AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_synecho_reg_100.orf -o00710_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 sll0938 40 aspartate transaminase. [EC:2.6.1.1] #2 ssl1792 33 hypothetical protein. #3 sll0936 83 hypothetical protein. #4 slr0969 102 cbiH; precorrin methylase. #5 sll1070 122 tktA; transketolase. [EC:2.2.1.1] #6 sll1275 187 pykF; pyruvate kinase. [EC:2.7.1.40] #7 sll0807 152 rpe; ribulose-phosphate 3-epimerase (pentose-5-phosphate 3- #8 sll0920 300 ppc; phosphoenolpyruvate carboxylase. [EC:4.1.1.31] #9 slr0943 121 fda; fructose-bisphosphate aldolase. [EC:4.1.2.13] #10 slr0952 206 fbp; fructose-1,6-bisphosphatase (D-fructose-1,6-bisphosphate 1- #11 sll1525 300 prk, ptk; phosphoribulokinase (phosphopentokinase) (PRK). #12 slr0394 268 pgk; phosphoglycerate kinase. [EC:2.7.2.3] [SP:PGK_SYNY3] #13 sll0325 222 hypothetical protein. #14 sll0018 283 fda; fructose-bisphosphate aldolase. [EC:4.1.2.13] [SP:ALF_SYNY3] #15 slr0009 201 rbcL; ribulose bisphosphate carboxylase large chain precursor. #16 slr0012 300 rbcS; ribulose bisphosphate carboxylase small chain. [EC:4.1.1.39] #17 sll0006 103 aspC; aspartate aminotransferase. [EC:2.6.1.1] #18 sll0402 122 aspC; aspartate aminotransferase. [EC:2.6.1.1] #19 slr0194 55 rpiA; ribose 5-phosphate isomerase. [EC:5.3.1.6] #20 slr0195 35 hypothetical protein. #21 slr0197 103 comE ORF1. #22 sll0587 42 pyk1; pyruvate kinase 1. [EC:2.7.1.40] [SP:KPY1_SYNY3] #23 sll0586 300 hypothetical protein. #24 sll0034 62 hypothetical protein. #25 sll0033 160 hypothetical protein. Motif number 1 CCCTACCTCACTCCGCATCCCAGGCTACAGC 8 203 0 CTCGCATCCC 0.763589 -98 TGAAACTTGCCCCTGCCATCCTCTTGTCTGA 9 39 0 CCTGCCATCC 0.909639 -83 ACTTTGAACACTATTCCCCCCAGAATTGGGG 10 126 1 CTTTCCCCCC 0.990319 -81 TTAAAAGCCCCCTAGCCCCCCAATTCTGGGG 10 143 0 CCAGCCCCCC 0.981396 -64 TAGTCATAGGGCGCGCCCCCCCTTGAATCGG 11 16 1 GCCGCCCCCC 0.908421 -285 TCTAGTCATCCTGGTCAACCCCAGATAACGC 11 134 0 CTGTCAACCC 0.758168 -167 TAGAAAATTTCTCCTCACCCCAGATGGCGTG 11 237 0 CTCTCACCCC 0.972992 -64 CGGAGTCAACCCCCTCCATCCCTGATCCTTA 13 28 0 CCCTCCATCC 0.900153 -195 AGTTTGGGAGCTTTTCCACCCTTGGTCAAAC 13 99 0 CTTTCCACCC 0.97489 -124 GGTTCTATATCTCTTCCCCCCGGCAATAGGC 14 29 0 CTTTCCCCCC 0.990319 -255 AAAATTTTCTCCATTCAACCCTTATTTTCAA 16 42 1 CCTTCAACCC 0.938529 -259 TGGCGTCACACTTTTCCCCCTGGGGAGCAGA 23 65 1 CTTTCCCCCT 0.905075 -236 ACGTAAGTTTCCGTTCACTCCTCACACCACA 23 131 0 CCTTCACTCC 0.889584 -170 AAACTTACGTCTCCGCCCTCTTCATTGTACA 23 152 1 CTCGCCCTCT 0.688864 -149 GGCAAAAACCCTATGCCCCCCGTCCCAACCT 23 182 0 CTTGCCCCCC 0.991482 -119 GAAAATGGATCTAATCACCCCAAAAATCCCT 23 246 0 CTATCACCCC 0.933698 -55 CACTCGATCGCCGAGCCACCCCCTACTGAAT 25 47 0 CCAGCCACCC 0.952429 -114 ** ******** Masking position 6 Map Score: 24.0849 Number of sites scoring better than the average of aligned sites = 1666 Number in coding regions = 1458 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 2 TGGAAAATACTCCCGGTCAACGGACTCACTTCT 4 10 1 CTCCCGGCGG 0.975868 -93 CTACCATCTTCCCACGGTTCGGGAAATTTTTCGG 5 15 0 CCCACGGGGA 0.851464 -108 GGGTCAATATCCACCGGGGGGCGGTAATGGTAGG 5 69 0 CCACCGGCGG 0.932833 -54 TCTTCTTCCTCCCCCTGCTCCAGGGGTTTTTTTC 8 134 1 CCCCCTGAGG 0.952197 -167 GTCGATGCCCCTCCCAGATTAGGGCAGAAAAAAA 8 160 0 CTCCCAGGGG 0.958748 -141 AACACTATTCCCCCCAGAATTGGGGGGCTAGGGG 10 132 1 CCCCCAGGGG 0.942702 -75 AGGGCGCGCCCCCCCTTGAATCGGTCAATCTTGT 11 23 1 CCCCCTTCGG 0.949882 -278 TATAGCCTGACCCTCTGAATACTGAGTATGAATT 11 80 0 CCCTCTGCTG 0.80029 -221 GGCTTGTTAACCCCCTGTCAAGGGCCGAAGGAAA 11 178 0 CCCCCTGGGG 0.986729 -123 CATTATATCGCCCCGAGAAAAGTGCATCAATAAC 12 81 0 CCCCGAGGTG 0.796069 -188 CAGCTTCAAGCCCTGGGGAAAGGGAAGTCCGGCT 13 167 1 CCCTGGGGGG 0.894131 -56 ATATCTCTTCCCCCCGGCAATAGGCGATCGGGGA 14 20 0 CCCCCGGAGG 0.979307 -264 TCAGCCAAAACCCACTGCTTACTGATGTTCAACT 15 41 0 CCCACTGCTG 0.800261 -161 CAACAAAAAACCCGCGGGAGCGGGCTAACATTGA 16 239 1 CCCGCGGGGG 0.74137 -62 TCAATTCCAGCTCCCTTGCTGGGGTTGGCATGCT 18 42 1 CTCCCTTGGG 0.83688 -81 TCACACTTTTCCCCCTGGGGAGCAGATAAGAAGA 23 70 1 CCCCCTGGCA 0.766483 -231 ******* *** Masking position 1 Map Score: 19.567 Number of sites scoring better than the average of aligned sites = 1369 Number in coding regions = 1228 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 TAGAAGTGAGTCCGTTGACCGGGAGTATTTTCC 4 12 0 TCCTTGCGGG 0.983984 -91 CTACCATCTTCCCACGGTTCGGGAAATTTTTCG 5 16 0 CCCCGGCGGG 0.967717 -107 CAGAAAAAAACCCCTGGAGCAGGGGGAGGAAGA 8 137 0 CCCTGGCAGG 0.965534 -164 GGCGCGCCCCCCCTTGAATCGGTCAATCTTGTA 11 25 1 CCCTGACGGT 0.809298 -276 TTTCCTTCGGCCCTTGACAGGGGGTTAACAAGC 11 178 1 CCCTGAGGGG 0.82215 -123 AAAAAGTTATCCCGTGGTCCAGTCTGCAAACTG 12 209 1 CCCTGGCAGT 0.95067 -60 AGCCGGACTTCCCTTTCCCCAGGGCTTGAAGCT 13 168 0 CCCTTCCAGG 0.889151 -55 TCCCCGATCGCCTATTGCCGGGGGGAAGAGATA 14 20 1 CCTTTGGGGG 0.704636 -264 TAGCACAAATTCCTTGGGGCAGGACAAAAAAGA 14 156 1 TCCTGGCAGG 0.982598 -128 TACGGCCCTGTTCTTTGGACAGTTTTTGTATAA 16 170 0 TTCTTGCAGT 0.684457 -131 CTTTTATTGTCTCATTGACCGGCACTGGCTTGA 17 56 0 CTCTTGCGGC 0.842602 -48 CAATTCCAGCTCCCTTGCTGGGGTTGGCATGCT 18 43 1 TCCTTGGGGG 0.955394 -80 ATTCTAATTCTCTTGGCCCAGGAGTTTTGCAA 20 10 1 CTCTGGCAGG 0.971167 -26 ATAACTCACATCCTTTGGCCGGGAAATTTATGA 21 56 0 TCCTTGCGGG 0.989236 -48 TTATTGCTGTTTCCTTGGTCGGGATTTTT 21 85 1 TTCTTGCGGG 0.963944 -19 CTCCGCCCTCTTCATTGTACAGGTTGGGACGGG 23 162 1 TTCTTGCAGG 0.928744 -139 *** *** **** Masking position 12 Map Score: 20.363 Number of sites scoring better than the average of aligned sites = 1453 Number in coding regions = 1337 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 4 CCTGCCTTGGCCCCTACCATTACCGCCCCCCGGT 5 57 1 CCCTACATCC 0.900352 -66 GGAAAAATTGCCCAAAGCCCAGCCTACCATCGTT 6 41 1 CCCAACCCCC 0.993969 -147 ATTTAACTGCCCCTAATTTCAGCCCATT 6 170 1 CCCAATTCCC 0.948661 -18 TGTAGTAGGCCCCCAAACCCGGCCTTTAAAATAG 7 61 0 CCCAACCCCC 0.993969 -92 CTAAGGGGCACCCGAATCACAACACGGTGAAACT 9 63 0 CCCAACACCA 0.79032 -59 TGTTCAAAGTCCCCCAAATTTGCCGGAGCTTTAG 10 102 0 CCCCAATTCC 0.861356 -105 TTTTAAAAGCCCCCTAGCCCCCCAATTCTGGGGG 10 142 0 CCCTACCCCA 0.918605 -65 GCCAACTTTCCCCGAAAACTAACCT 12 2 0 CCCAAACTCC 0.950684 -267 AACTTGATTACCCAAAACCTTCCCCCATCCTGGA 14 62 1 CCCAACCTCC 0.987313 -222 TTGAATTCGACCCGTATTTTTACCCCCACCCTAG 14 117 0 CCCTATTTCC 0.837259 -167 TATAATGTTGACCGCATCCTGACCGGATTTTTTA 16 141 0 ACCCACCTCC 0.771321 -160 CATTCCCTTAATTCCTCCTCAGTAAGTT 22 5 1 CCCTATTCCC 0.915931 -38 GAAGAAACCGCCCGAACATCATCCAGGCGGAGTG 23 99 1 CCCAAATCCC 0.948661 -202 AACCCTATGCCCCCCGTCCCAACCTGTACAATGA 23 173 0 CCCCGCCCCC 0.944803 -128 *** ** *** ** Masking position 3 Map Score: 16.5761 Number of sites scoring better than the average of aligned sites = 1049 Number in coding regions = 970 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 5 CGTTGGAGATCGCCATCCTGGTCGGGCTAAA 3 24 1 CGCATCCTGG 0.963682 -60 CGAAAAATTTCCCGAACCGTGGGAAGATGGT 5 16 1 CCCAACCGTG 0.513905 -107 CAACTGAAACGGCGATCGTGGCGGATAATGA 6 92 1 GGCATCGTGG 0.940505 -96 CTATGGTTGCGGTGATTTTGGCTTTTAGTGT 8 91 1 GGTATTTTGG 0.577825 -210 TTTTTTCTGCCCTAATCTGGGAGGGGCATCG 8 161 1 CCTATCTGGG 0.816732 -140 CTAAAGCTCCGGCAAATTTGGGGGACTTTGA 10 102 1 GGCAATTTGG 0.742215 -105 CCCCTAGCCCCCCAATTCTGGGGGGAATAGT 10 135 0 CCCATTCTGG 0.751189 -72 AACCGAAGAGCGTTATCTGGGGTTGACCAGG 11 125 1 CGTATCTGGG 0.906298 -176 CTCTCCAACACGCCATCTGGGGTGAGGAGAA 11 229 1 CGCATCTGGG 0.982672 -72 TGGAAAAGCTCCCAAACTTGGCAAAAATGAG 13 112 1 CCCAACTTGG 0.852447 -111 CCCGGCAATAGGCGATCGGGGATCAAACAGT 14 11 0 GGCATCGGGG 0.962143 -273 CAAAACCTTCCCCCATCCTGGACTTGGTTAA 14 74 1 CCCATCCTGG 0.924444 -210 ATTGCCTAATGGGTATTTGGGTCGCAAGACA 14 246 0 GGGATTTGGG 0.563507 -38 TACCAAGGCAATTTGGGGACGTAACCT 17 87 0 GGCATTTGGG 0.929268 -17 AAAAGTGTGACGCCAACTGTGACAAAAGATG 23 49 0 CGCAACTGTG 0.757819 -252 GCAGTTGGCGATCGTTGCAGCTCATTG 24 46 0 GGCATCGTTG 0.708573 -17 *** ******* Masking position 5 Map Score: 11.1489 Number of sites scoring better than the average of aligned sites = 1931 Number in coding regions = 1803 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 6 CTGGTCGGGCTAAACCCGTTAAGCTAGAGAGCGTA 3 41 1 TAAACCAACT 0.733821 -43 GAGCGGTGCTCAAGCCCTCTAATCCCATAATTTTC 4 58 0 CAAGCCAACC 0.973077 -45 AGCAAACCCATCAAACTGTGCAGACTA 6 3 1 CAAACCAACT 0.95202 -185 CTACCTTCGTCAAACCCTGGAAACTTTAGCTTACT 8 29 1 CAAACCAACT 0.95202 -272 ACCCGAATCACAACACGGTGAAACTTGCCCCTGCC 9 53 0 CAACCGAACT 0.954577 -69 CCGCCGGAGTCAACCCCCTCCATCCCTGATCCTTA 13 28 0 CAACCCCACC 0.929613 -195 TAAAAATTGTCAAGGCGCAGAAACTAGCCTAAGAT 14 193 1 CAAGCGAACT 0.91547 -91 TTAGCAGACTCAACCCCGAAGAACTGTTCATCCTT 15 140 1 CAACCCGACT 0.919363 -62 CGGACGAGTACAACTCCGACAATCCAAACACCGGT 15 177 1 CAACCCAACC 0.985942 -25 CGATTTAGATCAACACGATTAAGCTCAGT 18 5 0 CAACCGAACT 0.954577 -118 ATGGATCTAATCACCCCAAAAATCCCTTTAAAAAA 23 238 0 TCACCCAACC 0.771536 -63 TTTGCCCTAACCAGACCAAGAAACC 25 146 1 CCAGCCAACC 0.926068 -15 **** ** ** ** Masking position 12 Map Score: 10.746 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 303 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 AAATACTCCCGGTCAACGGACTCACTTCTA 4 15 1 GGTCAACGGA 0.745271 -88 TAATGGTAGGGGCCAAGGCAGGCCAAATTG 5 49 0 GGCCAAGGCA 0.962589 -74 CGGCTTACAGGGCCAACGATGGTAGGCTGG 6 59 0 GGCCAACGAT 0.827688 -129 CCCTGTCAAGGGCCGAAGGAAAACTAATCC 11 170 0 GGCCGAAGGA 0.866389 -131 TTGCAGACTGGACCACGGGATAACTTTTTT 12 208 0 GACCACGGGA 0.894106 -61 ATGACGGTTTGACCAAGGGTGGAAAAGCTC 13 93 1 GACCAAGGGT 0.916805 -130 TACAAAAACTGTCCAAAGAACAGGGCCGTA 16 173 1 GTCCAAAGAA 0.689221 -128 AAAACTCCTGGGCCAAGAGAATTAGAAT 20 9 0 GGCCAAGAGA 0.953755 -27 TAAATTTCCCGGCCAAAGGATGTGAGTTAT 21 59 1 GGCCAAAGGA 0.974209 -45 AAAAATCCCGACCAAGGAAACAGCAATAA 21 85 0 GACCAAGGAA 0.962769 -19 GGCACAATGGGGCCAAGCAATGAGCTGCAA 24 29 1 GGCCAAGCAA 0.901128 -34 GCCCTAACCAGACCAAGAAACC 25 149 1 GACCAAGAAA 0.799355 -12 ********** Masking position 4 Map Score: 6.74507 Number of sites scoring better than the average of aligned sites = 1017 Number in coding regions = 922 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 8 GCATCGACAAATCGCTGGCTGTAGCCTGGG 8 186 1 ATCGCTGGCT 0.953452 -115 CTCACTCCGCATCCCAGGCTACAGCCAGCG 8 198 0 ATCCCAGGCT 0.95074 -103 ACAAAGTTGAATCTCCGGCGTTAGAGTATG 10 36 1 ATCTCCGGCG 0.91003 -171 GTCAGGCTATATCTCTGGCTAGAACCGAAG 11 103 1 ATCTCTGGCT 0.982451 -198 GGATGACTAGATCTCAGGATTAGTTTTCCT 11 154 1 ATCTCAGGAT 0.936926 -147 TATGGGTCTCATCTTAGGCTAGTTTCTGCG 14 208 0 ATCTTAGGCT 0.878355 -76 ACCAACCTTTATCTCTGGATTTCACTGGAA 23 274 0 ATCTCTGGAT 0.938206 -27 ********** Masking position 1 Map Score: 3.68833 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 84 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GACGCCCAAGTGCGCCACTACCTTCGTCAAACCCTGG 8 12 1 TGCCCTTCGT 0.826508 -289 TTCCTCCCCCTGCTCCAGGGGTTTTTTTCTGCCCTAA 8 139 1 TGCCCGTTTT 0.987719 -162 CATCCCAGGCTACAGCCAGCGATTTGTCGATGCCCCT 8 182 0 TACGCGTTGT 0.771411 -119 CCGAGAAAAGTGCATCAATAACATTTTTGAATAATGG 12 66 0 TGCTCTTTTT 0.638802 -203 TTTTTTGTCCTGCCCCAAGGAATTTGTGCTAGGGCAT 14 150 0 TGCCCGTTGT 0.990435 -134 GGCTAGTTTCTGCGCCTTGACAATTTTTAACGATCTT 14 185 0 TGCCCGTTTT 0.987719 -99 TGCTGTTGTTTACCCCAGGGATGTTTTGATT 18 102 1 TACCCGTTTT 0.940609 -21 GGCGATCGAGTGCTCCCTGTTTTTTTGGCGGCAAAAC 25 66 1 TGCCCGTTTG 0.949474 -95 TTAGTTGGATTGCTCCGTGTCCGTTGTTAACTTTTTG 25 113 1 TGCCCGTTGT 0.990435 -48 *** ** * **** Masking position 14 Map Score: 3.92741 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 120 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 GAATAGTAGATTTTTTGCCA 2 24 1 TTTTTTGCCA 0.962426 -10 ATTGCTAGTTTATTTTTCCAAACATT 5 107 1 TATTTTTCCA 0.890431 -16 GCTTTGGGCAATTTTTCCCAATAGTCTGCA 6 29 0 ATTTTTCCCA 0.750279 -159 AGGAATAGTTTATTATGCCAACTTTCCCCG 12 22 0 TATTATGCCA 0.745248 -247 ACGAGAAAAATCTTTTTCCAGTATCATCTA 12 242 1 TCTTTTTCCA 0.785451 -27 AGTAGTTCTCATTTTTGCCAAGTTTGGGAG 13 120 0 ATTTTTGCCA 0.87685 -103 TGATTAACAATTTTTTGACAATTGCCAATG 15 72 1 TTTTTTGACA 0.691151 -130 ATCCCTTCTATTTTCCCACCTTGACTCT 19 9 1 TATTTTCCCA 0.897675 -47 CGTTTCCAATTTATTTGCCATTGTTTAAAC 21 18 1 TTATTTGCCA 0.782804 -86 AGTTTCACGATATTTTTCCATACAGGG 23 8 0 TATTTTTCCA 0.890431 -293 ********** Masking position 6 Map Score: 3.98719 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 410 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 11 CCCTACCATTACCGCCCCCCGGTGGATATTG 5 68 1 ACCCCCCCCG 0.990761 -55 GAGAATATTTCCCTAACACCGCTTAAAAGCA 6 121 1 CCCAACACCG 0.902824 -67 GTAGTAGGCCCCCAAACCCGGCCTTTAAAAT 7 63 0 CCCAACCCGG 0.785899 -90 ATTGTCTTCTTCCTCCCCCTGCTCCAGGGGT 8 130 1 TCCCCCCCTG 0.883778 -171 GATTATCCCTACCTCACTCCGCATCCCAGGC 8 209 0 ACCCACTCCG 0.96327 -92 AGAAAATTTCTCCTCACCCCAGATGGCGTGT 11 236 0 TCCCACCCCA 0.879997 -65 GTTCTATATCTCTTCCCCCCGGCAATAGGCG 14 28 0 TCTCCCCCCG 0.955673 -256 TAGTTAGCAGACTCAACCCCGAAGAACTGTT 15 137 1 ACTAACCCCG 0.91255 -65 ACTCCGACAATCCAAACACCGGT 15 189 1 TCCAACACCG 0.918077 -13 CACTCCTCACACCACACTCCGCCTGGATGAT 23 116 0 ACCCACTCCG 0.96327 -185 CAAATACGGAACTCCCCACCGGCAAAAACCC 23 202 0 ACTCCCACCG 0.896965 -99 *** ******* Masking position 7 Map Score: 8.85492 Number of sites scoring better than the average of aligned sites = 714 Number in coding regions = 664 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 12 GAGAGCGTATTTGTTTAGACATCAGCC 3 67 1 TTGTTTAGAC 0.860992 -17 TTAAATATAATAGTTAAGGCCGTCTGCTTT 6 146 0 TAGTTAAGGC 0.885663 -42 TTGACCGTAATTGTTTACACTGAATTTCAA 7 96 1 TTGTTTACAC 0.807265 -57 GCCGGAGCTTTAGTGAAGACATTTGGAGAG 10 85 0 TAGTGAAGAC 0.685834 -122 GCCTATGGGCTTGTTAACCCCCTGTCAAGG 11 189 0 TTGTTAACCC 0.936013 -112 GCAAAACTGATTGTTAACCCGGTTTCCTAG 11 265 0 TTGTTAACCC 0.936013 -36 TCGTTAAAAATTGTCAAGGCGCAGAAACTA 14 189 1 TTGTCAAGGC 0.726001 -95 GACTAACTGTTAGTTAAGCCGCTGTTAATG 15 101 1 TAGTTAAGCC 0.936789 -101 TTTTTTGCTGTTGTTTACCCCAGGGATGTT 18 97 1 TTGTTTACCC 0.869277 -26 ACCTTGACTCTAGTTAAGACGATGGAGTTG 19 28 1 TAGTTAAGAC 0.903314 -28 ********** Masking position 4 Map Score: 5.38885 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 100 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 13 CTAGGACACTAAAAGCCAAAATCACCGCAAC 8 96 0 AAAGCCAAAA 0.927292 -205 CATCCCTCAAAAATGCAAAACTGATTGTTAA 11 278 0 AATGCAAAAC 0.869963 -23 AAAATTGTTAATCAGCCAAAACCCACTGCTT 15 55 0 ATAGCCAAAA 0.801203 -147 ACTATAGGTAATCAGCAACACAATACGGCCC 16 195 0 ATAGCAACAC 0.695327 -106 GTCACTGTGAAAAAGCAACAAAAAACCCGCG 16 224 1 AAAGCAACAA 0.897496 -77 GTTTTTTAGTAATTGCCAAAACTGTAAC 16 283 1 AATGCCAAAA 0.869961 -18 TGGGGTAAACAACAGCAAAAAATGGCTAAGG 18 88 0 AAAGCAAAAA 0.939254 -35 CAATTGCAAAACTCCTGGGCCA 20 24 0 AATGCAAAAC 0.869963 -12 CGACCAAGGAAACAGCAATAACTCACATCCT 21 75 0 AAAGCAATAA 0.762472 -29 ** ******** Masking position 8 Map Score: 1.31005 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 182 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 14 TCAGGCTATATCTCTGGCTAGAACCGAAGAG 11 104 1 TCTTGGCTAG 0.963346 -197 AATGGAGAGTGCTATAGCTAGGAATAGTTTA 12 40 0 GCTTAGCTAG 0.919011 -229 ATGGGTCTCATCTTAGGCTAGTTTCTGCGCC 14 206 0 TCTAGGCTAG 0.974133 -78 TCAAAATTTTGCTGAGGCGAGATCAAGCCAG 17 34 1 GCTAGGCGAG 0.974506 -70 GCAAAAAATGGCTAAGGCTAGTCAGACAGAG 18 74 0 GCTAGGCTAG 0.988352 -49 *** ******* Masking position 3 Map Score: 0.765826 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 44 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 CCATCCTGGTCGGGCTAAACCCGTTAAGCTAGA 3 36 1 CGGCTAACCG 0.955951 -48 CTCCGCATCCCAGGCTACAGCCAGCGATTTGTC 8 191 0 CGGCTAACCA 0.97392 -110 GGCTATATCTCTGGCTAGAACCGAAGAGCGTTA 11 107 1 CGGCTAACCG 0.991019 -194 TGTTAACCCCCTGTCAAGGGCCGAAGGAAAACT 11 175 0 CGTCAAGCCG 0.871904 -126 TCTCTTCCCCCCGGCAATAGGCGATCGGGGATC 14 18 0 CGGCAAAGCG 0.965108 -266 AATTGTTAATCAGCCAAAACCCACTGCTTACTG 15 51 0 CGCCAAACCA 0.917668 -151 GAACTCCCCACCGGCAAAAACCCTATGCCCCCC 23 192 0 CGGCAAACCC 0.976114 -109 * ***** * *** Masking position 7 Map Score: 2.42594 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 142 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172