AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00920_synecho_reg_300.orf -o00920_synecho_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/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 sll0712 112 cysM; cysteine synthase. [EC:4.2.99.8] #2 sll0711 98 hypothetical protein. #3 sll0710 40 hypothetical protein. #4 sll0709 300 llaI.2; 2nd component required for LlaI restriction activity. #5 slr0676 157 cysC; adenylylsulfate 3-phosphotransferase. [EC:2.7.1.25] #6 slr0677 110 exbB; biopolymer transport ExbB protein. #7 slr0678 35 hypothetical protein. #8 slr0679 162 sun, fmu; sun protein (fmu protein). [SP:SUN_SYNY3] #9 slr0681 237 hypothetical protein. #10 slr0682 33 hisD; histidinol dehydrogenase. [EC:1.1.1.23] #11 sll0650 159 transposase. #12 sll0648 127 lim; lipophilic protein. [EC:2.4.1.-] #13 sll0646 38 cyaA; adenylate cyclase. [EC:4.6.1.1] #14 sll0645 74 hypothetical protein. #15 sll0644 195 esterase. #16 slr0686 254 hypothetical protein. #17 sll0643 300 ureG; urease accessory protein ureG. [SP:UREG_SYNY3] #18 slr1842 106 cysK; cysteine synthase. [EC:4.2.99.8] #19 slr1843 157 zwf; glucose-6-phosphate 1-dehydrogenase (G6PD). [EC:1.1.1.49] #20 slr1844 137 uvrA; excinuclease ABC subunit A. [SP:UVRA_SYNY3] #21 sll1717 93 hypothetical protein. #22 sll1716 134 transposase. #23 sll1714 300 hypothetical protein. #24 slr1348 300 cysE; serine acetyltransferase (SAT). [EC:2.3.1.30] [SP:CYSE_SYNY3] #25 slr1165 42 met3; sulfate adenylyltransferase. [EC:2.7.7.4] #26 slr1166 49 hypothetical protein. #27 ssl2138 246 hypothetical protein. #28 sll1091 300 chlP; geranylgeranyl hydrogenase. [SP:CHLP_SYNY3] Motif number 1 TAACATTTTACGGCGATTGGCGAATCCTAAT 2 18 0 CGGCGATTGC 0.99067 -81 ACTAATCCCTTGGCGATCGGGCTTAACCACA 5 79 1 TGGCGATCGG 0.981271 -79 CAATCCTAACGGCGATCGACTCTTCCCCCC 8 143 0 CGGCGATCGC 0.997851 -20 GCTGGGGTAATGGCGGTAGGCAAGAAACTTT 17 38 1 TGGCGGTAGC 0.916162 -263 TCTAAGTAAATGGCGATCGCCAGCCAAGATT 19 63 0 TGGCGATCGC 0.997234 -95 AAGGGTATTGCGGCCATTGACTGCTGTGA 22 9 0 CGGCCATTGC 0.939128 -126 TAAGTTAATGTGGCGATCGCCATCTCGATGA 23 261 0 TGGCGATCGC 0.997234 -40 GGAAAAGCCTTGGCGATCGCCTTTTTTTGTC 24 115 0 TGGCGATCGC 0.997234 -186 GCCGTCCCAGCGGCGATCGCCTACCCCTAAG 28 64 1 CGGCGATCGC 0.997851 -237 ********* * Masking position 7 Map Score: 22.1543 Number of sites scoring better than the average of aligned sites = 6066 Number in coding regions = 5520 Number in noncoding regions = 546 Number of orfs with sites within 600 bp upstream = 345 Fraction of orfs with sites within 600 bp upstream = 0.0554128 Motif number 2 ATCCTACCCCAGGGAGGATGGGCTGATGTAGGGGG 1 39 0 AGGAGATGGG 0.684927 -74 GCTGAGTTGAGGTAAGGCGGTCAAGCGGGG 1 93 0 GTGAGTAGGG 0.912234 -20 TTCCAGGCTTGTTAGGATTGGGGAGGTTGATTGAG 6 68 0 GTAGGTTGGG 0.858604 -43 TTCCATCCCTGGGGGGTAATGCGCC 8 1 0 GGGGGAAGCC 0.73638 -162 TTTCTATTGTGGGGGGGAAGAGTCGATCGCCGTTA 8 132 1 GGGGGAAAGG 0.86258 -31 TCCGGTGCCCAATGGGCTTTGGTGGAAA 9 220 1 ATGGGTTGGG 0.851171 -18 GGGGCGGTTTTGGTTCCCATGGTTGG 11 2 1 GGCGGTTGGC 0.858309 -158 TGGTTCCCATGGTTGGCTTAGGCAGGTAGACCTTC 11 21 1 GTTGGTTGGG 0.774959 -139 GGGCAAAGATGGGATTGGGAAGGGTTTAGGAT 12 106 0 GTGGGTTGGG 0.985803 -22 TTTTTAAAAAGTTGAGTTTTGGCTGTTTAATCCCC 16 31 1 GTGAGTTGGG 0.949812 -224 CCCTTTCTAAGGGGGGCTAGGGGGGATTAAACAGC 16 52 0 GGGGGTAGGG 0.990454 -203 GAGCTTTAGTGAGGAGATTTAGGGGGCAGAATAAA 16 120 1 GGGAGTTAGG 0.858694 -135 TAGGGGTTAGCTGGGGTAATGGCGGTAGGCAAGAA 17 29 1 CGGGGAAGGG 0.786413 -272 TTATCTGATAGTGAGGCTTAGGGAGTTCAAAATTT 17 84 1 GGAGGTTGGG 0.942928 -217 CCGTTGATTTGCCGGGGCAGGGTTGGTTAGGCCGA 17 203 0 GCGGGCAGGG 0.746203 -98 AGGGGGAGACAAGGCTCTTAACTTTTC 19 3 1 GGGAGCAGGC 0.781696 -155 GTCCTCAAGGGCGGGGTTTCAGACCCATTT 24 6 0 GGGGGTTAGC 0.906761 -295 ATGGGATGTGGAGGGGCATAGGAGGTGACTATTTG 24 251 0 GGGGGATGGG 0.989779 -50 AAAGTAGAGAGGTGAGTTTTGGCTCACCTTTTTAT 27 46 1 GTGAGTTGGC 0.891957 -201 ACAGAGGGGAATTGCTCCACCACAGGGT 28 283 0 GGGGGATGCC 0.835691 -18 * **** ** ** * Masking position 6 Map Score: 19.544 Number of sites scoring better than the average of aligned sites = 1851 Number in coding regions = 1627 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 3 CATCAGCCCATCCTCCCTGGGGTAGGATAACC 1 46 1 TCCTCCTGGG 0.8695 -67 AAAACCGGACTCAATCCTGGGGAAGATGCCTA 6 28 1 TCAATCTGGG 0.964917 -83 CTGTACCATTCCATCCCTGGGGGGTAATGCGC 8 12 0 CCATCCTGGG 0.976201 -151 CAAAACAGAACCCTTACTAGGGTCAAAGGTTT 9 131 1 CCCTTCTGGG 0.985832 -107 GAATTTGGCTCCGATGCTGGGGG 12 2 0 CCGATCTGGG 0.977133 -126 GCATCGGAGCCAAATTCTAGGGGCCATACCAA 12 17 1 CAAATCTGGG 0.92426 -111 AAGAGTTCCCCCCTTTCTAAGGGGGGCTAGGG 16 65 0 CCCTTCTAGG 0.872934 -190 TAAAGCTCCGGCAATACTGGGGGTCTTTTGTA 16 96 0 GCAATCTGGG 0.958536 -159 AATTATTTCTCCAATTCTTGGGCATTAAAT 25 9 0 CCAATCTGGG 0.992842 -34 GTTGTGCCCGCCAATTCTAGGGACGT 26 34 1 CCAATCTGGG 0.992858 -16 ***** ** *** Masking position 8 Map Score: 12.2075 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 283 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 TTTCTTTTCATTGAATAGTTTTATTTACAT 3 18 1 TTGAATAGTT 0.697077 -23 TATGTGCGACTAGAAAAGTATTCAACTTTA 5 35 1 TAGAAAAGTA 0.650245 -123 CTAACAAGCCTGGAAAAGTTGATTCCAGCA 6 88 1 TGGAAAAGTT 0.964795 -23 GCTTTGGCTATGGAAAAGTCTCTGTACAAT 15 51 0 TGGAAAAGTC 0.799906 -145 TCAAGCTTAATGGCAAAATTTAACTTTAAA 15 136 0 TGGCAAAATT 0.686078 -60 TAAAACTTAATAGAAAAATTGTTTTGTTTC 15 166 1 TAGAAAAATT 0.773823 -30 AAGAGCCTTTTTAAAAAGTTGAGTTTTGGC 16 24 1 TTAAAAAGTT 0.728507 -231 TAGAACTTATTTGAAAAGTTTTATTCTGCC 16 144 0 TTGAAAAGTT 0.96415 -111 TTTCTTTTTCTGGCAAAGTTTTCAGGAAAA 18 71 1 TGGCAAAGTT 0.872496 -36 CAAAGTTTTCAGGAAAAATTTCTTTCTCAG 18 84 1 AGGAAAAATT 0.585561 -23 TAAAATCGTGAAGAAAAGTTAAGAGCCTTG 19 20 0 AAGAAAAGTT 0.633596 -138 TAGAAAGTGTTTGAAAAGTT 21 1 0 TTGAAAAGTT 0.96415 -93 TAGAGCGTGTTTGAAAAGTAGGGTGAAGAA 22 76 1 TTGAAAAGTA 0.823556 -59 CTCTACTTTATTGAAAAATTAGTTAAACTA 27 25 0 TTGAAAAATT 0.895719 -222 GTCGCATAAATTAAAAAATTGGTAAAAATA 27 86 0 TTAAAAAATT 0.4615 -161 AAGGAAGAAATTGAAAATTTAACGCAGATT 27 187 1 TTGAAAATTT 0.67939 -60 ********** Masking position 5 Map Score: 9.23737 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 364 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 TAAGTTGGGGGTGAAAGAGGGGCAATAAAT 2 79 0 GGGTGAAAGG 0.65142 -20 TCAACTTTACGGGGAAATAAGGGACTAATCCC 5 56 1 GGGGAATAGG 0.725629 -102 CTATTGTGGGGGGGAAGAGTCGATCGCCGTTA 8 135 1 GGGGAAATCG 0.669661 -28 CAGGGGGAATGGGCAACACAGGGAACTTCAGG 9 84 0 GGGCAAAAGG 0.970798 -154 CTATCTGAAAGGTCAAAACAGAACCCTTACTA 9 118 1 GGTCAAAAGA 0.559265 -120 TTTACTGCCTGGGTAACAGTGGCTAAGCACCG 12 53 1 GGGTAAATGG 0.970961 -75 GGGCAAAGATGGGATTGGGAAG 12 116 0 GGGCAAGTGG 0.977169 -12 TTGTTATCTTGGGTAAAAATGACTCTGTTTTT 14 23 1 GGGTAAATGA 0.827001 -52 GTGTATATTTGGTTAACATTGGACCATTGTAC 15 26 1 GGTTAAATGG 0.899265 -170 ACTAAAGCTCCGGCAATACTGGGGGTCTTTTG 16 98 0 CGGCAAATGG 0.83883 -157 GGGTTAGCTGGGGTAATGGCGGTAGGCAAGAA 17 32 1 GGGTAAGCGG 0.776266 -269 TGATTTGCCGGGGCAGGGTTGGTTAGGCCGAT 17 202 0 GGGCAGGTGG 0.853096 -99 GGTGCGACCCGGTCAACAGTGACTTTAGATTA 20 83 1 GGTCAAATGA 0.729932 -55 TGAAAAGTAGGGTGAAGAATGGAAAATGGTGA 22 87 1 GGTGAAATGG 0.880431 -48 AAAAACCCTAGGTTATTATTGGAACTGGAGGC 23 41 1 GGTTATATGG 0.590341 -260 GAGCAAAATGGGGCAAGTTTGGCGACAGTGTG 24 175 1 GGGCAATTGG 0.935327 -126 GGATGTGGAGGGGCATAGGAGGTGACTATTTG 24 251 0 GGGCATGAGG 0.764361 -50 ****** * *** Masking position 2 Map Score: 11.2955 Number of sites scoring better than the average of aligned sites = 1758 Number in coding regions = 1611 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 6 TAGGATTCGCCAATCGCCGTAAAATGTTAGGCGAT 2 20 1 CATCGTAAAT 0.574856 -79 TAGTTATTAACCACCCTTCAAATCTATAATCAACC 4 117 0 CCCCCAAATT 0.834676 -184 TCAATAGCAGCAATCTGCGAAATGTCAGTATTAGT 4 206 0 CATCGAAATT 0.834316 -95 CTATTCATTGCCTCCATTGCAATATGTGCGACTAG 5 13 1 CCCCGCAATT 0.872341 -145 CCAATCCTAACAAGCCTGGAAAAGTTGATTCCAGC 6 82 1 CAGCGAAAAT 0.782231 -29 GCCAGGGGATCAACGCCTCAAAAGTAATATATGGG 8 79 0 CACGCAAAAT 0.903958 -84 ACAATAGAAACAGTGAATCAAAATTCTGGCCAGGG 8 107 0 CATGCAAAAT 0.781287 -56 GGGAGCATATCAGTCAAGGCAAATTATCCGGTGCC 9 194 1 CATCGCAAAT 0.897334 -44 CCCCCAGCATCGGAGCCAAATTCTAGGGGCCA 12 8 1 CACGCCAAAT 0.875729 -120 CCACCGGAGAAAACTAAAGGAAATA 13 1 1 CCCCGAAAAT 0.954871 -38 CCCGGCAAATCAACGGAAGAAAATATAAATTAGAC 17 222 1 CACGGAAAAA 0.577455 -79 ATTTCTGCATCAGCGGACGAAATTTGCTCCGAAAA 23 146 0 CACGGAAATT 0.880088 -155 CAGGAAAAAACATCCGGCCAAAAATTGAGGACAAA 24 86 1 CACCCAAAAT 0.94449 -215 CCCGCAACACCAACCCCAGAAAATTCCCTCGGAGC 24 144 1 CACCGAAAAT 0.968512 -157 CCAGAAAATTCCCTCGGAGCAAAATGGGGCAAGTT 24 159 1 CCTCGCAAAT 0.857394 -142 GTTAACCACACACTGTCGCCAAACTTGCCCCATTT 24 180 0 CATGCCAAAT 0.727856 -121 GCTGGTTCTTCCGCCGCCGAAATTTTAGTAAAAGC 28 203 1 CCCCGAAATT 0.901253 -98 ** ** ***** * Masking position 11 Map Score: 10.7336 Number of sites scoring better than the average of aligned sites = 748 Number in coding regions = 666 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 GAAGAGGGATACAGCGGATACCCTATTAGT 4 11 1 ACAGCGGATA 0.883019 -290 TAATCAACCTACAGCGGTCATGCTTTCCAT 4 96 0 ACAGCGGTCA 0.970588 -205 GGCGAACTTAACACCGGTCAATCTCTCTAG 5 138 0 ACACCGGTCA 0.97737 -20 AGCCCATTGGGCACCGGATAATTTGCCTTG 9 208 0 GCACCGGATA 0.940211 -30 CAGTGGCTAAGCACCGTACAAATATGGGGT 12 69 1 GCACCGTACA 0.884765 -59 ACTGCAACGGTCATCGAAAGCGA 19 145 0 GCAACGGTCA 0.929446 -13 TGACCGGGTCGCACCGGACAGATCAACTTC 20 68 0 GCACCGGACA 0.985661 -70 TCACAGCAGTCAATGGCCGCAA 22 3 1 ACAGCAGTCA 0.786568 -132 ********** Masking position 3 Map Score: 5.83827 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 180 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 CTTTCCATCTGGTATACCAAAGTCATTGTAAAACAGT 4 67 0 GAACCAAGCT 0.992592 -234 TGGCGATCGGGCTTAACCACAGACAATCCTAACGCAA 5 89 1 GTACCAAGCT 0.980021 -69 TGACCTTTCAGATAGACCAGGGGGAATGGGCAACACA 9 96 0 GAACCAGGGT 0.894861 -142 TTTCCACCAAAGCCCATTGGGCACCGG 9 221 0 TCACCAAGCT 0.86892 -17 AATTCTAGGGGCCATACCAAAGTCTTTACTGCCTGGG 12 29 1 GAACCAAGCT 0.992592 -99 AAAACTAAAGGAAATACCAGAGAACATTA 13 20 1 GAACCAAGAT 0.937353 -19 AGGACAAAGGGCAAAAACAGAGTCATTTTTACCCAAG 14 30 0 GAAACAAGCT 0.921299 -45 GAACTTTGGTGGTTAACCACACACTGTCGCCAAACTT 24 189 0 GTACCAACCT 0.863976 -112 ACTGCTACCCGTAATACCAAAGCCTTTCTCCTAAATT 28 150 0 GAACCAAGCT 0.992592 -151 GAGGGGAATTGCTCCACCACAGGGTTTGGCGTTGTCT 28 271 0 GCACCAAGGT 0.958524 -30 * * **** ** * * Masking position 9 Map Score: 7.50973 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 74 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 CATCCTCCCTGGGGTAGGATAACCTAACAG 1 54 1 GGGGTAGGAT 0.944725 -59 CGGTCAAGCGGGGGTTAAAACCCTGTTAGG 1 76 0 GGGGTTAAAA 0.527676 -37 CACTCTGCCTGGGGTTGACTGTTTGGGAGC 9 23 0 GGGGTTGACT 0.929112 -215 GGGAACTTCAGGGGTAAAAACGTTAAGCTA 9 66 0 GGGGTAAAAA 0.684459 -172 GTACAAATATGGGGTAAACTTTATCCTAAA 12 84 1 GGGGTAAACT 0.890445 -44 GGGGTAGATAGTTTGTTATC 14 1 1 GGGGTAGATA 0.839123 -74 GGAGATTTAGGGGGCAGAATAAAACTTTTC 16 132 1 GGGGCAGAAT 0.811416 -123 TTCCGAAGTAGGGGTTAGCTGGGGTAATGG 17 21 1 GGGGTTAGCT 0.884422 -280 TGGGGTAATGGCGGTAGGCAAGAAACTTTC 17 40 1 GCGGTAGGCA 0.739166 -261 TTGATTTGCCGGGGCAGGGTTGGTTAGGCC 17 205 0 GGGGCAGGGT 0.779889 -96 AGGGGGAGACAAGGCTCTTAA 19 2 1 GGGGGAGACA 0.76039 -156 GGAATTTTCTGGGGTTGGTGTTGCGGGAAA 24 141 0 GGGGTTGGTG 0.827981 -160 GGAGCAAAATGGGGCAAGTTTGGCGACAGT 24 174 1 GGGGCAAGTT 0.658609 -127 TTTTTGCTTAGGGGTAGGCGATCGCCGCTG 28 71 0 GGGGTAGGCG 0.970694 -230 CTCCACCACAGGGTTTGGCGTTGTCTAGCT 28 267 0 GGGTTTGGCG 0.491156 -34 ********** Masking position 3 Map Score: 6.98691 Number of sites scoring better than the average of aligned sites = 1717 Number in coding regions = 1573 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 10 CAGCTAAAGTTCCCGACCAAGAAATAAGTCC 8 50 1 TCCCGCCAAG 0.940103 -113 TGAATCAAAATTCTGGCCAGGGGATCAACGC 8 98 0 TTCTGCCAGG 0.979579 -65 CAGGTAGACCTTCTGTCCAGAAACCTACAAC 11 43 1 TTCTGCCAGA 0.967918 -117 TTGCCCTTTGTCCTGCCCAGGCAGCGTTAAT 14 53 1 TCCTGCCAGG 0.964496 -22 ATTGTTTTGTTTCTGACCAAACC 15 183 1 TTCTGCCAAA 0.96847 -13 AGTTTTCTTTTTCTGGCAAAGTTTTCAGGAA 18 68 1 TTCTGCAAAG 0.845238 -39 AGGAAAAAACATCCGGCCAAAAATTGAGGAC 24 87 1 ATCCGCCAAA 0.757962 -214 ACCACCAAAGTTCTGTCCAAAATTCCTAAGT 24 213 1 TTCTGCCAAA 0.96847 -88 ***** ***** Masking position 9 Map Score: 5.19257 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 128 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 AATCGCCGTAAAATGTTAGGCGATAACTTGAGTGG 2 31 1 AAAGTTACAA 0.973904 -68 TTATATCTAAAAAGGTTATCCCACACAACAAAAAA 4 156 0 AAAGTTACAA 0.973904 -145 CCACAATAGAAACAGTGAATCAAAATTCTGGCCAG 8 109 0 AACGTGACAA 0.809965 -54 TCAGGGGTAAAAACGTTAAGCTAAAACAGAACTGG 9 54 0 AAAGTTACAA 0.973904 -184 GGTTTAGGATAAAGTTTACCCCATATTTGTACGGT 12 81 0 AAATTTACAA 0.924422 -47 AGACTTAAGTAAACTTTAACCGACAGTCAACAAGC 16 189 1 AAATTTACAA 0.924422 -66 TGAAAAGAATAAAATTTTCACCATAATTA 22 116 1 AAATTTTCAA 0.658487 -19 CTTCAAACGTTATTCCTTATACCTTACTC 23 5 1 AAAGTTACTA 0.854718 -296 AAGACAATAAAAAGGTGAGCCAAAACTCACCTCTC 27 52 0 AAAGTGACAA 0.948031 -195 *** **** * * * Masking position 6 Map Score: 2.85058 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 25 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 CCCCGCTTGACCGCCTTACCTCAACTCAGC 1 93 1 CCGCCTTACC 0.951105 -20 GGCGCATTACCCCCCAGGGAT 8 2 1 GCGCATTACC 0.92423 -161 CTTCACCAAACCGCAAAACCTGTGACTTCG 20 42 0 CCGCAAAACC 0.967917 -96 CAGTCAATGGCCGCAATACCCTTATGGTGA 22 17 1 CCGCAATACC 0.990026 -118 AAGGCTTTTCCCGCAACACCAACCCCAGAA 24 135 1 CCGCAACACC 0.978125 -166 CGACTGCTACCCGTAATACCAAAGCCTTTC 28 159 0 CCGTAATACC 0.938858 -142 ********** Masking position 8 Map Score: 4.43569 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 147 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 Motif number 13 TTCTGCCGCAATTGATTGATCCAGG 1 4 0 ATTGTTATCC 0.720631 -109 GATTGGGGAGGTTGATTGAGCCTATTTTTAGG 6 56 0 GTTGTTAGCC 0.952436 -55 AGGCAATGCAGTTTCAGCCAATTACTATC 7 8 1 GCAGTTAGCC 0.856364 -28 TAAAAATGACTCTGTTTTTGCCCTTTGTCCTG 14 36 1 TCTGTTTGCC 0.788751 -39 CATAGCCAAAGCTGGTTTATCCCCAGTTTAAG 15 69 1 GCTGTTATCC 0.972195 -127 TTGAGTTTTGGCTGTTTAATCCCCCCTAGCCC 16 42 1 GCTGTTATCC 0.972195 -213 CCGGGGCAGGGTTGGTTAGGCCGATGTTAGAA 17 195 0 GTTGTTGGCC 0.930914 -106 GTTTGGTGAAGTTGATCTGTCCGGTGCGACCC 20 61 1 GTTGTCGTCC 0.79397 -77 AGATGCCCTAACTGCTCGTGCCACGGAAATTG 23 211 1 ACTGTCTGCC 0.716465 -90 TTTTTGGCCGGATGTTTTTTCCTGTTTAATAA 24 78 0 GATGTTTTCC 0.78638 -223 AGGAGGCCCCGCTGGTTCTTCCGCCGCCGAAA 28 193 1 GCTGTTTTCC 0.965964 -108 **** ** **** Masking position 6 Map Score: 4.23439 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 267 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 14 TCAAGCGGGGGTTAAAACCCTGTTAGGTTA 1 73 0 GTTAAAACCC 0.84156 -40 CTCCCCAATCCTAACAAGCCTGGAAAAGTT 6 78 1 CTAACAAGCC 0.894495 -33 TTAATTCAAGCTTAAGAGCCTTTTTAAAAA 16 11 1 CTTAAGAGCC 0.920713 -244 GGAACTCTTACAAAAGACCCCCAGTATTGC 16 88 1 CAAAAGACCC 0.848485 -167 TTCTCAGCGACTAAAAGCCCTTGCGACAAA 17 127 1 CTAAAAGCCC 0.833879 -174 GTGAAGAAAAGTTAAGAGCCTTGTCTCCCC 19 13 0 GTTAAGAGCC 0.779591 -145 TAGAAATAGGCTTAAAACCCAGAACAGTTT 19 90 1 CTTAAAACCC 0.945765 -68 ATACCTTACTCAAAAAACCCTAGGTTATTA 23 29 1 CAAAAAACCC 0.871617 -272 ATTAGTTAAACTAACAAGCCATTAGCA 27 8 0 CTAACAAGCC 0.894495 -239 ********** Masking position 4 Map Score: 1.6316 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 111 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 CATTCTCCCACCTAGAGAGATTGACCGGTG 5 127 1 CCTAGAGAGA 0.883816 -31 CCTAGCCCCCCTTAGAAAGGGGGGAACTCT 16 66 1 CTTAGAAAGG 0.853593 -189 TTTCAGCGTTCTGAGAAAGTTTCTTGCCTA 17 54 0 CTGAGAAAGT 0.84677 -247 GATAGTGAGGCTTAGGGAGTTCAAAATTTC 17 90 1 CTTAGGGAGT 0.911708 -211 GAACTGAGAAAGAAATTTTTCCT 18 94 0 CTGAGAAAGA 0.867844 -13 TCGCCATTTACTTAGAAATAGGCTTAAAAC 19 78 1 CTTAGAAATA 0.807054 -80 GCTCACTCCTCTTAGAAAGTGTTTGAAAAG 21 13 0 CTTAGAAAGT 0.940986 -81 CTGCTAAGCTCTTAGAGCGTGTTTGAAAAG 22 64 1 CTTAGAGCGT 0.760242 -71 TCTTAAGACAATTAGAAAGATTTTATTAAA 24 56 1 ATTAGAAAGA 0.576191 -245 TGTTGGTTCACTTAGGAATTTTGGACAGAA 24 223 0 CTTAGGAATT 0.66305 -78 GCGACTTAAGCCTAGAGATATTGAGATTAA 27 111 1 CCTAGAGATA 0.626763 -136 CAAAAGGATACTTAGGGAGATTAGGATTAA 27 137 0 CTTAGGGAGA 0.924646 -110 ********** Masking position 4 Map Score: 3.52219 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 66 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084