AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_synecho_reg_100.orf -o02020_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 sll1672 193 sensory transduction histidine kinase. #2 slr1761 267 ytfC; FKBP-type peptidyl-prolyl cis-trans isomerase. [EC:5.2.1.8] #3 slr1728 56 kdpA; potassium-transporting ATPase A chain. [EC:3.6.1.36] #4 slr1729 28 kdpB; potassium-transporting ATPase B chain. [EC:3.6.1.36] #5 ssr2912 189 hypothetical protein. #6 slr1730 231 kdpC; potassium-transporting ATPase C chain. [EC:3.6.1.36] #7 slr1731 76 kdpD; potassium-transporting ATPase D chain. [EC:2.7.3.-] #8 sll1586 269 hypothetical protein. #9 slr2098 89 sensory transduction histidine kinase. [EC:2.7.3.-] #10 slr2099 226 regulatory components of sensory transduction system. #11 slr2100 164 regulatory components of sensory transduction system. #12 slr2104 222 sensory transduction histidine kinase. [EC:2.7.3.-] #13 sll1229 107 regulatory components of sensory transduction system. #14 sll1228 232 sensory transduction histidine kinase. #15 sll1871 183 sensory transduction histidine kinase. #16 slr1982 244 regulatory components of sensory transduction system. #17 sll1869 149 cbaB; 3-chlorobenzoate-3,4-dioxygenase. [EC:1.14.-.-] #18 slr0474 189 rcp1; response regulator for phytochrome 1. #19 sll0396 216 regulatory components of sensory transduction system. #20 slr0081 300 hisB; regulatory components of sensory transduction system. #21 slr0312 221 nitrate/nitrite response regulator protein. #22 sll0797 118 regulatory components of sensory transduction system. #23 sll0788 221 merR; hypothetical protein. #24 slr0533 98 sensory transduction histidine kinase. [EC:2.7.3.-] #25 slr0534 240 slt; soluble lytic transglycosylase. [EC:3.2.1.-] Motif number 1 ATGGCCCGTAGGCGATCGCCGTGGTGAACC 6 176 1 GGCGATCGCC 0.499999 -56 GGAATATTACGGCGATCGCCATACAGTCAC 11 113 1 GGCGATCGCC 0.499999 -52 AATTCCCGCAGGCGATCGCC 13 98 1 GGCGATCGCC 0.499999 -10 CTCACCAGTTGGGGACAGCCCCAAAGTGAT 14 91 0 GGGGACAGCC 0.956849 -142 TAGGAGGATAGGCGATCGCCGGGGGGAGGT 14 134 1 GGCGATCGCC 0.499999 -99 GTTTGGAAACGGCGATCGCCAAAATGGTTG 18 44 1 GGCGATCGCC 0.499999 -146 AAGAAGCCATGGCAACAGCCAATGAATTTG 19 59 0 GGCAACAGCC 0.93576 -158 GGCAAACTAGGCGATCGCATAGCAAATAT 19 198 0 GGCGATCGCA 0.51726 -19 ATTCAATATAGGCAATCGCCTTCAAACCGT 21 87 1 GGCAATCGCC 0.512177 -135 AGCATGAAAAGTCGACAGCCTATGAAACAG 23 46 0 GTCGACAGCC 0.890759 -176 ACGTTAGCTTGGGGATCGCAGCAAAAATCT 25 159 0 GGGGATCGCA 0.823869 -82 ********** Masking position 5 Map Score: 33.4268 Number of sites scoring better than the average of aligned sites = 5681 Number in coding regions = 5155 Number in noncoding regions = 526 Number of orfs with sites within 600 bp upstream = 315 Fraction of orfs with sites within 600 bp upstream = 0.0505943 Motif number 2 GGAGATTGTAAACCCCTCTTTTTGCCCAGAAGCGGGC 1 31 0 ACCCCTTCCC 0.989201 -163 AGGGCTGAAAGGTCGCCATTTTCCCCCTAAGAGCCGG 2 31 1 GCGCATCCCC 0.838774 -237 TTGTTTGAAAAGCCCCCCTGACCCCCCAAATTTGGGG 2 141 0 ACCCCCCCCC 0.994454 -127 GGAACTGGATAAGCCCCCTTGCTTCCTAATTTTGGGG 2 215 0 ACCCCCTCCT 0.902552 -53 GTTTTATTTTGCCCCCTAAATTTCCCAATAATGGAGG 5 38 1 GCCCATTCCA 0.687651 -152 CATCTTTCAAACGCCCCCTGCCCCCCCAAAAAAATTA 5 95 0 ACCCCCCCCC 0.994454 -95 GGCGCTATTCATTCCCCACAACCACCCTGTTAGGCTA 8 236 0 ACCCACCCCC 0.990037 -34 TAAATAGGGTAAACCCGCTTGTTGCCCTGCCCAAA 10 202 1 ACCCCTTCCC 0.989201 -25 TCAGCCCGTTAACCCCAAACTTTTCCCTTGGCTAGGC 11 68 1 ACCCATTCCC 0.980683 -97 TATGAACTCAGTACCCTCCCACTGCCCACTTTTTAGG 12 130 1 GCCCCCTCCC 0.987883 -93 GTTGGGGACAGCCCCAAAGTGATACCCTTAAAGATGG 14 77 0 GCCAAATCCC 0.664172 -156 TCCAACTTTTGCTCCAAAACCTCCCCCCGGCGATCGC 14 145 0 GCCAATCCCC 0.909396 -88 TTTATCTTTAGCCCCCAAAATTCACCCAGACAAGAAA 15 69 1 GCCCATCCCC 0.986869 -115 GGTGGAAATAACACCAGCATTTCCCCCATGGGTTAAA 15 120 0 ACCACTCCCC 0.956662 -64 GGTAACTTAAATACCCTTGATATGCCCTGACTAGATG 16 102 1 ACCCTATCCC 0.739943 -143 TCCTGACATTACTCCCAATATTCTCCTACTCTGACGT 20 145 1 ACCCATCCCT 0.895155 -156 ATGGCGAAAAATTCCCCCATTAGTCCCATTGAGGAAA 20 230 1 ACCCCAGCCC 0.883845 -71 AGCCAGAATAATCCCCGCTTACCTTCCCCAGTCAAAC 24 34 0 ACCCCCCTCC 0.893329 -65 * *** * ** *** Masking position 4 Map Score: 27.8133 Number of sites scoring better than the average of aligned sites = 1076 Number in coding regions = 896 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 3 CCGGCTCTTAGGGGGAAAATGGCGACCTTT 2 38 0 GGGGGAAAAT 0.979736 -230 CCCAAATTTGGGGGGAAAGAGAGGCGAAAT 2 124 0 GGGGGAAAGA 0.959275 -144 TTCCTAATTTTGGGGAAAATCAAAATCCCC 2 200 0 TGGGGAAAAT 0.959302 -68 GGGAAATTTAGGGGGCAAAATAAAACCTTT 5 34 0 GGGGGCAAAA 0.843916 -156 CAAAAAAATTAGGGGGAAGTTAAGTAAAAA 5 76 0 AGGGGGAAGT 0.919023 -114 TCAACTTTATGGGGGGAGCATGTTAGTGAC 7 30 1 GGGGGGAGCA 0.81663 -47 GACTATTTATGGTGGGAAATCATTGTTGAT 8 44 1 GGTGGGAAAT 0.734465 -226 AATTTATGGCTGGTGGAAATAAAATTCAGA 10 127 0 TGGTGGAAAT 0.859519 -100 AAGAAAGAAATGGTGAAAAAGGCTGAGGAT 12 67 1 TGGTGAAAAA 0.737068 -156 AATTGGTGGAGGGGGAAGAAAAGTTGAGTA 13 72 0 GGGGGAAGAA 0.956112 -36 GGCGATCGCCGGGGGGAGGTTTTGGAGCAA 14 144 1 GGGGGGAGGT 0.975007 -89 ATTTAACCCATGGGGGAAATGCTGGTGTTA 15 119 1 TGGGGGAAAT 0.968304 -65 CTGAAGATTTTGGTGGAAATAACACCAGCA 15 138 0 TGGTGGAAAT 0.859519 -46 GGTTAAGCCAAGGGGAAGGTCTCAAAACGT 19 133 0 AGGGGAAGGT 0.869184 -84 GATAGAAATATGGCGAAAAATTCCCCCATT 20 221 1 TGGCGAAAAA 0.699159 -80 TATGAAATTCAGGTGAAAATCTCCTTCCCC 22 63 1 AGGTGAAAAT 0.681279 -56 TGATCTTAGCGGGGGAAGGAGATTTTCACC 22 74 0 GGGGGAAGGA 0.947015 -45 TGGGTTTGACTGGGGAAGGTAAGCGGGGAT 24 31 1 TGGGGAAGGT 0.936199 -68 CCATTTTTCCGGGCGGAAATCAGTAAATCA 25 32 1 GGGCGGAAAT 0.912315 -209 ********** Masking position 7 Map Score: 19.4255 Number of sites scoring better than the average of aligned sites = 2827 Number in coding regions = 2442 Number in noncoding regions = 385 Number of orfs with sites within 600 bp upstream = 314 Fraction of orfs with sites within 600 bp upstream = 0.0504337 Motif number 4 ATTGTAAACCCCTCTTTTTGCCCAGAAGCGG 1 33 0 CCTCTTTTGC 0.953575 -161 AATAAATTATCCTAATTTTCCAGAGAGACTC 1 121 0 CCTATTTTCC 0.973778 -73 TATCTTGCTACCTAAATTTCCTCACAGCTCT 2 80 1 CCTAATTTCC 0.93234 -188 GGCGAAATCCCCCAGAATTGCAGAGCTGTGA 2 101 0 CCCAAATTGC 0.609255 -167 GGGGATTTCGCCTCTCTTTCCCCCCAAATTT 2 120 1 CCTCCTTTCC 0.735934 -148 TCTCTTTCCCCCCAAATTTGGGGGGTCAGGG 2 132 1 CCCAATTTGG 0.459571 -136 AATCAAAATCCCCAGTATGGCGGGAGTTTTA 2 182 0 CCCATATGGC 0.572796 -86 CCCCTTGCTTCCTAATTTTGGGGAAAATCAA 2 207 0 CCTATTTTGG 0.815158 -61 TATTTTGCCCCCTAAATTTCCCAATAATGGA 5 42 1 CCTAATTTCC 0.93234 -148 CCCTAGTTTAGCCTTCGGTCTA 8 2 1 CCTATTTAGC 0.748904 -268 TTCCTTTTACCCTAGTTTTTCTGCGCCGATA 8 114 0 CCTATTTTTC 0.764405 -156 TTTATGTTGCCCTATTTTTGATTGAATTAGC 10 46 0 CCTATTTTGA 0.6343 -181 TCTTCCCGTTCCAACTTTTGCTCCAAAACCT 14 160 0 CCAATTTTGC 0.772691 -73 AGTTGATCAACCTAGTTTTACGAATTATTTT 16 27 1 CCTATTTTAC 0.764405 -218 TATGCGATCGCCTAGTTTGCC 19 206 1 CCTATTTGCC 0.922185 -11 CTCAGAACCTCCTCCATTTCCTCAATGGGAC 20 252 0 CCTCATTTCC 0.884017 -49 GAATTTCATACCCCCTTTGGCAGACTGGGAA 22 42 0 CCCCTTTGGC 0.795028 -77 TGCTCTTACTCTTAGTTTTCCTTTTTTTCTT 23 89 1 CTTATTTTCC 0.608428 -133 GGAATGCTTACCTCCTATTCCTTCTCTAATT 23 200 0 CCTCTATTCC 0.797067 -22 GGGAACGGGACCCATTTTTCCGGGCGGAAAT 25 21 1 CCCATTTTCC 0.956475 -220 **** ****** Masking position 8 Map Score: 15.8472 Number of sites scoring better than the average of aligned sites = 927 Number in coding regions = 784 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 5 AACCGGCTCTTAGGGGGAAAATGGCGACCTTTCA 2 36 0 TAGGGGATGG 0.599369 -232 TTTTTGGCGGATTTTTGTCCTAGAACG 2 251 0 TTGGCGATTG 0.778479 -17 AATGGCAAAACCTTGCAGTCATCGG 4 2 1 ATGGCAATTG 0.881045 -27 AATGCAAACTCTGGCTAACCATGGCCCGTAGGCG 6 156 1 CTGGCAATGG 0.922197 -76 ACTATTTATGGTGGGAAATCATTGTTGATTCAGA 8 45 1 GTGGGAATTG 0.861706 -225 ATTAAGATTTATGGCGCAGAATTGGTTAAGACTA 11 33 0 ATGGCCATTG 0.719645 -132 AAGCCTAGCCAAGGGAAAAGTTTGGGGTTAACGG 11 73 0 AAGGGAATTG 0.850763 -92 AGGCGATCGCCGGGGGGAGGTTTTGGAGCAAAAG 14 143 1 CGGGGGATTT 0.765878 -90 GGGAATAAAACAGGGCAACTATTGCTATAATTCT 15 25 0 CAGGGAATTG 0.942839 -159 CATTTCTTGTCTGGGTGAATTTTGGGGGCTAAAG 15 74 0 CTGGGGATTG 0.987003 -110 CAACGACAATCTGGTGGACAATGGCTGGGTTAGC 18 149 1 CTGGTGATGG 0.703843 -41 CTGTAATTACCTGGGTGATATTTTC 19 2 0 CTGGGGATTT 0.96268 -215 GCTTCTTCCTCAGGGGAAATTTTTTCTGGGCCAT 19 82 1 CAGGGAATTT 0.848549 -135 GAAATTTTTTCTGGGCCATGTTTTTGAAAGGTTG 19 97 1 CTGGGCATTT 0.873379 -120 CAGCCTGCGGATGGGGAACGGTGGTCAGACCCTT 20 40 1 ATGGGAATGG 0.918035 -261 AATGGGACTAATGGGGGAATTTTTCGCCATATTT 20 226 0 ATGGGGATTT 0.899144 -75 CTTTGGCAGACTGGGAAAATCTTGGACAAATTCC 22 25 0 CTGGGAATTG 0.983219 -94 GCGATGCAGAATGGGCAATAGTTGAATCA 23 6 0 ATGGGAATTG 0.952942 -216 GGGGATTATTCTGGCTGAAAGTGTTACAAACATT 24 55 1 CTGGCGATGT 0.839182 -44 CTGATCGCCCCTGGGAAAATGTTTGTAACACTTT 24 72 0 CTGGGAATTT 0.952158 -27 ***** ** *** Masking position 12 Map Score: 20.0146 Number of sites scoring better than the average of aligned sites = 1018 Number in coding regions = 888 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 6 AATCTTAGGTAAAAATCGGATT 3 3 1 TCTTAGGTAA 0.713963 -54 GGTAGTCAGTTCCTAGGTAAAAATGAT 7 60 1 TCCTAGGTAA 0.926131 -17 GCCAGCAAAATCCTGGGCAAACCAGATCCA 8 200 0 TCCTGGGCAA 0.940924 -70 GCTGAGGATGACCCAAGCAAGCCCTCCTTA 12 88 1 ACCCAAGCAA 0.864977 -135 ATAAACAAATTCCTAGACAATCAGC 14 6 0 TCCTAGACAA 0.900685 -227 CCCAAAATTCACCCAGACAAGAAATGTTCC 15 82 1 ACCCAGACAA 0.935707 -102 ATTTTGTCAGACCTAGGTAACTTAAATACC 16 87 1 ACCTAGGTAA 0.915414 -158 GTCACGAAAGTCCCAAGCAATCCTGCTAGA 17 48 0 TCCCAAGCAA 0.881255 -102 AACTGATCCTACCCAGGTAAGGGCCGTCCC 17 94 0 ACCCAGGTAA 0.952651 -56 GAAAATATCACCCAGGTAATTACAGGTAA 19 10 1 ACCCAGGTAA 0.952651 -207 ACTGGGAAAATCTTGGACAAATTCCCAATT 22 20 0 TCTTGGACAA 0.476844 -99 CCCCAGTCAAACCCAGACAAAGATAAGGTA 24 16 0 ACCCAGACAA 0.935707 -83 GCACCGGGAATCTCGGGCAAGTTTTATGCC 25 193 0 TCTCGGGCAA 0.854972 -48 ********** Masking position 9 Map Score: 11.8634 Number of sites scoring better than the average of aligned sites = 1119 Number in coding regions = 979 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 7 TTTTTGGCGGATTTTTGTCC 2 258 0 TTTTTGGCGG 0.964453 -10 CCCCCTAATTTTTTTGGGGGGGCAGGGGGC 5 90 1 TTTTTGGGGG 0.943427 -100 ACCACAAGAATTTTTGCTTGAAACATCAGA 6 203 1 TTTTTGCTTG 0.614371 -29 AGGTCTCAACTTTATGGGGGGAGCATGTTA 7 25 1 TTTATGGGGG 0.918717 -52 TGCTGGACTATTTATGGTGGGAAATCATTG 8 39 1 TTTATGGTGG 0.940739 -231 TTTGCCCAGGATTTTGCTGGCTAGTGTTAG 8 209 1 ATTTTGCTGG 0.799636 -61 ACTTTAGCCGTTTATGTTGCCCTATTTTTG 10 57 0 TTTATGTTGC 0.582932 -170 CGTATCACAATTTATGGCTGGTGGAAATAA 10 135 0 TTTATGGCTG 0.663736 -92 GAAATTAAGATTTATGGCGCAGAATTGGTT 11 40 0 TTTATGGCGC 0.90353 -125 TTGGCTAGGCTTTTTGCCGGAATATTACGG 11 95 1 TTTTTGCCGG 0.945035 -70 GTCTGGGTGAATTTTGGGGGCTAAAGATAA 15 70 0 ATTTTGGGGG 0.817653 -114 ATTACTGAAGATTTTGGTGGAAATAACACC 15 142 0 ATTTTGGTGG 0.862972 -42 CACCTTTAAATTTTTGTTGCTCCCAATGGC 16 160 1 TTTTTGTTGC 0.673438 -85 CCAAAGAAGATTTTTGCTGCGATCCCCAAG 25 152 1 TTTTTGCTGC 0.883171 -89 TCGGGCAAGTTTTATGCCGCCGACGTTAGC 25 181 0 TTTATGCCGC 0.855807 -60 ********** Masking position 5 Map Score: 13.8591 Number of sites scoring better than the average of aligned sites = 1052 Number in coding regions = 936 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 8 CAAATTTGGGGGGTCAGGGGGGCTTTTCAA 2 144 1 GGGTCAGGGG 0.86503 -124 TTTTTTTGGGGGGGCAGGGGGCGTTTGAAA 5 98 1 GGGGCAGGGG 0.991249 -92 GGTGATGGGGCAGAGGGGATTTGCAG 6 7 1 GGGGCAGAGG 0.881804 -225 TAAGTTTTCATGGGCAGGACGATAGGTCGG 6 76 1 TGGGCAGGAC 0.651178 -156 TGCGCCGATATTGGCGCGGGAGAGTTGATC 8 94 0 TTGGCGCGGG 0.958834 -176 TTTGGGCAGGGCAACAAGCGGG 10 215 0 TGGGCAGGGC 0.970582 -12 ACCTAAAAAGTGGGCAGTGGGAGGGTACTG 12 138 0 TGGGCAGTGG 0.840888 -85 GCGGGAATTGGTGGAGGGGGAAGAAAAGTT 13 77 0 GTGGAGGGGG 0.906624 -31 GGAGCAAAAGTTGGAACGGGAAGATTGTCT 14 167 1 TTGGAACGGG 0.909004 -66 TAGTTCCAGTGTGGGACGGCCCTTACCTGG 17 82 1 GTGGGACGGC 0.723155 -68 CGTAAAGCGTTTGGCGCGGCCAAT 18 5 0 TTGGCGCGGC 0.905457 -185 GCCTGCGGATGGGGAACGGTGGTCAGACCC 20 42 1 GGGGAACGGT 0.670092 -259 CGGTCTGATCTTAGCGGGGGAAGGAGATTT 22 79 0 TTAGCGGGGG 0.600194 -40 AGTAAATGCGGGGAACGGGACCCATTTTT 25 10 1 GGGGAACGGG 0.962656 -231 ACTCAGAGCCTTGGCACCGGGAATCTCGGG 25 206 0 TTGGCACCGG 0.789993 -35 ********** Masking position 3 Map Score: 10.7323 Number of sites scoring better than the average of aligned sites = 2789 Number in coding regions = 2583 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 9 ATTTATTGTCATCTCAGACCGTGATTTAAGTATT 1 145 1 ATAACCGTGA 0.964612 -49 TTAGGTAGCAAGATAAGACCTTACAAACCGGCTC 2 61 0 ATAACCTTAC 0.753884 -207 TTAGGGGGCAAAATAAAACCTTTCAAAAAAACTC 5 23 0 ATAACCTTTC 0.925463 -167 TGCCCATGAAAACTTAGACCGTTCAACGACGGAC 6 58 0 ATAACCGTTC 0.941125 -174 CCGGGTTGGGAATTGAAACCTTGATCCGACCTAT 6 97 0 ATAACCTTGA 0.954898 -135 AAGACTAGCAACATTAGACCCTGAGCACC 11 6 0 ATAACCCTGA 0.934413 -159 ATAAATCTTAATTTCAGCCCGTTAACCCCAAACT 11 55 1 ATACCCGTTA 0.762971 -110 GACAGCCCCAAAGTGATACCCTTAAAGATGGCAA 14 74 0 ATAACCCTTA 0.899335 -159 TCTATATCAGACATGAAACCTTGCAATTAACTTG 21 20 1 ATAACCTTGC 0.951923 -202 TCCCCCGCTAAGATCAGACCGTTATAAAAAAGGC 22 88 1 ATAACCGTTA 0.944729 -31 GGAAATCAGTAAATCACACCTTGAGGGATGGATA 25 46 1 ATAACCTTGA 0.954898 -195 * * * ******* Masking position 6 Map Score: 7.87086 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 43 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 CTCTGCAATTCTGGGGGATTTCGCCTCTCTT 2 107 1 CTGGGGATTT 0.854681 -161 GCTATCGCTACTGTCTGAATTTTATTTCCAC 10 114 1 CTGCTGAATT 0.912812 -113 CAATTTATGGCTGGTGGAAATAAAATTCAGA 10 127 0 CTGTGGAAAT 0.770943 -100 TTGGGGTTAACGGGCTGAAATTAAGATTTAT 11 55 0 CGGCTGAAAT 0.761625 -110 AGAACCTGTGCTGTCTGCATTAAAAATGCTC 12 185 0 CTGCTGCATT 0.815721 -38 GGCGATCGCCTGCGGGAATTGGTGGAGGGG 13 88 0 CTGGGGAATT 0.971337 -20 GGAAGATTGTCTGCGGGCAATTGCGAGAACT 14 185 1 CTGGGGCAAT 0.942157 -48 CATTTCTTGTCTGGGTGAATTTTGGGGGCTA 15 77 0 CTGGTGAATT 0.948819 -107 GATTTAACCCATGGGGGAAATGCTGGTGTTA 15 118 1 ATGGGGAAAT 0.805263 -66 CTGTAATTACCTGGGTGATATTTTC 19 5 0 CTGGTGATAT 0.785295 -212 GGCGACTTTTCTGTGGGCATTTTCAACGTCA 20 176 0 CTGGGGCATT 0.93476 -125 AATGGGACTAATGGGGGAATTTTTCGCCATA 20 229 0 ATGGGGAATT 0.784368 -72 GGGGATTATTCTGGCTGAAAGTGTTACAAAC 24 55 1 CTGCTGAAAG 0.617559 -44 CCCATTTTTCCGGGCGGAAATCAGTAAATCA 25 31 1 CGGCGGAAAT 0.853814 -210 TGCCAAGGCTCTGAGTTAAATAAAAACGAGA 25 220 1 CTGGTTAAAT 0.543887 -21 *** ******* Masking position 3 Map Score: 11.2975 Number of sites scoring better than the average of aligned sites = 1147 Number in coding regions = 1004 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 11 AAATTAGGAAGCAAGGGGGCTTATCCAGTT 2 220 1 GCAAGGGGGC 0.95528 -48 GGTGATGGGGCAGAGGGGATTTGCAGAAA 6 10 1 GCAGAGGGGA 0.975743 -222 TTTGCAGAAAGCAGAGGGGCCTGCCTCGGT 6 30 1 GCAGAGGGGC 0.970702 -202 GTAGGCGATCGCCGTGGTGAACCACAAGAA 6 183 1 GCCGTGGTGA 0.85612 -49 AAAAAGCCTAGCCAAGGGAAAAGTTTGGGG 11 80 0 GCCAAGGGAA 0.857511 -85 ATAGGCGATCGCCGGGGGGAGGTTTTGGAG 14 141 1 GCCGGGGGGA 0.984965 -92 ATAATCCTTTGCCATTGGGAGCAACAAAAA 16 170 0 GCCATTGGGA 0.822097 -75 CCTGGGTTAAGCCAAGGGGAAGGTCTCAAA 19 137 0 GCCAAGGGGA 0.983962 -80 GTTGAAAGCCGCAATGGGGCCTTAGGATGA 19 166 1 GCAATGGGGC 0.951896 -51 ********** Masking position 2 Map Score: 9.48676 Number of sites scoring better than the average of aligned sites = 780 Number in coding regions = 677 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 12 CAGATCCTTGGTTGCTACCTTTTC 3 43 0 TCCTTGGTTG 0.849742 -14 GAAGGAACATTTCTTGTCTGGGTGAATTTT 15 85 0 TTCTTGTCTG 0.814561 -99 CAAGAAATGTTCCTTCGCTGATTTAACCCA 15 99 1 TCCTTCGCTG 0.945381 -85 CCATTCAAATTCATTGGCTGTTGCCATGGC 19 54 1 TCATTGGCTG 0.954984 -163 AATTTGCTGATCATTGCCTG 20 1 0 TCATTGCCTG 0.857653 -300 CCCAATATTCTCCTACTCTGACGTTGAAAA 20 158 1 TCCTACTCTG 0.901797 -143 TAAGTTAGAATCCTAGTCTGATCGAAAGTA 21 198 1 TCCTAGTCTG 0.971705 -24 TCCAAGATTTTCCCAGTCTGCCAAAGGGGG 22 33 1 TCCCAGTCTG 0.877479 -86 CAGGTCTGTTTCATAGGCTGTCGACTTTTC 23 41 1 TCATAGGCTG 0.935444 -181 CTCTACCTTATCTTTGTCTGGGTTTGACTG 24 13 1 TCTTTGTCTG 0.867047 -86 ********** Masking position 9 Map Score: 5.29538 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 268 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 13 CTTGTTCCTTTTACCCTAGTTTTTCTGCGCC 8 118 0 TTACCCTGTT 0.844379 -152 CTAAACCCAGTCACCCCTTTTAAGCCCCAGC 9 47 0 TCACCCCTTT 0.755444 -43 GCCGTTTATGTTGCCCTATTTTTGATTGAAT 10 50 0 TTGCCCTTTT 0.964143 -177 ACAAGCGGGTTTACCCTATTTAAATTCCGCT 10 193 0 TTACCCTTTT 0.933938 -34 TCAGCCTTTTTCACCATTTCTTTCTTTTTGA 12 62 0 TCACCATTCT 0.752619 -161 TTGGTCAAATTTGCCATCTTTAAGGGTATCA 14 64 1 TTGCCATTTT 0.908079 -169 ATAGCAATAGTTGCCCTGTTTTATTCCCCAT 15 31 1 TTGCCCTTTT 0.964143 -153 ACTTTTTTGATCACCCAATTTATTAATAGTT 16 208 0 TCACCCATTT 0.786105 -37 TCATTGGCTGTTGCCATGGCTTCTTCCTCAG 19 64 1 TTGCCATGCT 0.703678 -153 GGGGAATTTTTCGCCATATTTCTATCTATTG 20 216 0 TCGCCATTTT 0.902332 -85 GATTCAACTATTGCCCATTCTGCATCGCTCA 23 12 1 TTGCCCATCT 0.823988 -210 ******* *** Masking position 1 Map Score: 4.17095 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 415 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 14 TCCGATGACTGCAAGGTTTTGCCATT 4 6 0 GCAAGTTTTG 0.941359 -23 GGCAAAGTTTTAGAGTTTTTTT 5 2 1 GCAAGTTTTA 0.973909 -188 GAGTTTTTTTGAAAGGTTTTATTTTGCCCCC 5 23 1 GAAAGTTTTA 0.746298 -167 AAATAGTCCAGCACTGTTCTAGACCGAAGGC 8 21 0 GCACGTTCTA 0.878545 -249 AGGAACAAGAGCAAGGTTCTACTCCGTCTCC 8 140 1 GCAAGTTCTA 0.954278 -130 TCCTTTTCCAGCAAAGTTCTCGCAATTGCCC 14 199 0 GCAAGTTCTC 0.829822 -34 AGCAATAGTTGCCCTGTTTTATTCCCCATCA 15 33 1 GCCCGTTTTA 0.914122 -151 TTTTTTCTGGGCCATGTTTTTGAAAGGTTGC 19 101 1 GCCAGTTTTT 0.828817 -116 TTGAAAGGTTGCAACGTTTTGAGACCTTCCC 19 120 1 GCAAGTTTTG 0.941359 -97 CAAGTTAATTGCAAGGTTTCATGTCTGATAT 21 23 0 GCAAGTTTCA 0.865031 -199 AGGCACTCGGGCCAGGTTTTATCCATCCCTC 25 68 0 GCCAGTTTTA 0.968467 -173 GGGAATCTCGGGCAAGTTTTATGCCGCCGAC 25 187 0 GGCAGTTTTA 0.781979 -54 **** ****** Masking position 7 Map Score: 10.0424 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 120 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 15 ATGGCGACCTTTCAGCCCTTCTTTCGACGA 2 20 0 TTCAGCCCTT 0.647995 -248 GCTACCTTTTCTCTACCCTTAAATCCGATT 3 24 0 CTCTACCCTT 0.882341 -33 AGGCAGGCCCCTCTGCTTTCTGCAAATCCC 6 26 0 CTCTGCTTTC 0.679341 -206 AGCCGGAGGTCTCAACTTTATGGGGGGAGC 7 19 1 CTCAACTTTA 0.541894 -58 ATACGGTCTTTTTTACTTTTTAGATACATG 10 160 1 TTTTACTTTT 0.482461 -67 TTGGGTCATCCTCAGCCTTTTTCACCATTT 12 74 0 CTCAGCCTTT 0.918671 -149 TCAGTTCAACTTCTACTTTTACTCAACTTT 13 53 1 TTCTACTTTT 0.782421 -55 TCTACTTTTACTCAACTTTTCTTCCCCCTC 13 64 1 CTCAACTTTT 0.852759 -44 TACGAATTATTTTAGCCTTTACTGATAATT 16 45 1 TTTAGCCTTT 0.509084 -200 TGTTATTGATCTTTACTTTTTTGATCACCC 16 223 0 CTTTACTTTT 0.724698 -22 CAGTTTTTTGCTTTACCTTTACCGCTGTTG 17 119 1 CTTTACCTTT 0.808592 -31 CGCCTCTGCCTTTTTTATAACGG 22 106 0 CTCTGCCTTT 0.951934 -13 CTTTGTCTCCTTCTGCTCTTACTCTTAGTT 23 76 1 TTCTGCTCTT 0.667908 -146 AACTCTACCTTATCTTTGTCTG 24 3 1 CTCTACCTTA 0.768962 -96 ********** Masking position 2 Map Score: 3.6692 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 439 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983