AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_synecho_reg_100.orf -o00330_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 slr1312 150 speA; arginine decarboxylase. [EC:4.1.1.19] #2 sll0227 205 ppiB; peptidyl-prolyl cis-trans isomerase B. [EC:5.2.1.8] #3 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #4 sll0938 40 aspartate transaminase. [EC:2.6.1.1] #5 ssl1792 33 hypothetical protein. #6 sll0936 83 hypothetical protein. #7 slr0969 102 cbiH; precorrin methylase. #8 sll1508 300 lpxC; UDP-3-0-acyl N-acetylglcosamine deacetylase. [EC:3.5.1.-] #9 slr1134 300 hypothetical protein. #10 sll1077 300 speB; agmatine ureohydrolase. [EC:3.5.3.11] #11 slr0877 207 amidase. [EC:3.5.1.4] #12 sll1425 168 proS; proline-tRNA ligase. [EC:6.1.1.15] [SP:SYP_SYNY3] #13 sll1561 300 putA; delta-1-pyrroline-5-carboxylate dehydrogenase. [EC:1.5.1.12] #14 sll0006 103 aspC; aspartate aminotransferase. [EC:2.6.1.1] #15 sll0402 122 aspC; aspartate aminotransferase. [EC:2.6.1.1] #16 sll0827 266 hypothetical protein. #17 slr0092 117 hisB; hypothetical protein. #18 sll0107 119 eda; 4-hydroxy-2-oxoglutarate aldolase. [EC:4.1.3.16] #19 sll0034 62 hypothetical protein. #20 sll0033 160 hypothetical protein. #21 sll0502 197 argS; arginyl-tRNA synthetase (arginine--tRNA ligase) (argRS). #22 sll0902 112 argF; ornithine carbamoyltransferase chain f. [EC:2.1.3.3] #23 sll0626 196 lim17; LIM17. #24 slr0662 82 speA; arginine decarboxylase. [EC:4.1.1.19] #25 sll0623 45 hypothetical protein. #26 sll0622 92 nadA; quinolinate synthetase. [EC:4.6.1.3] [SP:NADA_SYNY3] #27 sll0621 284 dsbD; thiol:disulfide interchange protein DsbD. #28 slr0585 118 argG; argininosuccinate synthase (citrulline--aspartate ligase). #29 sll0572 300 hypothetical protein. Motif number 1 ACCAGGATGGCGATCTCCAACGAGAATTTG 6 16 0 CGATCTCCAA 0.946604 -68 CTAAGGATTTTGATCGCAAATTTGATGAAG 8 162 1 TGATCGCAAA 0.797103 -139 ATTGAGCAAACGATCGCCACTTTATAAAAA 9 104 1 CGATCGCCAC 0.982093 -197 GGATGAGAGACGATCGCCAATTTGGACCAG 9 184 1 CGATCGCCAA 0.996578 -117 TTTTTATCGGCGATCGCCAAACTAAAGTTT 10 41 0 CGATCGCCAA 0.996578 -260 TGTCCCGAACCGATCGCCGAAAGG 11 5 0 CGATCGCCGA 0.994848 -203 GGCGGGGCTACGACCGCAGAAAAAAGGCCC 11 65 1 CGACCGCAGA 0.866848 -143 ACCGCCACGGCGATCGCCAAGGAAAATAAT 11 123 0 CGATCGCCAA 0.996578 -85 CTCCGCCCTCCGATCGCCATGGTTAAAA 18 102 1 CGATCGCCAT 0.984906 -18 TGACCGCCAACATTCTCTGG 19 1 1 TGACCGCCAA 0.907563 -62 TGAGCTGCAACGATCGCCAACTGC 19 49 1 CGATCGCCAA 0.996578 -14 AGGGAGCACTCGATCGCCGAGCCACCCCCT 20 54 0 CGATCGCCGA 0.994848 -107 TCCATCTAGGCGATCGCCGTCCGGAAACCC 27 51 1 CGATCGCCGT 0.97741 -234 AGTTAGACCCCGATCGCCAGGGATATGAAC 28 34 0 CGATCGCCAG 0.982093 -85 ********** Masking position 3 Map Score: 40.0044 Number of sites scoring better than the average of aligned sites = 3701 Number in coding regions = 3322 Number in noncoding regions = 379 Number of orfs with sites within 600 bp upstream = 342 Fraction of orfs with sites within 600 bp upstream = 0.0549309 Motif number 2 TATGTTCAATTGGTCCCCATTTCCCCTAGAAAGTTATCTAAA 2 80 1 TCCTCCCCAA 0.988642 -126 GTTCTACAGATTCTTACCCTCCACCCAACTGTAA 3 3 0 TCCCACCCAT 0.897446 -298 AATGCCAAACTTTGCCCACAGCCGCCGACACTGGGCGGTTTT 3 101 1 TCACCGCCAT 0.844452 -200 GAGCGATCACTAAAGCCTTTGTCCCCCAACTATTTTCACTAA 3 180 1 TCTTCCCCAA 0.949655 -121 GAGGGAAGTGTAAGTCCAAATCCCCCAACCTTGCCGGAGCTT 3 221 0 TCACCCCCAT 0.964977 -80 GGCGATCGTCTCTCATCCGATTTCCCTAAGTACACCAACTGC 9 160 0 TCCTTCCCAA 0.920794 -141 CGATCGCCAATTTGGACCAGTTCCCCGACCATTGAACATAGG 9 194 1 TCCTCCCCAT 0.995438 -107 CGACAAGGTCTTTGATACCCATCCCCTATGTTCAATGGTCGG 9 218 0 TACTCCCCAT 0.910642 -83 ATCGGAACCCTAGAAACAATATCCCCTACCCTAGCTAGGGAT 10 98 0 TCATCCCCAT 0.973199 -203 TCCCCAGTATTTTGCTCCCGCTCCCCTATGATAATTTTTCTC 12 42 0 TCCTCCCCAT 0.995438 -127 TGGTGAGCACTCCGAGCTAATCTCCCAAAACTTCTGCCAGGG 16 167 1 TCTCTCCCAT 0.827335 -100 TTTGATTATTTAACGTTCACTTCCCCTAACATCATCGTCC 21 168 1 TTCTCCCCAT 0.910642 -30 TTTCTGACATCACTGCCATCCCCCCAAGACCATTAACCGAG 22 10 1 TCCCCCCCAC 0.960239 -103 GATAGTAGGGTTCTAGCTCGTTCCCTCAATATCCAATATCCC 23 77 0 TCTTCCCTAT 0.676062 -120 AGTTAGACATTCCCCCCCTGCCCCTCAATGGAGAGCAGATAA 27 98 0 TCCCCCTCAA 0.744597 -187 GCTAAGCAATTCCCAGCCATCTTGCCAAAGCTCATCGTCCTA 27 141 0 TCCTTGCCAT 0.851668 -144 TGCCAACTAGTTAGACCCCGATCGCCAGGGATATGAACTTTG 28 30 0 TCCTCGCCGT 0.820101 -89 AATCCACTTTTCCTCACTTACTCCCCGAATCA 29 1 0 TCTTCCCCAA 0.949655 -300 ATACTTTGCCTGGGAACCTTCTCCCCAATCTTGGTTCGGCCA 29 106 0 TCCTCCCCAT 0.995438 -195 * ** ***** * * Masking position 1 Map Score: 22.4784 Number of sites scoring better than the average of aligned sites = 844 Number in coding regions = 710 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 CGATCACTAAAGCCTTTGTCCCCCAACTATTTTCACTAA 3 183 1 ACTCCCCACA 0.889379 -118 GGGAAGTGTAAGTCCAAATCCCCCAACCTTGCCGGAGCT 3 222 0 ACTCCCCACT 0.975379 -79 TCGCCAATTTGGACCAGTTCCCCGACCATTGAACATAGG 9 197 1 GCTCCCCACT 0.995629 -104 CAAGGTCTTTGATACCCATCCCCTATGTTCAATGGTCGG 9 218 0 GATCCCCAGT 0.97963 -83 GGAACCCTAGAAACAATATCCCCTACCCTAGCTAGGGAT 10 98 0 ACTCCCCACT 0.975379 -203 TCCTCTCACTGACCTGTGTCCCGAACCGATCGCCGAAAG 11 12 0 GCTCCCGACA 0.869543 -196 CCAGTATTTTGCTCCCGCTCCCCTATGATAATTTTTCTC 12 42 0 GCTCCCCAGT 0.990624 -127 GATCTGTTTGGTAAGGTATTCCCAACCCTTCATTGTACA 13 256 0 GATTCCCACT 0.945224 -45 GCCATGGTTGCCATAGGTTCCAGTCAAAA 14 1 1 GATGCCAAGT 0.606409 -103 CCAATTCTAGGCAAGAAATTCCCAATGGTAAAATCATGG 16 55 0 GATTCCCAGT 0.888932 -212 GAATTGGGACGGAACAGTTTCCCAATTGTTTTTGCCTTT 16 87 1 GATTCCCATT 0.75778 -180 CTATGGAGTTGATCAAACTGCCCCAGCCTTACCCCTAAC 17 80 1 GCTGCCCACT 0.98739 -38 AAAACAGGGAGCACTCGATCGCCGAGCCACCCCCTACTG 20 50 0 GCTCGCCACA 0.751522 -111 GGCTGGGCTGGACAATAATGCCCCATGATAAGCCCCGAT 21 122 0 GATGCCCAGT 0.942955 -76 AGCCGTTATCCCCGATTGTCCAATGTGGT 22 94 0 ACTCCCCATT 0.877786 -19 AGCCTATCCCGTTAATAATCCCGGAGCCTGATTATGCCA 25 14 0 GATCCCGACT 0.9373 -32 GTCCTCACTGCCCTAGTTTTTCCTCCATT 28 100 0 GCTGCCCATT 0.934193 -19 CTTTGCCTGGGAACCTTCTCCCCAATCTTGGTTCGGCCA 29 106 0 GCTCCCCACT 0.995629 -195 AAACAGCAACGGGATTATTCCCAGAACCTTTGTTACAAT 29 146 0 GATCCCAACT 0.90623 -155 * * ***** * * * Masking position 9 Map Score: 26.4292 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 532 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 CATAACAAACCCCCGTTTCTGCCCTGAATTTGGTG 2 49 0 CCCCTTTCGT 0.600453 -157 TCGCTCGGTGCGCCATGGTTGGGATTAGCCGTTAA 3 151 0 CGCCTGGTGT 0.870732 -150 TCATTAAAGTCTCCCGGGCTTTTGTCCCGCCGTGT 10 211 0 CTCCGGGCTT 0.952985 -90 TCATTAATAACTCCTGGGCAGATTTTGTTGTTTAG 10 263 1 CTCCGGGCGT 0.996761 -38 GAACGGTTAACTCCTGGGCGGGGCTACGACCGCAG 11 49 1 CTCCGGGCGT 0.99676 -159 CCTTGGCGATCGCCGTGGCGGTTTTGATTGCAGCT 11 131 1 CGCCTGGCGT 0.988438 -77 TGCCACTTGAATCCGGGGATGTATTTGCTCTGTAT 12 86 0 ATCCGGGAGT 0.737965 -83 TCAATTCCAGCTCCCTTGCTGGGGTTGGCATGCTC 15 42 1 CTCCTTGCGT 0.968687 -81 CTGTTGTTTACCCCAGGGATGTTTTGATT 15 104 1 CCCCGGGAGT 0.942563 -19 CATGGAAAGCCTCCCTGGCAGAAGTTTTGGGAGAT 16 186 0 CTCCTGGCGT 0.99553 -81 CCTGGCTTTGCTCCAGGGCGGCAGTTTCAGGTCAC 17 26 0 CTCCGGGCGT 0.996761 -92 GTTTGATCAACTCCATAGCCGGTTTGGATAAACTT 17 63 0 CTCCTAGCGT 0.946094 -55 AGTTGGATTGCTCCGTGTCCGTTGTTAACTTTTTG 20 115 1 CTCCTGTCGT 0.965733 -46 **** **** * * Masking position 15 Map Score: 20.7724 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 267 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 CTGACAGCACGGGAATGGCAAT 2 2 0 GGAATGGCAA 0.989726 -204 CTCCGTAATTGCTAATGGCAACTGCCTTTCA 2 175 0 GCAATGGCAA 0.936978 -31 CTTTTCTGGCGGCAATGCCAAACTTTGCCCA 3 88 1 GGAATGCCAA 0.876248 -213 TGGTGATGTGGGGAATGGCTGGTCCGAGAGA 10 143 1 GGAATGGCTG 0.938755 -158 CCGCCGTGTAGCTAGTGGCAAAAATCTTTAC 10 189 0 GCAGTGGCAA 0.776279 -112 CTCAATTTTTGGGTGTGGCAAAAATTTTTGG 13 11 0 GGTGTGGCAA 0.93225 -290 TTCATCCTAATGAAATGGCAAAATTAGTCTC 13 202 0 TGAATGGCAA 0.835847 -99 AGCAAAAAATGGCTAAGGCTAGTCAGACAGA 15 75 0 GGTAAGGCTA 0.772283 -48 AGCCTCTAATGGCAAAGGCAAAAACAATTGG 16 108 0 GGAAAGGCAA 0.95993 -159 AGTTGGAAATGGCAAAATGCTTGAA 16 252 0 GGAATGGCAA 0.989726 -15 AGTTAGTTAGGGGTAAGGCTGGGGCAGTTTG 17 93 0 GGTAAGGCTG 0.699962 -25 TTCTTGGTCTGGTTAGGGCAAAAAGTTAACA 20 137 0 GGTAGGGCAA 0.895838 -24 ATGGTCTTGGGGGGATGGCAGTGATGTCAGA 22 13 0 GGGATGGCAG 0.925812 -100 ACCATTAACCGAGTATGGCAAAATGGGGCTT 22 39 1 GATATGGCAA 0.769372 -74 GACGATGGTGGGGAATGGTAGAGCATTACAA 24 59 0 GGAATGGTAG 0.766698 -24 AAACCAGGGGCGAAATGGCAGCCGGCAAATT 27 229 1 CGAATGGCAG 0.838484 -56 AAAACCGCTAGGATATGGCAAATTTAAACTT 29 51 0 GGTATGGCAA 0.983322 -250 ** ******** Masking position 7 Map Score: 19.947 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 974 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 6 GGAGATCGCCATCCTGGTCGGGCTAAACCC 6 28 1 ATCCTGGTCG 0.853385 -56 TGGAAAATACTCCCGGTCAACGGACTCAC 7 10 1 CTCCCGGTCA 0.883133 -93 TCATTAAAGTCTCCCGGGCTTTTGTCCCGC 10 216 0 CTCCCGGGCT 0.938257 -85 TCATTAATAACTCCTGGGCAGATTTTGTTG 10 263 1 CTCCTGGGCA 0.980788 -38 GAACGGTTAACTCCTGGGCGGGGCTACGAC 11 49 1 CTCCTGGGCG 0.992816 -159 GGCGTTCCTGCTCCTTGGGCCTTTTTTCTG 11 81 0 CTCCTTGGGC 0.790213 -127 GACAATTATTTTCCTTGGCGATCGCCGTGG 11 119 1 TTCCTTGGCG 0.878488 -89 GGCTTATCTTCTGGGCGATCTGTTTGG 13 284 0 CTTCTGGGCG 0.932056 -17 AATCAAAACATCCCTGGGGTAAACAACAG 15 104 0 ATCCCTGGGG 0.867553 -19 CATGGAAAGCCTCCCTGGCAGAAGTTTTGG 16 191 0 CTCCCTGGCA 0.958261 -76 CCTGGCTTTGCTCCAGGGCGGCAGTTTCAG 17 31 0 CTCCAGGGCG 0.936507 -87 AGATAGCTGACTCCTGGGGGCAACCAAAAT 18 74 0 CTCCTGGGGG 0.98252 -46 CAAAGTTCATATCCCTGGCGATCGGGGTCT 28 30 1 ATCCCTGGCG 0.953395 -89 ********** Masking position 2 Map Score: 17.5704 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 521 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 7 TGCCCACAGCCGCCGACACTGGGCGGTTTTTCTCTA 3 113 1 CGCCACATGG 0.891401 -188 TAACGGCTAATCCCAACCATGGCGCACCGAGCGATC 3 152 1 TCCCACCTGA 0.954488 -149 AGTCCAAATCCCCCAACCTTGCCGGAGCTTTAGTGA 3 215 0 CCCCACCTCA 0.971245 -86 TGGACCAGTTCCCCGACCATTGAACATAGGGGATGG 9 206 1 CCCCACCTGA 0.973994 -95 TTCCCTGCATTTCTTATTGAGCAAATA 9 284 0 TCCCGCATCT 0.633879 -17 GAAACAATATCCCCTACCCTAGCTAGGGATGATTAA 10 92 0 CCCCACCTGG 0.990856 -209 GACCAGCCATTCCCCACATCACCAGGAATCGGAACC 10 131 0 TCCCACACCG 0.907229 -170 GGTAAGGTATTCCCAACCCTTCATTGTACATTCAGA 13 250 0 TCCCACCTCG 0.982055 -51 AAAGGTTACGTCCCCAAATTGCCTTGGTA 14 85 1 TCCCAAATCG 0.588707 -19 AGACAGAGCATGCCAACCCCAGCAAGGGAGCTGGAA 15 46 0 TGCCACCCGG 0.723708 -77 ACCTTATTTTTCCCTGCAATGGTGAGCACTCCGAGC 16 148 1 TCCCGCATGG 0.938168 -119 GATCAAACTGCCCCAGCCTTACCCCTAACTAACTTA 17 90 1 CCCCGCCTCT 0.846658 -28 GTTAATTCGACCACCACATTGGACAATCGGGGATAA 22 82 1 CCACACATGA 0.480711 -31 ATATCCAATATCCCAACACTGGCAGATTTTTACCCG 23 55 0 TCCCACATGA 0.921531 -142 GCTCTACCATTCCCCACCATCGTCAAT 24 66 1 TCCCACCTGA 0.954488 -17 AGACATTCCCCCCCTGCCCCTCAATGGAGAGCAGAT 27 100 0 CCCCGCCCCG 0.933002 -185 ATTAACACTTCTCCGACAATGCTAAGCAATTCCCAG 27 167 0 CTCCACATCG 0.730749 -118 AGCAAAAACCCCGACAGTCCAAAGTTCATATCCC 28 9 1 CCCCACATCG 0.982055 -110 GGAACCTTCTCCCCAATCTTGGTTCGGCCAAAAAAT 29 100 0 CCCCATCTGG 0.835022 -201 **** *** * * * Masking position 4 Map Score: 20.7468 Number of sites scoring better than the average of aligned sites = 1291 Number in coding regions = 1190 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 8 TAATGGCAACTGCCTTTCATCGTTTATGTAAA 2 162 0 TGCCTTCATG 0.969893 -44 GGGAATTTCTTGCCTAGAATTGGGACGGAACA 16 71 1 TGCCTAAATG 0.751015 -196 TAGCTCGGAGTGCTCACCATTGCAGGGAAAAA 16 154 0 TGCTCACATG 0.974543 -113 CTGCCAGGGAGGCTTTCCATGGCTAACCTTAA 16 200 1 GGCTTTCATG 0.929679 -67 GTTTGGAATTTGTCCATCATTGATGATTTTGG 18 49 1 TGTCCACATG 0.738278 -71 GTTACATCGGGGCTTATCATGGGGCATTATTG 21 117 1 GGCTTACATG 0.940157 -81 GCAAACCAAATGCTTTACATCGTCAGACTAGT 23 129 1 TGCTTTCATG 0.971789 -68 GCTCTACCATTCCCCACCATCGTCAAT 24 66 1 TCCCCACATG 0.806981 -17 TTCTATTATCTGCTCTCCATTGAGGGGCAGGG 27 93 1 TGCTCTCATG 0.969893 -192 GGCTGGGAATTGCTTAGCATTGTCGGAGAAGT 27 165 1 TGCTTACATG 0.976153 -120 TTTTTTCTCTTGCTTTGCATTGATCCCCGGTT 29 205 0 TGCTTTCATG 0.971789 -96 ****** *** * Masking position 9 Map Score: 10.1775 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 96 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 AATTGGTCCCCATTTCCCCTAGAAAGTTATCT 2 87 1 CATTCCCTAG 0.939647 -119 AGTGTAAGTCCAAATCCCCCAACCTTGCCGGA 3 225 0 CAATCCCCAA 0.612158 -76 TCATCAGAAGGACTTACCCTCAGAGCCTAAGT 3 272 1 GATTCCCTCA 0.771985 -29 AACTGGGATTGAATTGCCCTGATATAGAAGGT 9 26 1 GATTCCCTGA 0.831413 -275 GTCTCTCATCCGATTTCCCTAAGTACACCAAC 9 163 0 CGTTCCCTAA 0.94518 -138 GTCTAGTTATCACTTTCCCCAGCTCTCTGCC 12 10 0 CATTCCCCAG 0.934041 -159 ATTTGCTCTGTATTTTCCCCAGTATTTTGCTC 12 67 0 TATTCCCCAG 0.898452 -102 TTTTTGCTGTTGTTTACCCCAGGGATGTTTTG 15 98 1 TGTTCCCCAG 0.88947 -25 TTGATGATTTTGGTTGCCCCCAGGAGTCAGCT 18 68 1 TGTTCCCCCA 0.772504 -52 CGTTGTTAACTTTTTGCCCTAACCAGACCAAG 20 134 1 TTTTCCCTAA 0.624976 -27 TTATGGCCATTGATTACCCTGGAAGTTAGTGT 21 28 1 TGTTCCCTGG 0.817067 -170 TATATTAGATTAGTTGCCCTAAGTGATTTATA 21 82 0 TATTCCCTAA 0.92214 -116 ATTTAACGTTCACTTCCCCTAACATCATCGTC 21 175 1 CATTCCCTAA 0.94989 -23 ATTTTTACCCGGCTTTCCCTGAAACTGGTGGA 23 34 0 GGTTCCCTGA 0.817704 -163 TACACAGTTGCCCAAAAAGCCAAAAA 27 269 0 CATTCCCAAA 0.727321 -16 ** ** ****** Masking position 5 Map Score: 8.36535 Number of sites scoring better than the average of aligned sites = 721 Number in coding regions = 637 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 10 TTGGCATTGCCGCCAGAAAAGCTGACGGGA 3 79 0 CGCCAGAAAA 0.854129 -222 GTTTGGCGATCGCCGATAAAAAGTAGCACA 10 49 1 CGCCGATAAA 0.951168 -252 GGGCTACGACCGCAGAAAAAAGGCCCAAGG 11 69 1 CGCAGAAAAA 0.79641 -139 GGAGCAGGAACGCCGAGAAAAAGACAATTA 11 97 1 CGCCGAGAAA 0.977722 -111 CCACGGCGATCGCCAAGGAAAATAATTGTC 11 119 0 CGCCAAGGAA 0.851617 -89 TGAATGACTGCGCCGAGAATCCCTTAATTC 12 135 0 CGCCGAGAAT 0.860633 -34 TAATGAAAATTGCCGAAAAAGTGAGCTTTT 13 149 0 TGCCGAAAAA 0.814453 -152 AAGGTTTTGCCGCCAAAAAAACAGGGAGCA 20 76 0 CGCCAAAAAA 0.965609 -85 GGTTTGACCCCGCCAATAAACCAGGGGCGA 27 212 1 CGCCAATAAA 0.924324 -73 ATCTTGGTTCGGCCAAAAAATTGCCCATTT 29 91 0 GGCCAAAAAA 0.803133 -210 ********** Masking position 9 Map Score: 7.22197 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 289 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 11 GGGATTAGCCGTTAAGCTAGAGAAAAACCG 3 136 0 GTTAAGCTAG 0.90962 -165 GGCTAAACCCGTTAAGCTAGAGAGCGTATT 6 48 1 GTTAAGCTAG 0.90962 -36 TTGTCCCGCCGTGTAGCTAGTGGCAAAAAT 10 195 0 GTGTAGCTAG 0.843448 -106 AGATTTTGTTGTTTAGCTAGTAACTACCT 10 282 1 GTTTAGCTAG 0.922838 -19 GGCATGCTCTGTCTGACTAGCCTTAGCCAT 15 68 1 GTCTGACTAG 0.937655 -55 TAACCTTAAAGTCTGGTTAGCGGCCATCAT 16 223 1 GTCTGGTTAG 0.891443 -44 GGTTTCTTGGTCTGGTTAGGGCAAAAAGT 20 142 0 GTCTGGTTAG 0.891443 -19 CCTACTATCTGTCAGCCTAGCAAACCAAAT 23 110 1 GTCAGCCTAG 0.88129 -87 GCTTTACATCGTCAGACTAGTTCAGGAAAA 23 140 1 GTCAGACTAG 0.926773 -57 TTATTAACGGGATAGGCTAGT 25 35 1 GATAGGCTAG 0.708644 -11 GGCGATCGGGGTCTAACTAGTTGGCAATTG 28 46 1 GTCTAACTAG 0.887734 -73 ********** Masking position 9 Map Score: 7.5917 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 159 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 TAGTCGAGTTTAAGCAAAATTGCGATGGGAT 1 48 1 TAAGCAAATT 0.892625 -103 GATGGGATAGTAAGCAAAATTAATCCAATTT 1 71 1 TAAGCAAATT 0.892625 -80 ACCTTCTATATCAGGGCAATTCAATCCCAGT 9 27 0 TCAGGCAATT 0.86942 -274 TTTGTATAAATCAGCTAAGTTTTCGACAAGG 9 252 0 TCAGCAAGTT 0.866037 -49 ATCCCTTAATTCAGCTAAAATCGGAGTGCCA 12 116 0 TCAGCAAAAT 0.813497 -53 GCGCAGTCATTCAACACAATTTAACTG 12 152 1 TCAACCAATT 0.689718 -17 CTTTGTTGACTAAGCTCAATTTTTGGGTGTG 13 25 0 TAAGCCAATT 0.872431 -276 TAACTAATTTTCAGCCAAATCAACCGACAAT 13 57 0 TCAGCAAATC 0.866037 -244 TCTCTCAAGAACAGCTAAATTTCCATAATGA 13 173 0 ACAGCAAATT 0.813497 -128 TGATCTCGCCTCAGCAAAATTTTGACTGGAA 14 28 0 TCAGCAAATT 0.974132 -76 TTGATCTAAATCGGCTCAATTCCAGCTCCCT 15 27 1 TCGGCCAATT 0.84173 -96 TCAGACTAGTTCAGGAAAATTAAGTTTGACC 23 151 1 TCAGGAAATT 0.89003 -46 ***** ***** Masking position 8 Map Score: 7.5729 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 399 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 13 ATCTAAAGTGGACTAAGGTTCCTAACAAGG 2 115 1 GACTAAGGTT 0.869332 -91 AATACATGAAGTCTAAGGATTTTGATCGCA 8 150 1 GTCTAAGGAT 0.93529 -151 GGTGTTTAAGGATGATTGACAAA 8 288 0 GTTTAAGGAT 0.945753 -13 GCTAACCAGACTTTAAGGTTAGCCATGGAA 16 214 0 CTTTAAGGTT 0.881774 -53 CAACTAATCAGTTTAAGGTTTTGCCGCCAA 20 90 0 GTTTAAGGTT 0.970175 -71 TCGAGCTGGTGTTTAAGGTTGAAAATTTGA 29 256 1 GTTTAAGGTT 0.970175 -45 ********** Masking position 5 Map Score: 2.16834 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 14 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 14 AATTCAGGGCAGAAACGGGGGTTTGTTATGTTC 2 54 1 AGAACGGGTT 0.967028 -152 AGCTCCGGCAAGGTTGGGGGATTTGGACTTACA 3 222 1 AGTTGGGGTT 0.682849 -79 ACAAAGTAACTGTAACTGGATTTGAGATCCGGA 8 260 0 TGAACGGATT 0.604536 -41 GCTATGCTAAAGCAACTGGGATTGAATTGCCCT 9 13 1 AGAACGGGTT 0.967028 -288 GAGTGCCACTTGAATCCGGGGATGTATTTGCTC 12 91 0 TGATCGGGAT 0.955167 -78 ATTAGGATGAAGAATCAGAGCATCACTTTCTGA 13 222 1 AGATCGAGAT 0.677876 -79 ATATACTGGTTACATCGGGGCTTATCATGGGGC 21 109 1 TAATCGGGTT 0.677881 -89 CTGAAACTGGTGGATCAGGGGATTTTTAAAATT 23 15 0 TGATCGGGAT 0.955167 -182 TGGCATAATCAGGCTCCGGGATTATTAACGGGA 25 14 1 AGCTCGGGTT 0.893778 -32 TAGAATTCTGTGAAAGTGGGTTTCCGGACGGCG 27 65 0 TGAAGGGGTT 0.82075 -220 ATTGTAACAAAGGTTCTGGGAATAATCCCGTTG 29 146 1 AGTTCGGGAT 0.879186 -155 AAGGTAGAAAAGCAACCGGGGATCAATGCAAAG 29 192 1 AGAACGGGAT 0.955167 -109 ** *** *** ** Masking position 13 Map Score: 5.38343 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 327 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 15 TTCACTAAAGCTCCGGCAAGGTTGGGGGATT 3 214 1 CTCCGCAAGG 0.97552 -87 AACGGGTTTAGCCCGACCAGGATGGCGATCT 6 30 0 GCCCGCCAGG 0.921592 -54 ACTTAATCATCCCTAGCTAGGGTAGGGGATA 10 90 1 CCCTACTAGG 0.760658 -211 GCGGTCGTAGCCCCGCCCAGGAGTTAACCGT 11 51 0 CCCCGCCAGG 0.987068 -157 AGCATGCCAACCCCAGCAAGGGAGCTGGAAT 15 45 0 CCCCACAAGG 0.970034 -78 TCTCCCAAAACTTCTGCCAGGGAGGCTTTCC 16 187 1 CTTCTCCAGG 0.703376 -80 TGGGCCAGCGCTTCATCTAGG 26 1 0 CTTCACTAGG 0.832254 -92 CCATAACAAACTCCATCTAGGCGATCGCCGT 27 40 1 CTCCACTAGG 0.961828 -245 ATTAACACTTCTCCGACAATGCTAAGCAATT 27 172 0 CTCCGCAATG 0.796669 -113 ***** ***** Masking position 9 Map Score: 2.95099 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 535 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516