AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_bsub_reg_100.orf -o00252_bsub_100.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yccC 216 similar to asparaginase #2 ycnG 106 similar to 4-aminobutyrate aminotransferase #3 dal 114 D-alanine racemase #4 purE 300 phosphoribosylaminoimidazole carboxylase I #5 ykrV 94 similar to aspartate aminotransferase #6 ylaO 205 similar to cell-division protein #7 pycA 74 pyruvate carboxylase #8 pyrB 145 aspartate carbamoyltransferase #9 yncD 300 similar to alanine racemase #10 asnS 143 asparaginyl-tRNA synthetase #11 aspB 22 aspartate aminotransferase #12 ypmA 142 ypmA #13 panB 245 ketopantoate hydroxymethyltransferase #14 ansB 44 L-aspartase #15 ansA 181 L-asparaginase #16 alaS 300 alanyl-tRNA synthetase #17 hisS 300 histidyl-tRNA synthetase #18 nadB 102 L-aspartate oxidase #19 argG 169 argininosuccinate synthase #20 asnB 149 asparagine synthetase #21 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #22 ywfB 151 alternate gene name: ipa-80d #23 yxbB 300 alternate gene name: yxaP; similar to hypothetical proteins #24 purA 205 adenylosuccinate synthetase Motif number 1 AAAGACAAAAAAAGAAGGATATGACAACAAA 1 106 1 AAGAAGGATA 0.803331 -111 TTTGATGGTATCAGAAGGAGAAACTACAAA 2 10 0 TAGAAGGAGA 0.803398 -97 GAAAATACCGACAGGGGGATATTCAC 2 91 1 AAGGGGGATA 0.940352 -16 ACAAGTGTGTACAGGGGAAGGATATTCCGCT 7 14 1 AAGGGGAAGG 0.802273 -61 TCCATTCGGGTAAGGGGGAGAAAAGT 7 59 1 TAGGGGGAGA 0.940376 -16 AGGGTTATGAAGAGAAGGAAGCTTCAATGCT 8 43 1 AAGAAGGAAG 0.894054 -103 AGTTGAAAAGAGAGGGGAAAGAAC 8 132 1 AAGGGGAAAG 0.717118 -14 TTATAATCCATAAGAAGGAAGGAAGCGTTG 9 281 1 TAGAAGGAAG 0.874159 -20 CTTTCTTGTTTTGGAGGGAAATATG 10 129 1 TGGAGGGAAA 0.583273 -15 GACGAATTAGGGGGAGTTCAAG 11 7 1 TAGGGGGAGT 0.738657 -16 ATTTGTTCAAACTGGAGGATGAAAAA 12 127 1 ATGGAGGATG 0.694743 -16 AAGGACTGGGACAGAGGGATGAAACTCGCCG 13 124 1 AAGAGGGATG 0.94715 -122 CCTCTAAACATGAGGAGGAGAAAAC 13 231 1 TAGGAGGAGA 0.907238 -15 TTATCAGAAGATCGGAGGAAGCTAATCCTGA 16 96 1 ACGGAGGAAG 0.719209 -205 GTTGGTTTGCATAGGGGGAGGGCTTTTTTGC 16 237 1 AAGGGGGAGG 0.981178 -64 CGATTTTTATAGAGGAGGAAATACA 16 286 1 AAGGAGGAAA 0.881282 -15 GGTGTAAACAACAGGAGGATGGCAT 18 88 1 AAGGAGGATG 0.963767 -15 TACTCTATTTTAGGAGGGATGCTCAATGAAA 23 37 1 TGGAGGGATG 0.833754 -264 TACTCTATTTTAGGAGGGATGCTCAATGAAA 23 155 1 TGGAGGGATG 0.833754 -146 GCCAACTTGATAAGGAGGATGCTGAAG 23 284 1 TAGGAGGATG 0.956323 -17 * ********* Masking position 9 Map Score: 18.5789 Number of sites scoring better than the average of aligned sites = 800 Number in coding regions = 502 Number in noncoding regions = 298 Number of orfs with sites within 600 bp upstream = 327 Fraction of orfs with sites within 600 bp upstream = 0.0525217 Motif number 2 AATGCAGAGCGGGTATTTTTTATTTTCTGA 4 251 1 GGGTATTTTT 0.599953 -50 CTATCATTTCAAGATTTTTTTAGAAGGTGA 5 69 1 AAGATTTTTT 0.786017 -26 TTAACAGTTTGGGTTTTTTTATAACCGCTA 6 30 1 GGGTTTTTTT 0.866375 -176 ATCTTAGACCGGGGTTTTTTTTCAGCCTTA 8 102 1 GGGGTTTTTT 0.957548 -44 TTACAACGAGAAGGATTCTTCACTTTCTAA 13 159 0 AAGGATTCTT 0.689472 -87 GTTGTAACGGAAGGTTTTTTGGCTTGCAGA 13 182 1 AAGGTTTTTT 0.943329 -64 CATAGGGGGAGGGCTTTTTTGCTGTCACTG 16 246 1 GGGCTTTTTT 0.886744 -55 CAACACTCCGGAGGTTTCCTGCTGAACGCG 17 84 1 GAGGTTTCCT 0.650994 -217 GTAGGGGCGGGAGTTTTTTTCATTTTCATC 17 232 1 GAGTTTTTTT 0.89523 -69 AAATAAACTCAAGAGTTTTTTATGGAGAAC 18 28 0 AAGAGTTTTT 0.478462 -75 AATTTAGGTGAAGTTTTTTTTATAAAAGGC 19 40 1 AAGTTTTTTT 0.827132 -130 ACGGTTGAGAGGGGATTTTTATC 19 157 1 GGGGATTTTT 0.83916 -13 ATAATGTCATGAGATTTCTTGACATTGCAA 21 115 1 GAGATTTCTT 0.795111 -33 ACCCTTTAAAAAGGGTTTTTAATTATAGGA 22 26 0 AAGGGTTTTT 0.806067 -126 CCCTTTTTAAAGGGTTTTTTTGTTTGTATG 22 41 1 AGGGTTTTTT 0.926637 -111 GGTTTCTTATAAGCTTTTTTCATTGAGCAT 23 55 0 AAGCTTTTTT 0.852465 -246 TCAAAAAGGCGAGGTTTCTTATAAGCTTTT 23 67 0 GAGGTTTCTT 0.946207 -234 GGTTTCTTATAAGCTTTTTTCATTGAGCAT 23 173 0 AAGCTTTTTT 0.852465 -128 TCAAAAAGGCGAGGTTTCTTATAAGCTTTT 23 185 0 GAGGTTTCTT 0.946207 -116 ********** Masking position 6 Map Score: 17.6815 Number of sites scoring better than the average of aligned sites = 678 Number in coding regions = 389 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 3 CTTTTCTGTCAGCCGCTTTTTGATCTG 10 8 0 AGCCGCTTTT 0.989743 -136 CTGACAGAAAAGCCGCTTTTTATCTGCATT 10 26 1 AGCCGCTTTT 0.989743 -118 ACACCGCAAAAGCCGCTTTATGCGGCTT 12 9 0 AGCCGCTTTA 0.976732 -134 AGAGCGGGAAATCCGCTTTTAAATAAAACA 12 52 0 ATCCGCTTTT 0.969347 -91 GCGAGAAGGTATTCGCTTTTCGCATACTTT 15 127 0 ATTCGCTTTT 0.756113 -55 AGTTAATCACTGCCGCTTATCCTGCGTTAC 16 131 1 TGCCGCTTAT 0.888631 -170 ACGCAATGGGATCCGCTTTCAGCCTGGGGC 17 43 0 ATCCGCTTTC 0.955117 -258 TTTTATAGCCGCTTACTGGTTAAGCG 20 7 1 AGCCGCTTAC 0.971478 -143 AAAAAGGGAAAGCCGCTTAACCAGTAAGCG 20 20 0 AGCCGCTTAA 0.956558 -130 ********** Masking position 7 Map Score: 13.2041 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 196 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 GCATTGCACTTATGAGGAAGCAATACAAAC 4 226 0 TATGAGGAAG 0.785784 -75 AAAACAAAAGCATTAGAAGGTGGGGAACAG 4 280 1 CATTAGAAGG 0.933492 -21 TTCAAGATTTTTTTAGAAGGTGAGAATAG 5 76 1 TTTTAGAAGG 0.68014 -19 ATCTCTATACGATTCGGAAGGAATGTGTAA 6 93 0 GATTCGGAAG 0.633228 -113 ATTTATAATCCATAAGAAGGAAGGAAGCGT 9 279 1 CATAAGAAGG 0.866678 -22 ACAAGAAAGACATTCGGAAGCTCATTGCCC 10 108 0 CATTCGGAAG 0.864937 -36 ACTCGCCGAACTTTAGAAAGTGAAGAATCC 13 147 1 CTTTAGAAAG 0.738213 -99 CTCCTCTAAACATGAGGAGGAGAAAAC 13 229 1 CATGAGGAGG 0.944053 -17 ATCATATAGGTATTAGGAAGTGTACGCGAA 15 46 1 TATTAGGAAG 0.905281 -136 TGAATAACGCCATTAGGCAGTGAACGTGAA 17 114 1 CATTAGGCAG 0.765442 -187 ATAAGGAATACATAAGGAGGTCTACCT 17 284 1 CATAAGGAGG 0.95317 -17 TAGTACTCTATTTTAGGAGGGATGCTCAAT 23 34 1 TTTTAGGAGG 0.869416 -267 TAGTACTCTATTTTAGGAGGGATGCTCAAT 23 152 1 TTTTAGGAGG 0.869416 -149 ACGCCAACTTGATAAGGAGGATGCTGAAG 23 282 1 GATAAGGAGG 0.844784 -19 CATCCTTTAGCATAAGAAAGAA 24 3 0 CATAAGAAAG 0.7805 -203 ********** Masking position 3 Map Score: 10.8993 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 223 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 5 GTTGTCATATCCTTCTTTTTTTGTCTTTTCAT 1 102 0 CTCTTTTTTT 0.945442 -115 GCTTTTCTCTCAGTATTTTTTGTTGTCATATC 1 123 0 CTATTTTTTG 0.426554 -94 CAAACATGATTTGGCCTTTTTTTCGTTAGACA 3 22 1 TGCCTTTTTT 0.775815 -93 ACGACACTTCCTAGCTTTTATTCAATATCATT 3 92 0 CGCTTTTATT 0.621654 -23 CCAAATTTTTCTTTACTTTTTTCATTTAACCA 5 23 1 CTACTTTTTT 0.713556 -72 ACTATCATTTCAAGATTTTTTTAGAAGGTGAG 5 68 1 CGATTTTTTT 0.750397 -27 TCATAAAAGACGGTCTTTTTTTACACATTCCT 6 73 1 CTCTTTTTTT 0.945442 -133 TATCTTAGACCGGGGTTTTTTTTCAGCCTTAA 8 101 1 CGGTTTTTTT 0.638137 -45 GTTCTTTCCCCTCTCTTTTCAACTTAAGGC 8 126 0 CTCTCTTTTC 0.701783 -20 TTGGATGATTCGATCTTATTTTATTCAACTTT 9 214 0 CTCTTATTTT 0.540361 -87 TTCCGAATGTCTTTCTTGTTTTGGAGGGAAAT 10 119 1 CTCTTGTTTT 0.635358 -25 CCCTCTGTCCCAGTCCTTTTTTGGATCAAGGC 13 110 0 CTCCTTTTTT 0.954767 -136 GAACTTCCGCTCCTTTTTCACCTTGAGCT 15 8 1 CTCCTTTTTC 0.909779 -174 TTCGTTTTTTCAAGCCTTTTATAAAAAAAACT 19 51 0 CGCCTTTTAT 0.78777 -119 GGTTAAGCGGCTTTCCCTTTTTTATCGTTGTA 20 28 1 CTCCCTTTTT 0.857144 -122 TCTGTGTCACTCCCTTTTTTTGATGGTTG 21 8 1 CTCCCTTTTT 0.857144 -140 AGGTTTCTTATAAGCTTTTTTCATTGAGCATC 23 54 0 TGCTTTTTTC 0.575781 -247 TATAAGAAACCTCGCCTTTTTGAACTGCGCCG 23 74 1 CGCCTTTTTG 0.918604 -227 AGGTTTCTTATAAGCTTTTTTCATTGAGCATC 23 172 0 TGCTTTTTTC 0.575781 -129 TATAAGAAACCTCGCCTTTTTGAATTGCGCCG 23 192 1 CGCCTTTTTG 0.918604 -109 GAAAGTTTCGCAAGCTTTTTATGACAAAGCAG 24 32 1 CGCTTTTTAT 0.752927 -174 * ********* Masking position 9 Map Score: 12.3714 Number of sites scoring better than the average of aligned sites = 2171 Number in coding regions = 1660 Number in noncoding regions = 511 Number of orfs with sites within 600 bp upstream = 467 Fraction of orfs with sites within 600 bp upstream = 0.075008 Motif number 6 AAATAAAAAATACCCGCTCTGCATTGCACT 4 246 0 TACCCGCTCT 0.97932 -55 GCATTGAAGCTTCCTTCTCTTCATAACCCT 8 43 0 TTCCTTCTCT 0.927227 -103 GTTCTTTCCCCTCTCTTTTCAACTTA 8 130 0 TCCCCTCTCT 0.969907 -16 CACTTTATTATACCCGCTCTTAACTAACCG 10 60 0 TACCCGCTCT 0.97932 -84 AAAAGCGGATTTCCCGCTCTGTGATACTAG 12 62 1 TTCCCGCTCT 0.984042 -81 GAAAAGCGAATACCTTCTCGCAACCCATCT 15 136 1 TACCTTCTCG 0.847118 -46 TGTATTTCCTCCTCTATAAAAATCG 16 286 0 TTCCTCCTCT 0.851627 -15 TACGTTCATATTCCCGCTCGATCCTTTAAC 17 149 0 TTCCCGCTCG 0.972159 -152 GATAAAAATCCCCTCTCAACCGTGTTTC 19 152 0 TCCCCTCTCA 0.869981 -18 ********** Masking position 8 Map Score: 10.1825 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 81 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 7 CTTTTCATCATACCAAAGAGAAGTCAGAATG 2 56 1 TACAAAGAGA 0.569392 -51 CCGGACTATGCAGGAAAGTGATCGATAAAAC 4 142 1 CAGAAAGTGA 0.776558 -159 AAGTTAGAAGCAGGGAAGAGGATGTT 6 190 1 CAGGAAGAGG 0.970485 -16 AAACGATAACCAGCAAAGAGAAAGAAGGTTA 14 18 1 CAGAAAGAGA 0.956609 -27 TCTTTAGATACAGTGAAGAGGTGCATGGT 15 163 1 CAGGAAGAGG 0.970485 -19 AACGTTTACACAGGGACGAGAGCTGTCTCGC 16 209 0 CAGGACGAGA 0.970485 -92 TTTTTGCTGTCACTGAAGAGAATTTCGATTT 16 261 1 CACGAAGAGA 0.953465 -40 TACATGATAGTAGGGACGAGAGTTATACCCG 17 199 0 TAGGACGAGA 0.866215 -102 TCAAGTTTATCAGTGAAGAAACAGAAAGTCA 24 138 0 CAGGAAGAAA 0.868328 -68 *** ******* Masking position 6 Map Score: 5.35499 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 172 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 CGATGTCTAACGAAAAAAAGGCCAAATCATGT 3 25 0 CGAAAAAGGC 0.809092 -90 AAGCGGCTGACAGAAAAGCCGCTTTTTATCTG 10 20 1 CAAAAACCGC 0.918597 -124 ACTCCCACACCGCAAAAGCCGCTTTATGCGGC 12 13 0 CGAAAACCGC 0.982849 -130 TATCACAGAGCGGGAAATCCGCTTTTAAATAA 12 56 0 CGGAAACCGC 0.991196 -87 AGACACGGAAAATAAAATACGCAAGACATTAT 15 83 0 AAAAAAACGC 0.653068 -99 GCATGATTAGAGAGGAACCCGCCCCAGGCTGA 17 23 1 AGGGAACCGC 0.896068 -278 AGTGTTGTTTCGAGAAAGACGCAATGGGATCC 17 59 0 CGGAAAACGC 0.982849 -242 CTGCTGAACGCGTGAATAACGCCATTAGGCAG 17 102 1 CGGAATACGC 0.900339 -199 ACGATAAAAAAGGGAAAGCCGCTTAACCAGTA 20 24 0 AGGAAACCGC 0.973615 -126 ** **** **** Masking position 6 Map Score: 5.81998 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 268 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 GCAATTCAGTAAGGTGGGAATGTT 1 5 0 AAGGTGGGAA 0.961826 -212 ATATGGATGTAAGGAGAGAAATAG 1 203 1 AAGGAGAGAA 0.957389 -14 AAAGCATTAGAAGGTGGGGAACAGA 4 286 1 AAGGTGGGGA 0.948721 -15 ATTTTTTTAGAAGGTGAGAATAG 5 82 1 AAGGTGAGAA 0.92981 -13 TGGAAGTTAGAAGCAGGGAAGAGGATGTT 6 187 1 AAGCAGGGAA 0.806639 -19 AATCCATAAGAAGGAAGGAAGCGTTG 9 285 1 AAGGAAGGAA 0.737853 -16 CAAGGTGAAAAAGGAGCGGAAGTTC 15 6 0 AAGGAGCGGA 0.857802 -176 AAGCCCTGTTAAAGAGAGAAGCTCCATAAG 16 54 1 AAAGAGAGAA 0.596752 -247 TGACATTGCAAAGGTGTGAATCAA 21 134 1 AAGGTGTGAA 0.765705 -14 TACTCTATTTTAGGAGGGATGCTCAATGAA 23 37 1 TAGGAGGGAT 0.80161 -264 GCAGTTCAAAAAGGCGAGGTTTCTTATAAG 23 72 0 AAGGCGAGGT 0.788732 -229 TACTCTATTTTAGGAGGGATGCTCAATGAA 23 155 1 TAGGAGGGAT 0.80161 -146 GCAATTCAAAAAGGCGAGGTTTCTTATAAG 23 190 0 AAGGCGAGGT 0.788732 -111 ********** Masking position 2 Map Score: 7.50152 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 302 Number in noncoding regions = 240 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 10 TAAAATTAAAGGCTAAAGGGAAACGATGTCTAAC 3 46 0 GGTAAGAAAC 0.970055 -69 CATCATATATGGTTAAATGAAAAAAGTAAAGAAA 5 30 0 GGTAAGAAAA 0.78344 -65 TTCAACTTAAGGCTGAAAAAAAACCCCGGTCTAA 8 105 0 GGTAAAAAAC 0.738927 -41 TTTTTTCTAAGGGTAGATGATAACGAGAAATCTA 9 26 0 GGTGAGTAAC 0.879621 -275 TTAACTAACCGGGTCAATGCAGATAAAAAGCGGC 10 37 0 GGTAAGAGAT 0.937297 -107 GTCCTTTTTTGGATCAAGGCAGACTGCTGCAATG 13 96 0 GGTAAGAGAC 0.986998 -150 CTGCGTTACAGGGTTAAAGGTGACGGGCGCATGA 16 152 1 GGTAAGTGAC 0.975503 -149 ACCCGCCCCAGGCTGAAAGCGGATCCCATTGCGT 17 39 1 GGTAAGGGAT 0.821414 -262 TATGGAGAACGGATGGAGGAAGACCGG 18 4 0 GGTGAGAGAC 0.970275 -99 TATAAATAGGGGTTCAATGATGACAATTTTAATT 20 112 1 GGTAAGTGAC 0.975502 -38 ** * ** * **** Masking position 7 Map Score: 7.22991 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 59 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TGATTCAATCATCAATTGTCAAGAAAAATTCATTGTATGAA 1 66 1 ATCATGCATC 0.943359 -151 TATAATCTTGGGAATATGGCCCATAAGTTTCTACCCGGCAA 4 91 1 GGAATGCATC 0.900599 -210 ATGTGATACGAGAAGGTGCCTATCAATGTTCGAATAATAGC 9 147 0 AGAATGCATC 0.971521 -154 CAGATCAAAAAGCGGCTGACAGAAAAGCCGCTTTTTATCTG 10 11 1 AGCGTGCAGC 0.913208 -133 AATCTCATATAGCATTTGACATCTAGTACTCTATTTTAGGA 23 11 1 AGCATGCATC 0.99334 -290 GCCGTGCTGTAGCAGCTGGCGGCCATTAATCTCATATAGCA 23 102 1 AGCATGCATC 0.993339 -199 AATCTCATATAGCATTTGACATCTAGTACTCTATTTTAGGA 23 129 1 AGCATGCATC 0.99334 -172 GCCGCGCTGTAGCAGCTGGCGGTCATTAATCTTATCCAAAA 23 220 1 AGCATGCATC 0.993339 -81 **** ** * * ** Masking position 15 Map Score: 5.98533 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 11 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 12 TATCGTCAGTCGTTCGCTTCTGCGATATATC 4 180 0 CGTCGCTTCT 0.953956 -121 AACATCCTCTTCCCTGCTTCTAA 6 193 0 CATCTCTTCC 0.883665 -13 ATTCAATTCGCGTACACTTCCTAATACCTAT 15 51 0 CGTCACTTCC 0.989202 -131 ACCATGCACCTCTTCACTGTATC 15 169 0 CATCACCTCT 0.82103 -13 CGCAGGTTCACGTTCACTGCCTAATGGCGTT 17 119 0 CGTCACTGCC 0.96574 -182 AATCTATATTCGTTCGCTTCCATTCGTTTTA 24 78 0 CGTCGCTTCC 0.987004 -128 GTCCGTGCACCTCCGTTAACCTTT 24 192 0 CGTCACCTCC 0.984037 -14 *** ******* Masking position 3 Map Score: 4.4551 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 55 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 GAAAAATTCATTGTATGAAAAGACAAAAAAAGA 1 88 1 TTTTGAAAAA 0.938622 -129 GACTGATCTTTTGACTGAATAGATAAAATGTAC 1 156 1 TTATGAATAA 0.727717 -61 GTATTTTTTATTTTCTGAAAACAAAAGCATTAG 4 263 1 TTTTGAAAAA 0.93847 -38 TCATATATGGTTAAATGAAAAAAGTAAAGAAAA 5 29 0 TTATGAAAAA 0.864222 -66 TTATTCAACTTTATTTGAAATCATTCAACAGCA 9 193 0 TTTTGAAATA 0.740527 -108 TCAAATAAAGTTGAATAAAATAAGATCGAATCA 9 208 1 TTATAAAATA 0.361614 -93 TATTTTATCCTTGTGTAAATATAGGTGTCAAGA 18 53 1 TTTTAAATAA 0.75118 -50 TTTTCAAGCCTTTTATAAAAAAAACTTCACCTA 19 44 0 TTTTAAAAAA 0.87173 -126 AAAATACATTTTGTATGTATACACTTTAACAAG 19 88 0 TTTTGTATAA 0.386218 -82 ATAAATTATATTTAATAAAAATACATTTTGTAT 19 105 0 TTATAAAAAA 0.75113 -65 TGTTTCTATTTTGTATAAAAATAAATTATATTT 19 125 0 TTTTAAAAAA 0.878368 -45 GGTTTCACAGTTATGTAAAAAAATAAACATGAA 20 60 0 TTTTAAAAAA 0.877109 -90 ACTGTCAATGTTTTTTGAAAATATTGATAATTA 22 75 0 TTTTGAAAAA 0.931524 -77 TAAACTTGATTTGTTTGAATAGAATCGTTTTGA 24 160 1 TTTTGAATAA 0.864673 -46 ** * ****** * Masking position 9 Map Score: 11.5235 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 219 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 14 CTTGAACTCCCCCTAATTCGTC 11 9 0 AACTCCCCCT 0.942619 -14 ATCGCCTGCGAACTGCACCTATTATTAAAA 13 58 1 AACTGCACCT 0.935951 -188 GAACTTCCGCTCCTTTTTCAC 15 2 1 AACTTCCGCT 0.964924 -180 TGCAGTTAATCACTGCCGCTTATCCTGCGT 16 128 1 CACTGCCGCT 0.784483 -173 AATACTATGAAACTTCACCTGAAATTTAGG 19 18 1 AACTTCACCT 0.962753 -152 TTATAAAAAAAACTTCACCTAAATTTCAGG 19 35 0 AACTTCACCT 0.962753 -135 AACGAGGAGAAACTTCCGCTAGAATTGACA 21 56 0 AACTTCCGCT 0.964924 -92 GCTTATAAGAAACCTCGCCTTTTTGAACTG 23 71 1 AACCTCGCCT 0.931692 -230 GCTTATAAGAAACCTCGCCTTTTTGAATTG 23 189 1 AACCTCGCCT 0.931692 -112 ********** Masking position 2 Map Score: 8.59801 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 44 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 AGAAAATAAAAAATACCCGCTCTGCATTGC 4 249 0 AAATACCCGC 0.769447 -52 TTGGGTTTTTTTATAACCGCTATTTTTCTC 6 38 1 TTATAACCGC 0.899462 -168 TAAATACCACCTATTGCCGCAAGAATAAAT 9 254 0 CTATTGCCGC 0.851572 -47 CATCACTTTATTATACCCGCTCTTAACTAA 10 63 0 TTATACCCGC 0.983002 -81 CCTAATGGCGTTATTCACGCGTTCAGCAGG 17 101 0 TTATTCACGC 0.8566 -200 GAATACGTTCATATTCCCGCTCGATCCTTT 17 152 0 ATATTCCCGC 0.917393 -149 GGGACGAGAGTTATACCCGTGGTGCCACCC 17 188 0 TTATACCCGT 0.850061 -113 TTTTATAGCCGCTTACTGGTTA 20 3 1 TTATAGCCGC 0.972637 -147 GAACCCCTATTTATAGACGCTGTGAATAGT 20 97 0 TTATAGACGC 0.874989 -53 ********** Masking position 4 Map Score: 5.77651 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 126 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049