AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_synecho_reg_100.orf -o00860_synecho_100.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 sll1678 74 spore maturation protein A. #2 sll1677 65 spore maturation protein B. #3 sll1676 97 malQ; 4-alpha-glucanotransferase. [EC:2.4.1.25] #4 sll1675 49 hypothetical protein. #5 slr1787 300 hypothetical protein. #6 sll1185 222 hemF; coproporphyrinogen III oxidase, aerobic #7 sll1184 134 ho; heme oxygenase. [EC:1.14.99.3] #8 slr1887 129 hemC; porphobilinogen deaminase (PBG) (hydroxymethylbilane synthase) #9 slr1808 161 hemA; glutamyl-tRNA reductase (GLUTR). [EC:1.2.1.-] [SP:HEM1_SYNY3] #10 slr0260 78 cobA; cob(I)alamin adenosyltransferase. [EC:2.5.1.17] #11 ssl0467 95 hypothetical protein. #12 sll0252 221 hypothetical protein. #13 sll1994 300 hemB; delta-aminolevulinic acid dehydratase (porphobilinogen #14 sll1237 105 hemK protein homolog. [EC:1.3.3.4] [SP:HEMK_SYNY3] #15 sll1875 64 ho; heme oxygenase. [EC:1.14.99.3] #16 sll1874 300 AT103; AT103. #17 slr1643 91 petH; ferredoxin--NADP reductase (FNR). [EC:1.18.1.2] #18 sll1524 300 hypothetical protein. #19 sll0163 300 beta transducin-like protein. [SP:Y163_SYNY3] #20 slr0772 131 chlB; protochlorophyllide reductase ChlB subunit. [EC:1.3.1.33] #21 sll0017 300 hemL, gsa; glutamate-1-semialdehyde 2,1-aminomutase (GSA) #22 sll0461 300 proA; gamma-glutamyl phosphate reductase. [EC:1.2.1.41] #23 sll0378 195 cysG; uroporphyrin-III C-methyltransferase. [EC:2.1.1.107] #24 sll0373 125 proA; probable gamma-glutamyl phosphate reductase (GPR) (glutamate- #25 sll0179 169 gltX; glutamyl-tRNA synthetase (glutamate--tRNA ligase) (gluRS). #26 slr0839 71 hemH; probable ferrochelatase (protoheme ferro-lyase) (hemE #27 sll0827 266 hypothetical protein. #28 slr0506 56 pcr; protochlorophyllide oxido-reductase. [EC:1.3.1.33] #29 sll0481 71 hypothetical protein. [SP:Y481_SYNY3] #30 sll0480 182 hypothetical protein. #31 slr0536 146 hemE; uroporphyrinogen decarboxylase. [EC:4.1.1.37] [SP:DCUP_SYNY3] #32 slr0750 119 chlN; protochlorophyllide reductase 46 kD chain (orf 469). Motif number 1 TTCTATATCCTGGGGGAAGTAAAAAGCACTAAC 1 47 0 TGGGGGAATA 0.837892 -28 GCCCATAGGTTTGGGGCATTTGGGAGTGCCTTG 2 17 1 TTGGGGCATG 0.899585 -49 TAAAACAAGTCTGGGGGCTAATATTTATCTCTC 5 53 1 CTGGGGGCAA 0.805952 -248 CCAATCAATCTTGGGGAATTTTGGGTCTGATCC 6 145 0 TTGGGGAATG 0.8855 -78 TCTGGCCTTGATGGGGGAAACAGCTTCACTCAT 8 31 0 ATGGGGGAAG 0.953084 -99 AAACGACTCCATGGGGAACACAGAGCCAGTTTT 9 98 1 ATGGGGAAAG 0.848983 -64 AGTTTTGCTGGGGGTGAGAAAACTGGAATA 11 76 0 CTGGGGGTAA 0.763373 -20 CGCCGGCCTTTTGGGGGAAACCGGCCTACAATA 12 130 1 TTGGGGGAAG 0.940248 -92 TCGGTCAGCCCTGGGGAAAAGCCTGGCAACCCA 13 115 0 CTGGGGAAAC 0.595249 -186 TAACCAGTTCTTGGGGGCAAAAACTAGTCAATT 13 183 1 TTGGGGGCAA 0.834899 -118 GGTTAAATGGAGGGGGAAATATAAATCATTGTA 18 207 1 AGGGGGAATA 0.869668 -94 GGACGGGGATAGGGGGGACTAAATCACCACTAA 19 103 0 AGGGGGGATA 0.960179 -198 CCAAGGTTTGATGGGGAAATTTGAGGGTTGAGT 20 80 1 ATGGGGAATG 0.908958 -52 AGGGGGGCGTTTAAAACGGGCTC 21 1 1 AGGGGGGCTA 0.900027 -300 CGAAAATTATAGGGGGCAAAGCCCACCCGCAAA 22 278 0 AGGGGGCAAC 0.675249 -23 TCCCCCATTATTGGGGAATTTAGGGGGCGGAAT 23 71 0 TTGGGGAATG 0.8855 -125 TTCCCCAATAATGGGGGACTTTCACTCAGTATT 23 86 1 ATGGGGGATC 0.936848 -110 CGGCTTGAACCTGGGGGAATGGCT 24 2 0 CTGGGGGATC 0.904196 -124 AGGGCAACTTTGGGGGGCAAACAGCAAAGCGCA 24 59 0 TGGGGGGCAA 0.797023 -67 ACCCCCAATGATGGGGGAATTAGATTATTGCAA 26 28 0 ATGGGGGATG 0.97303 -44 TCCCCCATCATTGGGGGTTTGGGGACTTTCAAA 26 43 1 TTGGGGGTTG 0.890164 -29 TGGTAAAATCATGGGGGTATAGATATCTTGTTT 27 36 0 ATGGGGGTTA 0.900054 -231 CCCCCCAGCCTTGGGGGGGTCAGGGGGGCAGTT 28 20 0 TTGGGGGGTG 0.74769 -37 CCCCCAAGGCTGGGGGGAATTTATCGGTGAA 28 36 1 TGGGGGGATA 0.949181 -21 AAATGTTCGATGGGGGTGTTAAGGATAGGTTT 30 10 1 ATGGGGGTTA 0.900054 -173 CTTGGGGACCAGGGGGCTTTTTAAACACACTCT 31 35 0 AGGGGGCTTA 0.691514 -112 GAGGAGATTTAGGGGGCAGAATAAAACTTTTCC 31 115 1 AGGGGGCAAA 0.813168 -32 TGGCGATCGCCTGGGGCAATGGATTTCTTTAGA 32 38 0 CTGGGGCATA 0.863632 -82 ******** * * Masking position 6 Map Score: 37.6848 Number of sites scoring better than the average of aligned sites = 2037 Number in coding regions = 1658 Number in noncoding regions = 379 Number of orfs with sites within 600 bp upstream = 289 Fraction of orfs with sites within 600 bp upstream = 0.0464182 Motif number 2 TATTTTTCTATATCCTGGGGGAAGTAAAA 1 56 0 ATATCCTGGG 0.625007 -19 GCAAGCCTAGGAAGGAAAATC 3 87 0 CAAGCCTAGG 0.897113 -11 CTTAGTAAAACAAGTCTGGGGGCTAATATT 5 48 1 CAAGTCTGGG 0.961287 -253 GAAAAACTGGCAACTCTAGGTTGATTCGAT 6 60 0 CAACTCTAGG 0.871075 -163 GTCCGCCAATCAATCTTGGGGAATTTTGGG 6 153 0 CAATCTTGGG 0.943949 -70 AAATACCTGTATATCTTGGGTTGAATGAAA 7 110 0 ATATCTTGGG 0.552386 -25 CTCGACAATTCTAGCTTAGGAATCTGGCGG 9 41 1 CTAGCTTAGG 0.664477 -121 AACACAGAGCCAGTTTTGGGACATTTATTG 9 114 1 CAGTTTTGGG 0.939294 -48 TAACTGAGAACTGGTCTGGGTTGGGTTGCC 13 94 1 CTGGTCTGGG 0.911407 -207 AGAATTCGGTCAGCCCTGGGGAAAAGCCTG 13 123 0 CAGCCCTGGG 0.982504 -178 AGTAAAAGTTCAGCCTTAGGGATTAGTTAG 13 234 0 CAGCCTTAGG 0.908526 -67 AAATTATTACCTGGCCTGGGTTTTGATTAT 16 111 0 CTGGCCTGGG 0.937976 -190 GGCTCCTTTTCAGTTTTGGGCCAACAA 17 8 0 CAGTTTTGGG 0.939294 -84 ATAGCGAGGAAAGCCCTAGGCGTTAGCTTC 19 173 0 AAGCCCTAGG 0.76215 -128 GGCACTGTGACAAGACTGGGCAAGCCTAGT 19 208 0 CAAGACTGGG 0.742007 -93 TCGGACAGGGCAACTTTGGGGGGCAAACAG 24 68 0 CAACTTTGGG 0.954426 -58 AATGGAGGCAAAGCTTTGGGTTAGGATGGA 25 107 1 AAGCTTTGGG 0.871075 -63 TGTTCCGTCCCAATTCTAGGCAAGAAATTC 27 73 0 CAATTCTAGG 0.787058 -194 TCCCTGGCAGAAGTTTTGGGAGATTAGCTC 27 180 0 AAGTTTTGGG 0.787058 -87 AAATTCCCCCCAGCCTTGGGGGGGTCAGGG 28 28 0 CAGCCTTGGG 0.976514 -29 ACCTAGGGAAAAACTTTGGGAAA 31 4 0 AAACTTTGGG 0.833406 -143 CCCTGGTCCCCAAGTTTGGGGGGACGCATT 31 54 1 CAAGTTTGGG 0.948414 -93 ********** Masking position 7 Map Score: 26.9702 Number of sites scoring better than the average of aligned sites = 1713 Number in coding regions = 1507 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 3 TAAATATTAGCCCCCAGACTTGTTTTACTAA 5 49 0 CCCCCGACTT 0.816459 -252 TTTTTCCTAAACCCTTGCCTCAATAGTTTTT 10 11 1 ACCCTGCCTC 0.880225 -68 GAAGAATAGCGCCCTAACCCCTAGGGTAACC 10 47 0 GCCCTACCCC 0.801132 -32 GCAGTAATGCCGCCTTGCCTCCCCAATGGCC 12 85 0 CGCCTGCCTC 0.907037 -137 TTGGTGATCCCCGCCGGCCTTTTGGGGGAAA 12 119 1 CCGCCGCCTT 0.84306 -103 TTTAAGAACCCCCCTGGCCTCCAAATTTGGT 16 34 0 CCCCTGCCTC 0.993685 -267 TCCAGCATAGCCGCCCGACCCTAGAAGTCCA 18 154 1 CCGCCGACCC 0.875486 -147 GATTTAGTCCCCCCTATCCCCGTCCCTGGCA 19 111 1 CCCCTTCCCC 0.934881 -190 AGAATTTTGGCCCACAGACCC 20 121 1 CCCACGACCC 0.798033 -11 CGATTGGCTACCTCTAACCTCCAAAACCCCT 22 184 1 CCTCTACCTC 0.770826 -117 ACCTCCAAAACCCCTAGCCTTTCCTTTTTGT 22 200 1 CCCCTGCCTT 0.971191 -101 TTTAAAAGCCCCTCTGGCCCCTCAAATTAGG 23 122 0 CCTCTGCCCC 0.95943 -74 TTACCATTACCCGATCGCCTCCGGTGGTGGG 25 61 0 CCGATGCCTC 0.795901 -109 TTTTGAAAGTCCCCAAACCCCCAATGATGGG 26 46 0 CCCCAACCCC 0.851356 -26 TTGAACTGCCCCCCTGACCCCCCCAAGGCTG 28 17 1 CCCCTACCCC 0.983106 -40 CGATAAATTCCCCCCAGCCTTGGGGGGGTCA 28 31 0 CCCCCGCCTT 0.962377 -26 AGGTGAGTTACCCCTCGCCCCAGGGGAAATG 30 128 0 CCCCTGCCCC 0.996074 -55 TTTAAAAAGCCCCCTGGTCCCCAAGTTTGGG 31 43 1 CCCCTGTCCC 0.93061 -104 TGAATGCGTCCCCCCAAACTTGGGGACCAGG 31 55 0 CCCCCAACTT 0.505012 -92 TCTAAAGAAATCCATTGCCCCAGGCGATCGC 32 38 1 TCCATGCCCC 0.583092 -82 ***** ***** Masking position 9 Map Score: 29.0275 Number of sites scoring better than the average of aligned sites = 1915 Number in coding regions = 1630 Number in noncoding regions = 285 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 4 CGGGGCTTTTGCCAGGGGCACCAAAGGGAA 9 68 1 GCCAGGGGCA 0.971018 -94 ATATGGCATGGCCATTGGGGAGGCAAGGCG 12 76 1 GCCATTGGGG 0.883792 -146 CCCCCAAAAGGCCGGCGGGGATCACCAAAG 12 117 0 GCCGGCGGGG 0.94418 -105 AAATTTGGAGGCCAGGGGGGTTCTTAAAAT 16 37 1 GCCAGGGGGG 0.998406 -264 CTAATCCGTTGCCAGGGAGTTTAACA 18 285 1 GCCAGGGAGT 0.931313 -16 CGTTGACACTGCCAGGGACGGGGATAGGGG 19 121 0 GCCAGGGACG 0.981775 -180 GGGACAGTCAGCCAGGGTGGATAATCTGGC 22 88 0 GCCAGGGTGG 0.98398 -213 AATTTGAGGGGCCAGAGGGGCTTTTAAAAC 23 125 1 GCCAGAGGGG 0.982057 -71 CAAAACTTCTGCCAGGGAGGCTTTCCATGG 27 192 1 GCCAGGGAGG 0.993598 -75 CCTTGGGGGGGTCAGGGGGGCAGTTCAAAA 28 15 0 GTCAGGGGGG 0.978239 -42 ATTCCCCCCAGCCTTGGGGGGGTCAGGGGG 28 26 0 GCCTTGGGGG 0.95575 -31 AATGGCGATCGCCTGGGGCAATGGATTTCT 32 43 0 GCCTGGGGCA 0.892624 -77 ********** Masking position 3 Map Score: 20.6102 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 518 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 TACTAAGTATTATTTAAATATCTACCAAAGGGATGAT 5 18 0 TTTTAATCCA 0.82639 -283 TCATTCATCTTTTTTTAACAATCTCCACC 6 204 1 TTTTAACCCA 0.950718 -19 ACCATTAAGTTTTTTTAACGTCCTCCCTTTGGCC 7 8 0 TTTTAACCCC 0.987371 -127 CCTCAATAGTTTTTTCAGTGGTTACCCTAGGGGTTAG 10 28 1 TTTTAGTCCC 0.723564 -51 AGAGATTTTCTCATTAAAACCACACCACATCTCTGCC 12 29 0 TATTAACCCA 0.806607 -193 ACCAGAAAAATTTTTCAAACCACACCCCGCTCCAGCC 12 192 0 TTTTAACCCC 0.987371 -30 TTTATTCAACTTTTAACTTACTCCAATTGTTTGCT 15 9 1 ATTTAACCCA 0.862011 -56 CCTCAGAGCCTATTTTAAGAACCCCCCTGGCCTCCAA 16 41 0 TTTTAACCCC 0.987371 -260 AAATTTACAATGATTTATATTTCCCCCTCCATTTAAC 18 208 0 TATTATCCCC 0.79633 -93 TCTGAGAGCCCGTTTTAAACGCCCCCCT 21 2 0 CTTTAACCCC 0.919389 -299 CTATGGGAATTTATTGAACCTGTGCCCACATCAAAAA 21 179 0 TATTAATCCC 0.806607 -122 GTGTTTAAAAAGTTTTATTCCGCCCCCTAAATTCCCC 23 55 1 ATTTATCCCC 0.854146 -141 TTTTAGAGCCTGTTTTAAAAGCCCCTCTGGCCCCTCA 23 129 0 TTTTAACCTC 0.872405 -67 GCCGTAAATATTTTTAAATACTTTCCCCTGCGCTTTG 24 31 1 TTTTAATCCC 0.950718 -95 TCGTTTTTGAACTGCCCCCCTGACCCCCCC 28 4 1 TTTTAACCCC 0.987371 -53 ACCAGGGGGCTTTTTAAACACACTCTAACCTAGGGAA 31 24 0 TTTTAACCTA 0.627843 -123 ATACTGAGAAACTTTGAATGCGTCCCCCCAAACTTGG 31 63 0 ATTTAATCCC 0.862011 -84 TTGTTGGAAAAGTTTTATTCTGCCCCCTAAATCTCCT 31 116 0 ATTTATCCCC 0.854146 -31 * *** ** * *** Masking position 5 Map Score: 23.1051 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 203 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 AAGTCATTTCTTGGCCCGTTGGATATGTTAAA 3 45 1 TTCCCGTTGG 0.979992 -53 TTCTGCCATCATCCCTTTGGTAGATATTTA 5 9 1 TCCCCTTTGG 0.987604 -292 TTTTTTAACGTCCTCCCTTTGGCC 7 3 0 TCCCCTTTGG 0.987607 -132 ATGGAGTCGTTTTTCCCTTTGGTGCCCCTGGC 9 78 0 TTCCCTTTGG 0.980381 -84 TGCCGCCTTGCCTCCCCAATGGCCATGCCATA 12 77 0 CCCCCAATGG 0.79811 -145 GTGATCCCCGCCGGCCTTTTGGGGGAAACCGG 12 122 1 CCCCTTTTGG 0.79727 -100 ACACCCCGCTCCAGCCCATTGGAAGCAAAACA 12 176 0 CCCCCATTGG 0.968851 -46 GGTAATAATTTTTCCCCTTTGGAAACTATGGG 16 130 1 TTCCCTTTGG 0.980381 -171 CTTTCACCCGTTGGATAACAGGCT 20 3 1 TTCCCGTTGG 0.979992 -129 ACCCCCATGATTTTACCATTGGGAATTTCTTG 27 51 1 TTACCATTGG 0.710514 -216 CAATCAATACTGCTCCCGTTGGTTTAATCATG 30 75 0 TGCCCGTTGG 0.947117 -108 ** ******** Masking position 10 Map Score: 13.5776 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 337 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 7 AAATCACCAGTTTTTCCTGGATAAGTTGTC 6 24 0 TTTTTCCTGG 0.926226 -199 CTGGCGGGGCTTTTGCCAGGGGCACCAAAG 9 64 1 TTTTGCCAGG 0.904936 -98 TTGCCAGGCTTTTCCCCAGGGCTGACCGAA 13 119 1 TTTCCCCAGG 0.956993 -182 ACATCAAAAATTTTCCCTGGGTTTTCACCC 16 217 1 TTTTCCCTGG 0.991184 -84 GGACTTTTGCCTGGGCATTAAGTA 17 78 0 TTTTGCCTGG 0.971627 -14 TCGAATAGGCTTTTCCCTGCCCATAATTGT 19 266 1 TTTTCCCTGC 0.980346 -35 TTTTAAATACTTTCCCCTGCGCTTTGCTGT 24 42 1 TTTCCCCTGC 0.972615 -84 GAAACCTTATTTTTCCCTGCAATGGTGAGC 27 145 1 TTTTCCCTGC 0.980346 -122 CCCATTGCCATTTCCCCTGGGGCGAGGGGT 30 120 1 TTTCCCCTGG 0.987662 -63 TTCCCAAAGTTTTTCCCTAGGTTAGAGTGT 31 12 1 TTTTCCCTAG 0.9076 -135 ********** Masking position 3 Map Score: 16.728 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 354 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 8 CAACGAAACTCTTTTGCAATTTTTCTTAATG 22 53 1 CTTTGCAATT 0.835612 -248 TGTCCCTTGGCGATCGCCATTTTGACTAAAT 22 112 1 CATCGCCATT 0.976429 -189 TACCTCAAGACATTTACCATTACCCGATCGC 25 74 0 CTTTACCATT 0.909567 -96 TACCCCCATGATTTTACCATTGGGAATTTCT 27 50 1 ATTTACCATT 0.634865 -217 ATTGTTTTTGCCTTTGCCATTAGAGGCTATT 27 111 1 CTTTGCCATT 0.983103 -156 TCATTCAAGCATTTTGCCATTTCCAACT 27 249 1 ATTTGCCATT 0.909567 -18 ACGCCTTTATCAATTGCCATTCCAGTTTGAA 29 39 1 CATTGCCATT 0.983103 -33 GAGCATAAACCCATTGCCATTTCCCCTGGGG 30 111 1 CATTGCCATT 0.983103 -72 GATTAAAGGGCGATCGCCATTATAAAAGGTG 30 154 0 CATCGCCATT 0.976429 -29 TTGCCCCAGGCGATCGCCATTCAACCTGCTG 32 52 1 CATCGCCATT 0.976429 -68 * ********* Masking position 4 Map Score: 12.5203 Number of sites scoring better than the average of aligned sites = 462 Number in coding regions = 407 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 CAACCATTAAAACAGGGACA 4 1 1 CAACCATTAA 0.354639 -49 AGAAAGGGCTCAACGATCAACACTGTCCCT 4 24 0 CAACGATCAA 0.420259 -26 GAAGCTGTTTCCCCCATCAAGGCCAGATTA 8 37 1 CCCCCATCAA 0.978742 -93 AGTTTTCTCACCCCCAGCAAAACT 11 82 1 CCCCCAGCAA 0.972172 -14 GCCACCAGAAAAATTTTTCAA 12 211 0 CCACCAGAAA 0.762235 -11 GCCATGTATGCCACCATCAACCGTAAACCC 14 75 1 CCACCATCAA 0.979721 -31 CAACCGTAAACCCCCGTAAACACA 14 92 1 CCCCCGTAAA 0.501331 -14 AGGATGAAAGGCAACATCAAAAATTTTCCC 16 204 1 GCAACATCAA 0.434094 -97 AAGGAGCCCGCCAACAGCAAACTCCCCTTC 17 30 1 CCAACAGCAA 0.893707 -62 GTCACAGTGCCCACCGTCAATTAAGCAAAA 19 227 1 CCACCGTCAA 0.923451 -74 TGGGGATTGGCCACCATCAATTTTCGTGAA 20 50 0 CCACCATCAA 0.979721 -82 CCCTCAAATTTCCCCATCAAACCTTGGTGG 20 77 0 TCCCCATCAA 0.682586 -55 GTTGCTTACTCAACCCTCAAATTTCCCCAT 20 90 0 CAACCCTCAA 0.801201 -42 TGAACCTGTGCCCACATCAAAAAAACAGAC 21 172 0 CCCACATCAA 0.913492 -129 TTTTTATTTCCAAACCGCAACGTTACACAA 22 26 1 CAAACCGCAA 0.412241 -275 GGGGCAAAGCCCACCCGCAAAGATGGATTT 22 269 0 CCACCCGCAA 0.930233 -32 CTTTGGGGGGCAAACAGCAAAGCGCAGGGG 24 55 0 CAAACAGCAA 0.658514 -71 TAATCTAATTCCCCCATCATTGGGGGTTTG 26 34 1 CCCCCATCAT 0.767118 -38 ATCCTTAACACCCCCATCGAACATTT 30 7 0 CCCCCATCGA 0.829994 -176 ********** Masking position 10 Map Score: 20.076 Number of sites scoring better than the average of aligned sites = 1707 Number in coding regions = 1573 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 10 TTTTTTTAACAATCTCCACC 6 213 1 AATCTCCACC 0.434318 -10 GCCCCTGGCAAAAGCCCCGCCAGATTCCTA 9 57 0 AAAGCCCCGC 0.842215 -105 TTTCTCATTAAAACCACACCACATCTCTGC 12 30 0 AAACCACACC 0.679746 -192 AAAATTTTTCAAACCACACCCCGCTCCAGC 12 193 0 AAACCACACC 0.679746 -29 CGCAGACCGTAAAGCAGACCAAGGGTGACC 13 32 0 AAAGCAGACC 0.440528 -269 AGAATTAATTAATCCCCATCCGCAGTAAAA 14 27 1 AATCCCCATC 0.44568 -79 GCCTATTTTAAGAACCCCCCTGGCCTCCAA 16 41 0 AGAACCCCCC 0.754156 -260 CTTTTCCAGCATAGCCGCCCGACCCTAGAA 18 150 1 ATAGCCGCCC 0.807192 -151 AAATGCGGAAAAAGCCGCCCGAATTTGTTT 19 18 1 AAAGCCGCCC 0.95632 -283 GTCTTGTCACAGTGCCCACCGTCAATTAAG 19 222 1 AGTGCCCACC 0.853524 -79 GATGGTGGCCAATCCCCACCAAGGTTTGAT 20 62 1 AATCCCCACC 0.923274 -70 GCCCGTTTTAAACGCCCCCCT 21 2 0 AACGCCCCCC 0.923393 -299 TATAGGGGGCAAAGCCCACCCGCAAAGATG 22 274 0 AAAGCCCACC 0.972755 -27 ATACTGAGTGAAAGTCCCCCATTATTGGGG 23 88 0 AAAGTCCCCC 0.858445 -108 GCCTGTTTTAAAAGCCCCTCTGGCCCCTCA 23 129 0 AAAGCCCCTC 0.863956 -67 CGCTTTGCTGTTTGCCCCCCAAAGTTGCCC 24 61 1 TTTGCCCCCC 0.605101 -65 TCTCCCATCGTAACCCCACCACCGGAGGCG 25 47 1 TAACCCCACC 0.774955 -123 GTTAGGATGGATAACCGCCCGGAAAATTGT 25 126 1 ATAACCGCCC 0.310049 -44 TTAGCCATGGAAAGCCTCCCTGGCAGAAGT 27 196 0 AAAGCCTCCC 0.880923 -71 TCGTTTTTGAACTGCCCCCCTGACCCCCCC 28 11 1 ACTGCCCCCC 0.852651 -46 ACTGCCCCCCTGACCCCCCCAAGGCTGGGG 28 21 1 TGACCCCCCC 0.73378 -36 TTCACCGATAAATTCCCCCCAGCCTTGGGG 28 37 0 AATTCCCCCC 0.758477 -20 AATCCCTCCCAAAGGTAGCT 29 1 1 AATCCCTCCC 0.713739 -71 GTGTGTTTAAAAAGCCCCCTGGTCCCCAAG 31 38 1 AAAGCCCCCT 0.766944 -109 ********** Masking position 10 Map Score: 20.8458 Number of sites scoring better than the average of aligned sites = 2050 Number in coding regions = 1738 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 11 TCCTGGGGGAAGTAAAAAGCACTAACAATTAG 1 41 0 AGTAAAAAGC 0.201332 -34 TCAGACTTAGGCCAAAAAGTGTGAAGATAAAT 5 189 0 GCCAAAAAGT 0.544862 -112 GCTAAAAATACCTGTATATCTT 7 123 0 GCTAAAAATC 0.382864 -12 TGGTGCCCCTGGCAAAAGCCCCGCCAGATTCC 9 59 0 GGCAAAAGCC 0.681293 -103 GGGCACCAAAGGGAAAAACGACTCCATGGGGA 9 83 1 GGGAAAAACC 0.903382 -79 GGGTGACCCCGGTAAAAACAGCAATATAA 13 8 0 GGTAAAAACC 0.854295 -293 AGTTCTTGGGGGCAAAAACTAGTCAATTAGCA 13 188 1 GGCAAAAACG 0.84352 -113 GTTTCCAAAGGGGAAAAATTATTACCTGGCCT 16 124 0 GGGAAAAATT 0.874295 -177 TGAAAACCCAGGGAAAATTTTTGATGTTGCCT 16 212 0 GGGAAAATTT 0.467367 -89 TAAGGATTATGGCAAAAAGCCTAAAAGAAAAT 16 249 0 GGCAAAAAGT 0.90862 -52 TAGTCTGGATGGTAAAAATTATCTTTGAGTCT 18 108 0 GGTAAAAATT 0.813481 -193 ATGCTGGAAAAGCAAAAATTGCTAGTCTGGAT 18 130 0 AGCAAAAATC 0.566566 -171 GGATTAGTTGGGCAAAAATTCTGTTAGAAAGC 18 260 0 GGCAAAAATT 0.937483 -41 GAATTTGTTTGGTAAAAACTTTGCCGCCTGGT 19 38 1 GGTAAAAACT 0.832286 -263 GGCAAGCCTAGTCAAAAATAGCGAGGAAAGCC 19 188 0 GTCAAAAATC 0.438845 -113 GGGTCTGTGGGCCAAAATTCTAGTTGCTTAC 20 111 0 GGCCAAAATT 0.589078 -21 GTTGAGCGGCGGCAAAAATCTCTTCTGATTTA 21 274 0 GGCAAAAATC 0.946574 -27 TAATGGCAAAGGCAAAAACAATTGGGAAACTG 27 101 0 GGCAAAAACT 0.944637 -166 CACCATTGCAGGGAAAAATAAGGTTTCAGCAA 27 140 0 GGGAAAAATG 0.687239 -127 AGTTGGAAATGGCAAAATGCTTGAATGATGGC 27 245 0 GGCAAAATGT 0.556434 -22 CTCTAACCTAGGGAAAAACTTTGGGAAA 31 7 0 GGGAAAAACT 0.887814 -140 ********* * Masking position 6 Map Score: 13.0629 Number of sites scoring better than the average of aligned sites = 1791 Number in coding regions = 1551 Number in noncoding regions = 240 Number of orfs with sites within 600 bp upstream = 273 Fraction of orfs with sites within 600 bp upstream = 0.0438484 Motif number 12 TTCTGCCATCATCCCTTTGGTAGA 5 5 1 GCCATCATCC 0.73363 -296 ATAAATATTAGCCCCCAGACTTGTTTTACT 5 51 0 GCCCCCAGAC 0.903593 -250 TGAAGCTGTTTCCCCCATCAAGGCCAGATT 8 36 1 TCCCCCATCA 0.903646 -94 CAGTTTTCTCACCCCCAGCAAAACT 11 81 1 ACCCCCAGCA 0.880211 -15 GCCACCAGAAAAATTTTTCA 12 212 0 GCCACCAGAA 0.93074 -10 TGCCATGTATGCCACCATCAACCGTAAACC 14 74 1 GCCACCATCA 0.979942 -32 CAGGATGAAAGGCAACATCAAAAATTTTCC 16 203 1 GGCAACATCA 0.683427 -98 AAAGGAGCCCGCCAACAGCAAACTCCCCTT 17 29 1 GCCAACAGCA 0.968307 -63 GTGGGGATTGGCCACCATCAATTTTCGTGA 20 51 0 GCCACCATCA 0.979942 -81 TAGAATTTTGGCCCACAGACCC 20 120 1 GCCCACAGAC 0.809252 -12 TTGAACCTGTGCCCACATCAAAAAAACAGA 21 173 0 GCCCACATCA 0.968307 -128 ACTTTGGGGGGCAAACAGCAAAGCGCAGGG 24 56 0 GCAAACAGCA 0.668039 -70 ATAATCTAATTCCCCCATCATTGGGGGTTT 26 33 1 TCCCCCATCA 0.903646 -39 ********** Masking position 7 Map Score: 11.7204 Number of sites scoring better than the average of aligned sites = 1373 Number in coding regions = 1291 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 13 GTTTTTATATTTATCAAACAAG 1 2 0 TTATCAACAA 0.590144 -73 TGGAAAGAGATTTTCCTTCCTAGGCTTGC 3 79 1 TTTTCCTCCT 0.856733 -19 AATTTCAGATTTTTCATTCATCTTTTTTTAA 6 191 1 TTTTCATCAT 0.698779 -32 AAAAGCCAATTTTTCATTCAACCCAAGATAT 7 99 1 TTTTCATCAA 0.671125 -36 CCAGAAAAATTTTTCAAACCACACCCCGCTC 12 197 0 TTTTCAACCA 0.853137 -25 TTTTATCTAGCTTTCCACCAAATTTGGAGGC 16 18 1 CTTTCCACAA 0.633229 -283 AGACTTAAATTTTTCAATCATTGCTTTAAGC 18 18 0 TTTTCAACAT 0.858907 -283 AAAGATAATTTTTACCATCCAGACTAGCAAT 18 114 1 TTTACCACCA 0.594973 -187 CAATTTTTGCTTTTCCAGCATAGCCGCCCGA 18 141 1 TTTTCCACAT 0.93534 -160 TTATCCCGAATTTGCCATCAAACCAGGCGGC 19 60 0 TTTGCCACAA 0.786942 -241 ATTAGCCAGATTATCCACCCTGGCTGACTGT 22 84 1 TTATCCACCT 0.808408 -217 AACCCAAAGCTTTGCCTCCATTAATACCTCA 25 98 0 TTTGCCTCAT 0.615398 -72 TTCCGGGCGGTTATCCATCCTAACCCAAAGC 25 119 0 TTATCCACCT 0.808408 -51 GTTTTCAAACCTTTCAAACTGG 29 60 0 TTTTCAACCT 0.868486 -12 AGAATAAAACTTTTCCAACAAGCTC 31 132 1 TTTTCCACAA 0.927139 -15 ******* *** Masking position 2 Map Score: 7.20738 Number of sites scoring better than the average of aligned sites = 856 Number in coding regions = 729 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 14 GATCGGCTTAAATAAGCTCTAAACAGACGG 6 91 0 AATAAGCTCT 0.754542 -132 TTGAATGAAAAATTGGCTTTTAACGAAGAT 7 90 0 AATTGGCTTT 0.83891 -45 AATGTCCCAAAACTGGCTCTGTGTTCCCCA 9 109 0 AACTGGCTCT 0.952373 -53 GGGTTCTTAAAATAGGCTCTGAGGCTTCAA 16 54 1 AATAGGCTCT 0.972364 -247 TTACAGGTCGAATAGGCTTTTCCCTGCCCA 19 259 1 AATAGGCTTT 0.908489 -42 CCCGTTGGATAACAGGCTTGATTGTAATGG 20 17 1 AACAGGCTTG 0.822216 -115 GGGCGTTTAAAACGGGCTCTCAGAGTCTTG 21 15 1 AACGGGCTCT 0.921441 -286 GGGCTTTTAAAACAGGCTCTAAAAACTGTT 23 142 1 AACAGGCTCT 0.974438 -54 GGGAGAAAGGAATTGCCTCGTCACCACCCA 25 23 0 AATTGCCTCG 0.679704 -147 AGGTTTCAGCAATAGCCTCTAATGGCAAAG 27 122 0 AATAGCCTCT 0.903924 -145 ********** Masking position 8 Map Score: 6.21246 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 117 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 GGTTAGGGCGCTATTCTTCCTGTACAGGGA 10 59 1 CTATTCCCTG 0.978457 -20 TTTGATGTTGCCTTTCATCCTGTCCAATTCCC 16 193 0 CCTTTCCCTG 0.980877 -108 TTTTCCCTGGGTTTTCACCCTGATTTTCTTTT 16 227 1 GTTTTCCCTG 0.901071 -74 TTGGTAAAAACTTTGCCGCCTGGTTTGATGGC 19 46 1 CTTTGCCCTG 0.936181 -255 AGGGAAAAGCCTATTCGACCTGTAACATTTTG 19 252 0 CTATTCCCTG 0.978457 -49 TGCGGGTGGGCTTTGCCCCCTATAATTTTCG 22 280 1 CTTTGCCCTA 0.693246 -21 CTTTCACTCAGTATTCCTCCTAATTTGAGGGG 23 104 1 GTATTCCCTA 0.625113 -92 AGCCATTCCCCCAGGTTCAAGCCG 24 3 1 CCATTCCCAG 0.885644 -123 GTTTTCAAACCTTTCAAACTGGAATGGCAAT 29 51 0 CCTTTCACTG 0.801645 -21 AAACCCATTGCCATTTCCCCTGGGGCGAGGGG 30 117 1 CCATTTCCTG 0.827663 -66 CAGGCGATCGCCATTCAACCTGCTGAGACAAT 32 58 1 CCATTCCCTG 0.983858 -62 ****** **** Masking position 4 Map Score: 8.37799 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 275 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974