AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_synecho_reg_300.orf -o00640_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 sll1022 146 hypothetical protein. #2 sll1021 39 hypothetical protein. #3 sll1020 95 hypothetical protein. #4 slr1090 44 GTP-binding protein. #5 ssr1789 79 hliA; high light inducible protein. #6 sll1019 60 gloB; probable hydroxyacylglutathione hydrolase (glyoxalase II). #7 sll1018 119 pyrC; dihydroorotase. [EC:3.5.2.3] #8 sll1017 241 putative ammonium transporter sll1017. [SP:YA17_SYNY3] #9 slr1400 119 regulatory components of sensory transduction system. #10 slr0670 117 hypothetical protein. #11 sll0656 130 nucH; extracellular nuclease. #12 sll0654 300 alkaline phosphatase. [EC:3.1.3.1] #13 sll1298 271 clcD; dienelactone hydrolase. [EC:3.1.1.45] #14 ssr2315 179 hypothetical protein. #15 ssr2317 28 hypothetical protein. #16 slr1384 134 hypothetical protein. #17 slr1385 178 hypothetical protein. #18 ssr2318 22 hypothetical protein. #19 ssl2559 120 hypothetical protein. #20 sll1296 56 cheA; chemotaxis protein CheA. [EC:2.7.3.-] #21 sll1294 146 pilJ; methyl-accepting chemotaxis protein (MCP). #22 sll1293 32 hypothetical protein. #23 sll1292 106 regulatory components of sensory transduction system. #24 sll1291 300 regulatory components of sensory transduction system. #25 sll1557 104 sucD; succinyl-CoA synthetase. [EC:6.2.1.5] #26 sll1556 171 hypothetical 37.5 kD protein sll1556. [SP:YF56_SYNY3] #27 sll1555 300 regulatory components of sensory transduction system. #28 sll0336 113 accD, zfpA; acetyl-coenzyme A carboxylase carboxyl transferase #29 sll0335 279 hypothetical 53.7 kD protein sll0335. [SP:Y335_SYNY3] #30 slr0373 90 hypothetical protein. #31 slr0374 132 cell division cycle protein. #32 slr0376 181 hypothetical protein. #33 slr0377 42 hypothetical protein. #34 slr0380 113 hypothetical protein. #35 slr0381 300 gloA; probable lactoylglutathione lyase (methylglyoxalase) #36 slr0435 229 accB; biotin carboxyl carrier protein of acetyl-CoA carboxylase. #37 slr0436 35 ccmK; carbon dioxide concentrating mechanism protein CcmK. #38 sll0405 300 hypothetical protein. #39 sll0891 37 citH; 2-ketoacid dehydrogenase (malate dehydrogenase, lactate #40 ssl1690 300 hypothetical protein. #41 sll0542 245 acs; acetyl-coenzyme A synthetase. [EC:6.2.1.1] #42 slr0579 124 hypothetical protein. #43 sll0541 110 des9; acyl-CoA desaturase 1. [EC:1.14.99.5] #44 slr0580 129 hypothetical protein. #45 sll0540 112 hypothetical protein. #46 sll0539 192 hypothetical protein. #47 slr0583 25 hypothetical protein. #48 slr0825 94 hypothetical protein. #49 ssr1398 96 rpmG, rpl33; 50S ribosomal protein L33. [SP:RL33_SYNY3] #50 ssr1399 265 rpsR, rps18; 30S ribosomal protein S18. [SP:RS18_SYNY3] #51 slr0827 294 alr; probable alanine racemase. [EC:5.1.1.1] [SP:ALR_SYNY3] #52 sll0834 284 low affinity sulfate transporter. #53 sll0832 300 hypothetical protein. #54 slr0092 117 hisB; hypothetical protein. #55 slr0093 28 dnaJ-like protein slr0093. [SP:DNJH_SYNY3] #56 slr0095 161 hisB; O-methyltransferase. [EC:2.1.1.-] #57 slr0096 29 hisB; low affinity sulfate transporter. #58 slr0498 246 hisB; hypothetical protein. #59 sll0489 286 hisB; ABC transporter. #60 sll0488 116 hypothetical protein. #61 sll0487 109 hypothetical protein. #62 sll0486 173 hypothetical protein. #63 sll0485 247 hypothetical protein. #64 sll0484 130 ABC transporter. #65 slr0502 62 cobW; CobW. #66 slr0505 121 hypothetical protein. #67 slr0506 56 pcr; protochlorophyllide oxido-reductase. [EC:1.3.1.33] #68 sll0481 71 hypothetical protein. [SP:Y481_SYNY3] #69 sll0480 182 hypothetical protein. #70 slr0509 131 alkaline phosphatase-like. #71 slr0510 222 hypothetical protein. #72 ssr0871 55 transposase. #73 slr0511 300 transposase. #74 sll0728 300 accA; acetyl-CoA carboxylase alpha subunit. [EC:6.4.1.2] Motif number 1 CCCTATCAGTAGCGATCGCCGTTGATCCCC 1 12 0 AGCGATCGCC 0.514098 -135 GCTGTCCGTTGGCGATCGCCAGCACCGATT 12 233 1 GGCGATCGCC 0.5 -68 AGCCGACAGAAGCGATCGCCGTTCTCAGAC 13 196 1 AGCGATCGCC 0.514098 -76 GCCCTGCAACGGTGATCGCCGGAATTTGAT 14 73 0 GGTGATCGCC 0.511517 -107 GTTCTATGTCGGCGATCGCCGACCTTGAAA 19 98 1 GGCGATCGCC 0.5 -23 AACTGAGTTTGGCGATCGCCTGATATTCTG 27 168 1 GGCGATCGCC 0.5 -133 CTGACAACCCGGCGATCGCCAAAGCGGGGT 28 25 1 GGCGATCGCC 0.5 -89 GGATTACCCCGGCGATCGCCACTGTCCCCG 28 87 1 GGCGATCGCC 0.5 -27 GCAAAATCTTGGCGATCGCCCTTGGCTTTA 34 52 1 GGCGATCGCC 0.5 -62 GGGCCGCTGTGGCGATCGCCTTCTATGATA 36 26 1 GGCGATCGCC 0.5 -204 TTCCCCAGGCGGCGATCGCCAGAAAAATAT 40 32 1 GGCGATCGCC 0.5 -269 TTGTTTTTCGGGCGATCGCCTGTGGGTAAA 51 153 1 GGCGATCGCC 0.5 -142 GATGATCCTTGGCGATCGCCAGTTTGGGAA 58 110 1 GGCGATCGCC 0.5 -137 CCATTCCTCTGGCGATCGCCAAAGCTCCAG 61 77 1 GGCGATCGCC 0.5 -33 CTTTTATAATGGCGATCGCCCTTTAATCAC 69 157 1 GGCGATCGCC 0.5 -26 ATGATAGAAGAGCGATAGCCTCTGATCTTT 71 141 1 AGCGATAGCC 0.794049 -82 ********** Masking position 5 Map Score: 82.9727 Number of sites scoring better than the average of aligned sites = 5646 Number in coding regions = 5126 Number in noncoding regions = 520 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 2 TAGACCCCCATCACCAAAGCCCCCAATAATGAG 1 45 1 TCCAAACCCC 0.820891 -102 CTCTGCAGGCCTCCACCTTCCCCT 1 133 1 CCACCTCCCC 0.887459 -14 GGCGGTTTTACTTCAACTTTCCCTAGAGTTAGC 12 96 1 CCAACTTCCC 0.544657 -205 GGCGGTTTGATTCCAACTACCCCAGTGAAGATT 14 157 0 TCAACTCCCC 0.759388 -23 TAATTCTATTTATCCCAGCTCCCCAATGAGCTG 17 46 1 TCCCAGTCCC 0.86573 -133 GAAACTGTTCCGACCCATTGCCCAATTGTTTTT 21 106 1 CCCCATGCCC 0.959067 -41 ATTATCATCGTTAGCAATTGCCCAGGGGGATAC 23 82 1 TGCAATGCCC 0.497706 -25 AGCACCATTTCATCCCTTATCCCATTTCTTCAA 24 97 0 CCCCTTTCCC 0.938004 -204 CTTAAAGTTGCTCCCCTACTCCCAAAAACTTGA 27 68 1 CCCCTATCCC 0.745088 -233 ACCCCGGCGATCGCCACTGTCCCCGAACAAAT 28 92 1 TCCACTTCCC 0.907106 -22 GCTTCAATTACAACCGCTGCCCCCGTTTCCTTC 29 125 1 CCCGCTCCCC 0.864952 -155 CGCTAACCCTTGGCCACGGTCCCATTATTCAGC 29 161 0 TCCACGTCCC 0.836988 -119 GGGACAGGTCTTGCCAGTCCCCCAAACTTACTG 35 78 0 TCCAGTCCCC 0.882286 -223 GTTTGAAAAGCCCCCCTGGCCCCCCAAGTTTGG 35 214 0 CCCCTGCCCC 0.966001 -87 CCCTTTAAAATGTCCTTTGCCCCGAAGTTTGCA 36 203 0 TCCTTTCCCC 0.777336 -27 GCCGGCTTCCAATAGCCCTCTAACGCCC 37 6 1 CCCAATGCCC 0.92697 -30 TTCCTGCAAATAACCTCTCCCCCGTTCTTCAGT 38 16 1 TCCTCTCCCC 0.849163 -285 AGTTTCTCCCCAGGCCATTCCCCAGACTTTCCC 40 196 0 CGCCATCCCC 0.862324 -105 TAGAGTTAATTTCCCAGTCTCCCAACGAGGGCA 40 273 1 TCCAGTTCCC 0.677279 -28 CCTTTACACGCAGCCCATAGCCCATTCACTCGG 41 22 0 CCCCATGCCC 0.959067 -224 GCAAAAATTTTTCCCCTTTCCCCAGATTTGTAA 41 173 0 TCCCTTCCCC 0.975563 -73 TACTCCTCTGCACCCAAATTCCCCAAGGGGATA 50 17 1 CCCAAATCCC 0.63464 -249 AACTGCCCAGTTGCCAAGCCCCCAGAATTTCGC 51 228 0 TCCAAGCCCC 0.925787 -67 ACCATAAATCTTCCCCAGCCCCCATTGAGCAAA 52 21 0 TCCCAGCCCC 0.958381 -264 TATTTGTTTTCCTCAACTACCCCTCGCTGTTTA 53 21 0 CCAACTCCCC 0.810316 -280 TCAAACTGCCCCAGCCTTACCCCTAACTAACTT 54 92 1 CGCCTTCCCC 0.85096 -26 GTTCTACCCCCGTCCACGTCCCCCATTACTAAA 56 112 1 CCCACGCCCC 0.961272 -50 TACCTGGTAATGTCCCTATGCCCGCAGTTTTGA 63 147 0 TCCCTAGCCC 0.752991 -101 TTTTGAACTGCCCCCCTGACCCCCCCAAGGCTG 67 15 1 CCCCTGCCCC 0.966001 -42 CATAAACCCATTGCCATTTCCCCTGGGGCGAGG 69 114 1 TCCATTCCCC 0.955804 -69 AAAAGGTGAGTTACCCCTCGCCCCAGGGGAAAT 69 129 0 TCCCCTGCCC 0.962187 -54 AATTTTTCAGTTACCCATCCCCCTATCCCCATG 70 73 0 TCCCATCCCC 0.977675 -59 GAAAAATCCTTCACCCTTAGCCCGGCTAATCCA 74 269 1 TCCCTTGCCC 0.940404 -32 * ***** **** Masking position 11 Map Score: 39.9241 Number of sites scoring better than the average of aligned sites = 3078 Number in coding regions = 2732 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 312 Fraction of orfs with sites within 600 bp upstream = 0.0501124 Motif number 3 TAGGATTTTAGGGGGATTTTTGTGCCGTCGTTCC 7 77 1 GGGGGTTTTG 0.991712 -43 AATTAGGAGTGGGGATATTACTTGTGGGAAAACT 10 17 0 GGGGAATTAG 0.685577 -101 TTTGCAGAGGTGGGGATTTTTTCGTATATGTGAT 10 50 1 TGGGGTTTTG 0.90304 -68 CTTCACCGATGGGGAATTTTGCTGTCCGTTGGCG 12 213 1 GGGGATTTTG 0.991406 -88 CTAATCTTCTTGGGGATTTTCGGGTTGTTAAAGG 16 50 1 TGGGGTTTTG 0.90304 -85 GGGGGGATTATTAAAGGAAAACTGTG 25 89 0 GGGGATATTG 0.956634 -16 GATTAAGGTGGGGGCATATTGTGGTGGTGCTGCT 26 67 0 GGGGCTATTG 0.874518 -105 TTTTTTGTTAGGGGAGTTTTCTGGGCGGCAGAAT 27 192 0 GGGGATTTTG 0.991406 -109 CCCCAGTATTGGGGGATTTAGGGGGCAGAATCAG 35 160 0 GGGGGTTTAG 0.941066 -141 GGGGGGCCAGGGGGGCTTTTCAAACACGCTCTTA 35 222 1 GGGGGTTTTA 0.840807 -79 AAATGATAGGGGGGGGGTTTACCGAAGTTCCTTG 36 171 1 GGGGGGTTTG 0.963255 -59 CGGAGTTGACGGGGCTTTTTCTTGGTGGTAGTCG 38 134 0 GGGGCTTTTG 0.973295 -167 CCTAGGGGTGGGGGAATTTTTTAGGGTTTTGACG 40 77 0 GGGGATTTTG 0.991406 -224 TAAGTTCAGCGGGGATTTTTGTTGCTATTAACTA 42 93 1 GGGGATTTTG 0.991406 -32 GTATCCCCTTGGGGAATTTGGGTGCAGAGGAGTA 50 17 0 GGGGATTTGG 0.928263 -249 CTTGGCAACTGGGCAGTTTTTCCGGTCAGCAATT 51 243 1 GGGCATTTTG 0.877359 -52 AATGGGGGCTGGGGAAGATTTATGGTTGCCAAGC 52 28 1 GGGGAGATTG 0.828555 -257 GTGCAACCAGGGGGACTTTTCAATTTTAGTCCTT 60 80 0 GGGGATTTTT 0.835854 -37 CCCAAGGCTGGGGGGAATTTATCGGTGAA 67 38 1 GGGGGATTTG 0.944281 -19 CTATTTCGATGGTGAATTTTTCAGTTACCCATCC 70 86 0 GGTGATTTTG 0.828378 -46 ***** **** * Masking position 9 Map Score: 27.5481 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 438 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 4 CACCAAAGCCCCCAATAATGAGGGAAGATGGTATGA 1 56 1 CCTTGAGGGA 0.945914 -91 GGCAACCTTTCCGGATTCTGGGGGTTAACTGTACTT 7 32 0 CCTTGGGGGT 0.97372 -88 TCATCGTTAGCAATTGCCCAGGGGGATACCA 23 86 1 CAGCAGGGGA 0.582277 -21 AGCAATTTTGCCATCAACTGGAGGGAGTGGAGCAAT 26 119 0 CCATGGAGGA 0.749076 -53 GGGTTCGACCAAAAATTGAGGGAAGGAAAGGAAT 30 9 1 CCATGAGGGA 0.861456 -82 GGAAATTTGGCGAGTTGATGGGGGAAAGTACAAAAC 35 43 0 CGTTGGGGGA 0.939005 -258 GTCAAAGTCCCCCAGTATTGGGGGATTTAGGGGGCA 35 167 0 CCTTGGGGGT 0.97372 -134 CCCCTGGCCCCCCAAGTTTGGGGGGAAACTAAGTCA 35 199 0 CCGTGGGGGA 0.994574 -102 CCGTGGGCACCCTAGGGGTGGGGGAATTTTTTAGGG 40 85 0 CCGTGGGGGA 0.994574 -216 GGGATAAAATCCGCTAACTGGGGGAATCACTGGGGA 40 164 1 CCATGGGGGA 0.975882 -137 TGGCTTGCATCCAGATAATGGAGAGAAATGA 46 172 1 CCTTGGAGAA 0.483595 -21 CGGCCAATGACCAGGGGCAGATTTTGTCC 48 76 0 CCGCAGGGGA 0.91752 -19 GACCTTCGAGCGAAATTCTGGGGGCTTGGCAACTGG 51 219 1 CGTTGGGGGT 0.833667 -76 CTATGACTAACCCATTTTTGGGGATATTGAATA 52 262 1 CCTTGGGGAA 0.92697 -23 TAATATCGGCCCACCGCCTAGGGGATAGCGG 61 6 0 CCGTAGGGGT 0.901674 -104 TGGCGATCGCCAGAGGAATGGGGGCAAAATTTTCGC 61 62 0 CAGTGGGGGA 0.958278 -48 TCCATCATGACCTTTTGTCGAGGGGAAAACCACGGC 64 73 0 CCTCGAGGGA 0.873531 -58 CCCTGACCCCCCCAAGGCTGGGGGGAATTTATCGGT 67 28 1 CCGTGGGGGA 0.994574 -29 TTGCCATTTCCCCTGGGGCGAGGGGTAACTCACCTT 69 124 1 CCGCGAGGGT 0.783628 -59 ATTCAAACATCCCGATTCTGGGGAAACTTACT 70 7 0 CCTTGGGGAA 0.92697 -125 GTCTAAGGTTCATGGGGATAGGGGGATGGGTAACTG 70 63 1 CAGTAGGGGA 0.779226 -69 ** * ****** * Masking position 13 Map Score: 26.4149 Number of sites scoring better than the average of aligned sites = 1248 Number in coding regions = 955 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 5 GGTGTGCCTCCGGAGGATAAAAGTTGTAGTT 2 19 0 CCCAGGAAAA 0.933941 -21 TTAACCTTTTAACCTCGGGGGAACGACGGCACAA 7 96 0 TCCGGGGAAC 0.85346 -24 CACAATTTGCCGGCCCGGGAAAAGCAGTACTCTGA 8 116 0 CCCGGAAAGC 0.72623 -126 CATTATCTGCCAACGCCGGGAAAAACGTTAAAATC 13 82 0 CCGGGGAAAA 0.744592 -190 TGGATTTAGGCTCCCAGAGGGAAAACATTATCTGC 13 107 0 CCCAGGGAAA 0.961901 -165 TCATTAGCAACGGCCACGGAGAAGACCTCAACGCC 14 118 0 CCCGGAGAGA 0.936888 -62 TCGTTAGCAATTGCCCAGGGGGATACCA 23 89 1 TCCGGGGATA 0.642366 -18 CAATAGATACTTCCCAAGGGATAGATTTCCCATAG 24 27 1 TCCGGGAAGA 0.866709 -274 GGTGGATTTCCTCCAGAGAAAAAAGTCAACAACA 31 10 1 CCCAGAAAAA 0.805651 -123 AAAACCTTAACCTCCTGGGGATAAAATCCGCTAAC 40 147 1 CCCGGGAAAA 0.978052 -154 GTCTGGGGAATGGCCTGGGGAGAAACTAGCCAAAA 40 202 1 TCCGGGAAAA 0.910878 -99 TATCCTAGATCGCCCCCAGGGTAAACAGCAGAGGC 41 122 1 CCCAGGGAAA 0.961901 -124 ATGCGTCTTTCTACCTCAGGGTAGCAAATACGGGG 50 185 0 CCCAGGGAGC 0.836756 -81 TCTTCCCCAGCCCCCATTGAGCAAATTTTTCTCTA 52 11 0 CCCTGAGAAA 0.605814 -274 CCTAGACTGACTGCCCAGGGAAAAATTCACTTTCA 53 138 1 CCCGGGAAAA 0.978052 -163 CCTGAAACTGCCGCCCTGGAGCAAAGCCAGGAAAA 54 30 1 CCCGGAGAAA 0.958904 -88 ACAGAATCGGCTACCATGGAGCAGAGAAACACAAG 65 22 0 CCCGGAGAGA 0.936888 -41 GAGTTACCCCTCGCCCCAGGGGAAATGGCAATGGG 69 120 0 TCCAGGGAAA 0.842539 -63 CTATCTAGCACCACCCAGGGACAAATGAAAGACCC 74 110 0 CCCGGGAAAA 0.978052 -191 * ** **** *** Masking position 13 Map Score: 19.5162 Number of sites scoring better than the average of aligned sites = 1151 Number in coding regions = 1023 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 6 AGGGGGGTAGACCCCCATCACCAAAGCCCC 1 38 1 ACCCCCATCA 0.7311 -109 ACAGTAAAGTGCCGCCCTTGAGCTTAGCTT 12 46 1 GCCGCCCTTG 0.830701 -255 TTGAAGTAAAACCGCCATTGTCAACGGGGA 12 82 0 ACCGCCATTG 0.835386 -219 GACAGCAAAATTCCCCATCGGTGAAGGACG 12 209 0 TTCCCCATCG 0.713277 -92 TCCGTTGGCGATCGCCAGCACCGATTGAAG 12 237 1 ATCGCCAGCA 0.274649 -64 AGTTTTTTGATCCCCCATTGCCGTGATGTT 19 36 1 TCCCCCATTG 0.864764 -85 TGGTATCCCCCTGGGCAATTGCTA 23 93 0 ATCCCCCTGG 0.721604 -14 TATTTGTTCAACCGCCATTGTTGTCCC 24 284 1 ACCGCCATTG 0.835386 -17 GGTTCCCCATCGATGGTGGTCT 29 268 0 TTCCCCATCG 0.713277 -12 AGTGGGAAATGCCGCCATCAAAACGGCTTA 31 55 1 GCCGCCATCA 0.719043 -78 AATCTTGGCGATCGCCCTTGGCTTTATCTT 34 56 1 ATCGCCCTTG 0.590579 -58 TTTTGTACTTTCCCCCATCAACTCGCCAAA 35 44 1 TCCCCCATCA 0.666408 -257 TAAGTCAAAGTCCCCCAGTATTGGGGGATT 35 176 0 TCCCCCAGTA 0.550838 -125 TGTTTGAAAAGCCCCCCTGGCCCCCCAAGT 35 218 0 GCCCCCCTGG 0.898135 -83 CTTGGTGGTAGTCGCCAGTGCTACCGATTA 38 118 0 GTCGCCAGTG 0.661765 -183 AGCGGATTTTATCCCCAGGAGGTTAAGGTT 40 149 0 ATCCCCAGGA 0.453542 -152 TCCCCAGACTTTCCCCAGTGATTCCCCCAG 40 181 0 TTCCCCAGTG 0.604304 -120 ATCCTAGATCGCCCCCAGGGTAAACAGCAG 41 123 1 GCCCCCAGGG 0.88107 -123 ATCTTCCCCAGCCCCCATTGAGCAAATTTT 52 17 0 GCCCCCATTG 0.93355 -268 ACCTGAAACTGCCGCCCTGGAGCAAAGCCA 54 29 1 GCCGCCCTGG 0.837168 -89 CCCGTCCACGTCCCCCATTACTAAATTCGA 56 120 1 TCCCCCATTA 0.709035 -42 TTGTCGCCGCACCGCCAGTAATGGTATTAA 58 41 0 ACCGCCAGTA 0.493229 -206 CCCATTCTTTGTCCCCATTGTCGCCGCACC 58 58 0 GTCCCCATTG 0.869572 -189 AAATTGAAAAGTCCCCCTGGTTGCACAGAG 60 88 1 GTCCCCCTGG 0.807106 -29 GGGCAAAATTTTCGCCCTGGTTTTTAATAA 61 47 0 TTCGCCCTGG 0.526185 -63 CGAAAATTTTGCCCCCATTCCTCTGGCGAT 61 63 1 GCCCCCATTC 0.478918 -47 TTTTTGAACTGCCCCCCTGACCCCCCCAAG 67 14 1 GCCCCCCTGA 0.770642 -43 TATCCTTAACACCCCCATCGAACATTT 69 8 0 ACCCCCATCG 0.877067 -175 TTAAAGGGCGATCGCCATTATAAAAGGTGA 69 153 0 ATCGCCATTA 0.478563 -30 CCATCCCCCTATCCCCATGAACCTTAGACT 70 62 0 ATCCCCATGA 0.622524 -70 ********** Masking position 5 Map Score: 30.6672 Number of sites scoring better than the average of aligned sites = 2549 Number in coding regions = 2246 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 313 Fraction of orfs with sites within 600 bp upstream = 0.050273 Motif number 7 AAAACATTATCTGCCAACGCCGGGAAAAACGTT 13 88 0 CCCAACCCGG 0.987611 -184 TGCCCTGCAACGGTGATCGCCGGAATTTGATCT 14 71 0 CTGATCCCGG 0.703873 -109 CACGGAGAAGACCTCAACGCCGGCCTGATCATC 14 106 0 ATCAACCCGG 0.914841 -74 GTTTTTTGATCCCCCATTGCCGTGATGTTTGCT 19 37 1 CCCATTCCGT 0.779854 -84 CTTGTCAACACACCCAACCCCGAATTTGGTCAA 20 31 1 CCCAACCCGA 0.932344 -26 AACCTCATCACCGTAGTCAGCATT 22 19 0 ATCATCCCGT 0.756382 -14 CCCCCTAAATCCCCCAATACTGGGGGACTTTGA 35 169 1 CCCAATCTGG 0.568235 -132 CGTTTGGGTGCTTCCAACTCGGTGGGTTATCAT 36 50 0 CCCAACCGGT 0.772529 -180 AGAAAAAGCCCCGTCAACTCCGGAGTAAGAAAG 38 146 1 CTCAACCCGG 0.980227 -155 AGAGGCCACGCAATCAACTCCGTGCCAACCTAC 38 277 1 CTCAACCCGT 0.959033 -24 TCAATCTTCGAGATCATCACCGATTCGATTTTC 43 64 1 ATCATCCCGA 0.531971 -47 AGGGCTAGGAAGACCATCGCCGGTCATAGAATC 44 67 0 ACCATCCCGG 0.91359 -63 GGGTCATTGCTCCCAACTCTGTGCCATCGAAG 45 91 0 CCCAACCTGT 0.801611 -22 GGCAAAAAATCAGCCAATGCCGGTTAGGAAAAT 51 54 1 CCCAATCCGG 0.924568 -241 GAAAAATTCACTTTCAACCCCGGTCAAGAAGTT 53 157 1 CTCAACCCGG 0.980227 -144 AAGACTACTTCGGTCATCACCGTGGTAGTCGTC 74 170 0 CTCATCCCGT 0.934757 -131 * ***** **** Masking position 6 Map Score: 13.4368 Number of sites scoring better than the average of aligned sites = 616 Number in coding regions = 583 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TTTTGTTACTGTTTGTCCACAATTTGCCGG 8 138 0 GTTTGTCCAC 0.423805 -104 GCTCCTAGTTTTCCCACAAGTAATATC 10 8 1 GTTTTCCCAC 0.90479 -110 GAGTTTTCCGTTTTGCCCACATTAACTGAC 11 68 1 TTTTGCCCAC 0.913089 -63 GATTGAAGGTTTTGCCCCACTTTTTCCTGA 12 259 1 TTTGCCCCAC 0.865571 -42 GGCAGATAATGTTTTCCCTCTGGGAGCCTA 13 106 1 GTTTTCCCTC 0.755734 -166 TAGGCTTTACTTTCTCCCACCAAAGGCAGA 14 35 1 TTTCTCCCAC 0.638974 -145 AGTTTTGTACTTTCCCCCATCAACTCGCCA 35 42 1 TTTCCCCCAT 0.371218 -259 CTTTGACTTAGTTTCCCCCCAAACTTGGGG 35 196 1 GTTTCCCCCC 0.838704 -105 GTTGCTTTTCTCCACCATCAACACC 39 6 1 TTTTCTCCAC 0.602144 -32 GGTTTTGCCCTCGTTGGGAGAC 40 289 0 TTTTGCCCTC 0.773777 -12 TTTCTTGATCTTTTCCCCACTGTCCAATTA 41 64 1 TTTTCCCCAC 0.95772 -182 TCGCAAAAATTTTTCCCCTTTCCCCAGATT 41 178 0 TTTTCCCCTT 0.496204 -68 CATCACTAAGGTTTCCCCATAAGCAACCGT 42 46 1 GTTTCCCCAT 0.760187 -79 AGGGTAACTAGTTTCCCCTCTCCT 47 5 0 GTTTCCCCTC 0.885417 -21 AGGGGCAGATTTTGTCCCAAGACTAATTTG 48 63 0 TTTGTCCCAA 0.309552 -32 TTGGCTGATTTTTTGCCCAAAAAACATATT 51 41 0 TTTTGCCCAA 0.646274 -254 GTTAGAGTCTGTTTTCCCAAAACTCCAGTA 59 98 1 GTTTTCCCAA 0.623016 -189 AGGGCGAAAATTTTGCCCCCATTCCTCTGG 61 59 1 TTTTGCCCCC 0.69712 -51 AAGCTCCAGTTTTTTCCCAATT 61 98 1 TTTTTCCCAA 0.611985 -12 TTAGCCGTGGTTTTCCCCTCGACAAAAGGT 64 70 1 TTTTCCCCTC 0.880592 -61 ATACAAGCTCTTTTTCCCACTATCTATTTG 64 108 1 TTTTTCCCAC 0.90069 -23 AGTAAGTTTCCCCAGAATCGGGATG 70 6 1 GTTTCCCCAG 0.650278 -126 GTGGTATATGGTTGCCCCACGTGAAGCAAA 71 69 0 GTTGCCCCAC 0.870911 -154 ********** Masking position 3 Map Score: 19.1462 Number of sites scoring better than the average of aligned sites = 896 Number in coding regions = 756 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 9 GGTGTGCCTCCGGAGGATAAAAGTT 2 25 0 GCCTCCGGAG 0.547885 -15 ACAATTTGCCGGCCCGGGAAAAGCAGTACT 8 120 0 GGCCCGGGAA 0.76758 -122 CAACAACCATGCCAGCGGAGGGCAGATTTT 9 14 0 GCCAGCGGAG 0.699068 -106 TAAAAATGCTTGCCAGGGAGTATGGCTCTA 11 24 0 TGCCAGGGAG 0.690645 -107 CATTAGCAACGGCCACGGAGAAGACCTCAA 14 122 0 GGCCACGGAG 0.872502 -58 GTTAGCAATTGCCCAGGGGGATACCA 23 91 1 GCCCAGGGGG 0.887539 -16 CAGTACTATTGCCCTTGGAGTC 26 3 0 GCCCTTGGAG 0.206549 -169 TACCAGAAGAGGCTTGGGAACGCACCAAAA 32 127 1 GGCTTGGGAA 0.636811 -55 GAATTGAACCGCCAACGGAGATTTTCAGGA 33 14 0 GCCAACGGAG 0.726892 -29 AAAAGATAAAGCCAAGGGCGATCGCCAAGA 34 58 0 GCCAAGGGCG 0.634515 -56 AAACTTGGGGGGCCAGGGGGGCTTTTCAAA 35 216 1 GGCCAGGGGG 0.895176 -85 GGCGATCGCCGCCTGGGGAATCCCAGAAAA 40 22 0 GCCTGGGGAA 0.903603 -279 ACTGGGGAAAGTCTGGGGAATGGCCTGGGG 40 192 1 GTCTGGGGAA 0.381729 -109 CTGGGGAATGGCCTGGGGAGAAACTAGCCA 40 204 1 GCCTGGGGAG 0.946323 -97 TCTGTGGCAGGGCTAGGAAGACCATCGCCG 44 78 0 GGCTAGGAAG 0.401212 -52 AATGTTCACAGACCAGGGAAA 49 86 1 GACCAGGGAA 0.462839 -11 CCAATTTCTATCCTAGGGAACTGGAACTTT 50 75 0 TCCTAGGGAA 0.473879 -191 GCTCAATGGGGGCTGGGGAAGATTTATGGT 52 24 1 GGCTGGGGAA 0.910256 -261 TAGACTGACTGCCCAGGGAAAAATTCACTT 53 140 1 GCCCAGGGAA 0.928977 -161 TATCCAAACCGGCTATGGAGTTGATCAAAC 54 68 1 GGCTATGGAG 0.605156 -50 TTAGGGGTAAGGCTGGGGCAGTTTGATCAA 54 88 0 GGCTGGGGCA 0.629724 -30 ATGCTTGATGGCCACGGAGCCAGGGATTT 57 11 0 GGCCACGGAG 0.872502 -19 TGGTATTAAATGCAAGGGAATTTGCGTTGC 58 20 0 TGCAAGGGAA 0.333142 -227 TTACCATTGTGCCAAGGGATGAATTTTCTC 58 218 1 GCCAAGGGAT 0.369423 -29 GGCAGGGGAAATTAGTGAGT 59 277 0 GGCAGGGGAA 0.838687 -10 TCGGCCCACCGCCTAGGGGATAGCGG 61 7 0 GCCTAGGGGA 0.775047 -103 ACCCCCCCAAGGCTGGGGGGAATTTATCGG 67 33 1 GGCTGGGGGG 0.859544 -24 ********** Masking position 7 Map Score: 17.3124 Number of sites scoring better than the average of aligned sites = 2757 Number in coding regions = 2460 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 10 CTCATTATTGGGGGCTTTGGTGATGGGGGT 1 48 0 GGGGCTTTGG 0.708096 -99 CGTTGACAATGGCGGTTTTACTTCAACTTT 12 86 1 GGCGGTTTTA 0.418163 -215 TGATCAGGCCGGCGTTGAGGTCTTCTCCGT 14 108 1 GGCGTTGAGG 0.428843 -72 GGCGGTTTGATTCCAACTAC 14 170 0 GGCGGTTTGA 0.902283 -10 TTCTGATAGAGCCACTTTGG 15 19 1 GCCACTTTGG 0.844699 -10 GATCGTTGACCCCGCTTTGGCGATCGCCGG 28 33 0 CCCGCTTTGG 0.740795 -81 TTTAAGATAAGCCGTTTTGATGGCGGCATT 31 62 0 GCCGTTTTGA 0.861512 -71 AAAGATCAGGGCCGCTGTGGCGATCGCCTT 36 18 1 GCCGCTGTGG 0.932694 -212 AAGGAAATGAGGCGCTTGGGATGGACTGAA 38 43 0 GGCGCTTGGG 0.786602 -258 CCGATTAATTGCCGGTGTGATTGAGTTATG 38 95 0 GCCGGTGTGA 0.805157 -206 CAACATATCAGCCGTTTAGGGAAGTGGTCT 44 105 0 GCCGTTTAGG 0.787988 -25 ATCAGCCAATGCCGGTTAGGAAAATTTGTA 51 62 1 GCCGGTTAGG 0.891436 -233 CAACTCCATAGCCGGTTTGGATAAACTTTT 54 61 0 GCCGGTTTGG 0.975881 -57 GTAAGGCTGGGGCAGTTTGATCAACTCCAT 54 82 0 GGCAGTTTGA 0.521468 -36 CTTGGCGATCGCCAGTTTGGGAAGTGGTTC 58 117 1 GCCAGTTTGG 0.82684 -130 CCGCAATACTGGAGTTTTGGGAAAACAGAC 59 104 0 GGAGTTTTGG 0.681511 -183 GGAAAAAACTGGAGCTTTGGCGATCGCCAG 61 85 0 GGAGCTTTGG 0.84338 -25 CCCTATGCCCGCAGTTTTGAGACAAATTAA 63 137 0 GCAGTTTTGA 0.519655 -111 CAATGTTGAAGCCGCTTTTGTGAAGGAGCT 66 71 1 GCCGCTTTTG 0.782002 -51 AATTTATTGGGCAGCTTTGAGATGCCTTGT 74 36 1 GCAGCTTTGA 0.73136 -265 ********** Masking position 6 Map Score: 8.97324 Number of sites scoring better than the average of aligned sites = 1200 Number in coding regions = 1142 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 11 GGGAACGAAAAAGCTAAGCTCAAGGGCGGCACT 12 53 0 AAGTAGCCAA 0.789672 -248 ACTCTAGGGAAAGTTGAAGTAAAACCGCCATTG 12 92 0 AAGTAAGAAA 0.907252 -209 AGACTATGAAAAGGTTAAGCAAATTTGCTAACT 12 122 0 AAGTAAGAAA 0.907252 -179 AATCCCCAAGAAGATTAGGATAAAAACATCTAG 16 35 0 AAGTAGGTAA 0.598588 -100 GACCAAGATTAAGTTGAGCAAAAACTTTGGGGA 21 21 0 AAGTAGCAAA 0.819877 -126 TAGTTAACTTAAGATTAAGAAAATAGTTAACTT 24 203 1 AAGTAAGAAA 0.907252 -98 GCCCATACCCAAGCTTAACGGAATATGGACAGA 32 64 1 AAGTAACGAA 0.836414 -118 GATCCTGGAAAAGATAAAGCCAAGGGCGATCGC 34 63 0 AAGTAAGCAA 0.889728 -51 CAGTGGGGAAAAGATCAAGAAAACATCGGACCC 41 53 0 AAGTAAGAAA 0.907252 -193 GGATACGCCTAAGATAAGGGCAAAGTTGGAAAA 50 45 1 AAGTAGGCAA 0.855589 -221 ATTTCGCTCGAAGGTCAACTAAATGGGGCCGAT 51 202 0 AAGTAACAAA 0.861088 -93 ATCCATTTTAAAGGTAAAGAGAAGATTGCCAAA 59 64 1 AAGTAAGGAA 0.889728 -223 TGAAATTGGGAAGATAAACTGAAACTTCGCAGA 60 39 1 AAGTAACGAA 0.836414 -78 *** * *** *** Masking position 7 Map Score: 6.68039 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 58 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 12 CTTGCTGAGTCCTGGTTTTTCCGGTCTATC 1 104 1 CCTGGTTTTT 0.926628 -43 AGTCTAGCCTGCTGGATTTCCCGACATCAC 10 79 0 GCTGGATTTC 0.727528 -39 CGGAAAACTCCCTGGTTATTAAGCTAAAAA 11 48 0 CCTGGTTATT 0.593958 -83 ATTTACGTCTGCTGGATTTAGGCTCCCAGA 13 124 0 GCTGGATTTA 0.76058 -148 AGCCACTATGCCTGCATTTTTGTAATATTT 29 62 1 CCTGCATTTT 0.792407 -218 TTGCAGGACGGCTGCTTTTTTCTGTCCATA 32 87 0 GCTGCTTTTT 0.935005 -95 TTTTGTGGTTGCTGCATTTTTCTTTACTCG 50 143 0 GCTGCATTTT 0.881813 -123 ACCGGCATTGGCTGATTTTTTGCCCAAAAA 51 48 0 GCTGATTTTT 0.733805 -247 ATATTCTAGGGCTGGTTTTTACTTCAGGCA 52 198 0 GCTGGTTTTT 0.961068 -87 GGGCTGCTTTTACGACTTCTCG 60 3 1 GCTGCTTTTA 0.781152 -114 AAATTTTCGCCCTGGTTTTTAATAATCACC 61 42 0 CCTGGTTTTT 0.926628 -68 TTTAAATAATGCTGGTTTTTCAAGTATAAA 73 15 0 GCTGGTTTTT 0.961068 -286 ********** Masking position 7 Map Score: 6.80107 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 157 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 TCCCGCCGAGGATTTTTCGCAGAATTTGCACAGTAAA 12 17 1 GATTGAAATT 0.873012 -284 TTTTCATAGAGAAATTAAGAAAAACTTATGGTTAGAC 12 151 0 GATTGAAATT 0.873013 -150 TCTCAGACAGGGCTTTCAGTACAGATTTTGAGATAGG 13 218 1 GGTTGAAGTT 0.854359 -54 ACTTTAAGAAGAGATTACGGAAAATTTAAGGAAAATA 27 39 0 GATTGAAATT 0.873013 -262 GCGGTAAAAAGGACTTGAATCAAGTTTTTGGGAGTAG 27 83 0 GGTTACAGTT 0.72495 -218 GGCAGAATCAGACTTTATAAACAGGTTCTGAGTACCC 35 134 0 GATTAAAGTT 0.841499 -167 AAATTGATGGGAGGTTAAGTACAGGTTAACGAAAGCT 45 33 1 GATTGAAGTT 0.906586 -80 GCAATAATCAGAGTTTGCGTATAAATTACCGTATTCC 48 25 0 GATTGAAATT 0.873012 -70 CCATTTAGTTGACCTTCGAGCGAAATTCTGGGGGCTT 51 209 1 GATTACAATT 0.755435 -86 GTCCTCTTTTGACATTTGGTATAGATTTTATCTATCT 52 154 1 GATTGAAGTT 0.906586 -131 TTGCAAAGGAGAATTTTCACAAAACTTCTTGACCGGG 53 175 0 GATTAAAATT 0.789921 -126 AAAAGGAAGGGGAATTGCATCAAGATTGCTAATCGTC 56 13 1 GGTTACAGTT 0.724951 -149 TTATTATATGGAGCTTTTAACTAAGTTTTTAATGTCG 63 23 0 GATTACAATT 0.755434 -225 TTTTGTGAAGGAGCTTTAAGCAAAATTCAGTTTTACC 66 86 1 GATTACAATT 0.755392 -36 GTTCGATGGGGGTGTTAAGGATAGGTTTTAGCAGAAA 69 15 1 GGTTGAAGTT 0.854359 -168 ** ** * * ** ** Masking position 13 Map Score: 7.78386 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 113 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 14 GGCGATCGCTACTGATAGGGGGGTAGACCCCCATC 1 22 1 ATGAGGGGGA 0.945778 -125 ACCTCTGCAAAATTAGGAGTGGGGATATTACTTGT 10 26 0 ATTAGTGGGA 0.474281 -92 TCTATGAAAAACTGGAGCGGGGCCAAGTGATCGTC 12 178 1 ATGGGGGGCA 0.957682 -123 TGATTTTAGAAATAGTATGGGGTTAAACTCTACTC 24 130 1 ATAGGGGGTA 0.604403 -171 ATAACCCAGGATTAAGGTGGGGGCATATTGTGGTG 26 75 0 ATAAGGGGGA 0.826206 -97 TTCAGCTTGGAAGGAAACGGGGGCAGCGGTTGTAA 29 132 0 AGGAGGGGGA 0.763461 -148 AAGCTGAATAATGGGACCGTGGCCAAGGGTTAGCG 29 159 1 AGGGGTGGCA 0.68462 -121 AACAACAACAATTGAGAAGTGGGAAATGCCGCCAT 31 38 1 ATGAGTGGGA 0.900417 -95 CTAAAACTCAAATGATAGGGGGGGGGTTTACCGAA 36 162 1 ATGAGGGGGG 0.866888 -68 CTTAACCCTGACTGGGCCGTGGGCACCCTAGGGGT 40 102 0 ATGGGTGGGA 0.935881 -199 AAGTCTGGGGAATGGCCTGGGGAGAAACTAGCCAA 40 200 1 ATGGGGGGAA 0.689306 -101 GTCCGGGTTAATTGGACAGTGGGGAAAAGATCAAG 41 67 0 ATGGGTGGGA 0.935881 -179 CAAAGTCTTTAATGGCTTGGGCCCAACGTTGATGA 41 211 0 ATGGGGGCCA 0.710543 -35 CGTTTAGGGAAGTGGTCTGTGGCAGGGCTAGGAAG 44 88 0 ATGGGTGGCG 0.814128 -42 CGGCCAATGACCAGGGGCAGATTTTGTCCC 48 75 0 ATGAGGGGCG 0.839597 -20 TCGAAGGTCAACTAAATGGGGCCGATTCGCTCTGT 51 193 0 ATAAGGGCCA 0.29301 -102 GTTCTGTCGGAATGATCGGTGGCGGAGACAACCAT 58 143 1 ATGAGTGGCG 0.730701 -104 GGCGATCGCCAGAGGAATGGGGGCAAAATTTTCGC 61 62 0 AAGGGGGGGA 0.656381 -48 ATCTAGCTCAATTAATCTGGGGTCAGTAACCTGAA 62 120 0 ATAAGGGGTA 0.486244 -54 ATTTGTAAAAATTAAATGGTGGCTATCTAGGGGCG 64 24 1 ATAAGTGGCA 0.664503 -107 GGGCAAATAGATAGTGGGAAAAAGAGCTTG 64 111 0 ATAGGTGGGA 0.79912 -20 ATTTTTAATTAATTGTTAGTGGTTAAACTTTGCCA 66 21 1 ATTGGTGGTA 0.224768 -101 * *** ***** * Masking position 1 Map Score: 14.1243 Number of sites scoring better than the average of aligned sites = 1039 Number in coding regions = 929 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 15 GCTAATGCTTTGCAGAAGAGGATTCATTCC 8 28 1 TGCAGAAGAG 0.855002 -214 CTCCTAATTTTGCAGAGGTGGGGATTTTTT 10 42 1 TGCAGAGGTG 0.983387 -76 ATCGATGCCCTGCAACGGTGATCGCCGGAA 14 79 0 TGCAACGGTG 0.83246 -101 GTTCACACTGCTGAGGTGCAGTCCTAAC 35 283 0 TGCTGAGGTG 0.924751 -18 GGAATTTGGGTGCAGAGGAGTAAACTTT 50 9 0 TGCAGAGGAG 0.978476 -257 GGAATTCCTTTGCAAAGGAGAATTTTCACA 53 191 0 TGCAAAGGAG 0.925381 -110 TAGTCTGAAATGCAGAGGTGGTATATGGTT 71 86 0 TGCAGAGGTG 0.983387 -137 ********** Masking position 1 Map Score: 4.20005 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 22 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432