAAAGGATAGGTAAAAA 36 67 1 AGCGAAAAGA 0.951025 -50 ATATAATTTCAGTGACAAATATTTTTTTAAA 43 29 0 AGTGACAAAA 0.598983 -165 ACAGACATCCAGCGAAAAAGACTGCTGCGCC 43 140 0 AGCGAAAAAA 0.912625 -54 AGTAGAATATAGTGAAAAGCACATCATATGG 47 59 1 AGTGAAAAGA 0.897851 -98 CATATATAATAGAGAAAAATAAGGGGTGACT 48 52 1 AGAGAAAAAA 0.5384 -24 ********* * Masking position 7 Map Score: 6.40482 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 199 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 TTGCTGCGCAGAATCCCGGCCGGACAGTGATTTACCG 3 41 1 GTCGGGACAG 0.917883 -186 GTTACTTGGAGGATACTGTGAGGAGAGACAATCAGAT 5 122 0 GTCGGGAGAG 0.989674 -110 TGCCTTAAAAGCGTGAGACAGGGAGAGGCACTACCCT 7 229 1 GTAAGGAGAG 0.956673 -72 TTTTGAAATAGAATGAAAGACGGTGAGGAC 9 178 1 GTAAGGTGAG 0.928666 -20 GTGTTTGTAGGGGTTTCGCTTGGAGAGTGCCCAAAAA 11 54 1 GTTGGGAGAG 0.936815 -51 GAATACAAATGTTTTAAGGGGGGAGACCGTTAA 14 12 1 GTAGGGAGAC 0.875285 -23 TCCTTCTCCTTCATAATGTGAGGTGAGGGGGGGACAG 18 88 1 TTAGGGTGAG 0.736285 -30 AAACCATCTGGTATGCTGATCGGTGAGAGCTGATTGC 40 150 1 GTCGGGTGAG 0.98261 -80 AGAGCTGATTGCTTTACATGTGGTGAGGACATTCTGC 40 175 1 GTAAGGTGAG 0.928666 -55 ACAAAGAACAGGATACGGATAGGAGAGGATCTCGCTG 46 180 1 GTCGGGAGAG 0.989673 -27 TATTTATAACGATTTCTAATTGGAGAGAGAATAACT 54 275 1 GTCAGGAGAG 0.972384 -26 * * * * ****** Masking position 16 Map Score: 8.78063 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 41 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 TATTTTTTAAAGGAAGAACAAACGAAAGAG 1 116 1 AGGAAGAACA 0.777546 -57 GGTATATTGAAGGAGGACCAATTTTTTTGA 6 115 1 AGGAGGACCA 0.975837 -37 TTGAAAAGATAGGAGGACATT 6 141 1 AGGAGGACAT 0.895342 -11 CTGAAAAGGAAGGAGGCACTTGC 11 92 1 AGGAGGCACT 0.718824 -13 CGACAGCACAAGGAGGAAGAAC 13 289 1 AGGAGGAAGA 0.852627 -12 ATTATGAAGGAGAAGGACAAGGTAGAACCC 18 75 0 AGAAGGACAA 0.640208 -43 GTCTTTGAATAGGAGGAACAAAT 19 27 1 AGGAGGAACA 0.96784 -13 TAGACAAGAAAGGAGGAGAAACTGCTTCGT 26 29 1 AGGAGGAGAA 0.947277 -272 TTTAGGAAAAAGGAGGAGAAAAA 38 173 1 AGGAGGAGAA 0.947277 -13 AAAAAATCTAAGGAGGAGATGTC 40 217 1 AGGAGGAGAT 0.84021 -13 TGTCAACCTAAGGGGGAACAACG 45 4 0 AGGGGGAACA 0.814471 -97 GTTAACAAAAAGGAGGCCCAT 45 90 1 AGGAGGCCCA 0.9214 -11 CACACACGCTGGGAGGAAAAGCAG 47 143 1 GGGAGGAAAA 0.760621 -14 GATAAAATGCAGGAAGACAACATTTATTTT 53 26 0 AGGAAGACAA 0.772473 -142 ********** Masking position 6 Map Score: 9.47774 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 154 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 15 TACCTTCCGCTATTATGAAAGCGT 2 4 0 TATTATGAAG 0.832791 -297 ATAATTACTGTATAATGGAGACTACAGAATC 2 34 1 TATAATGGAA 0.696142 -267 TATGAGTGAGTATAATGAAAAAAGAGTCTGC 5 75 0 TATAATGAAA 0.700361 -157 GAAAAATGGGTATATTGAAGGAGGACCAATT 6 107 1 TATATTGAAG 0.367165 -45 TAATACACACTATTATGCATAGGTATGATTA 12 147 1 TATTATGCAA 0.886285 -38 CAATTACTCCTATTATGAACGAAATGAATTG 17 115 0 TATTATGAAG 0.832791 -58 AAAGTTTGAATATTATGAAAATATACCTATA 20 16 1 TATTATGAAA 0.803844 -285 TGTTTGCGTTTATTCTGCAAA 29 1 0 TATTCTGCAA 0.572289 -124 CTCCGCCTTTTATTATGCAAGTTCCATGCCA 29 80 0 TATTATGCAG 0.904515 -45 ACAAAATAAGTATAATGGAGAAAACTTTAGG 32 43 1 TATAATGGAA 0.696142 -36 AAATAACGGGTATAATGCATGTAGGAAAAGC 35 123 0 TATAATGCAG 0.84382 -104 CAGATGGTTTTATTTTGCAAGGTGCTGGGAA 40 129 0 TATTTTGCAG 0.659258 -101 TTAGATTTTTTATTATGCAGAATGTCCTCAC 40 197 0 TATTATGCAA 0.886291 -33 TTTCTAGCCCTATTATGGACAAGGAGAGCCT 52 91 0 TATTATGGAA 0.800671 -50 ********* * Masking position 9 Map Score: 5.76602 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 109 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714