AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -inarL_bsub_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 nasF 60 uroporphyrin-III C-methyltransferase #2 nasE 31 assimilatory nitrite reductase (subunit) #3 nasD 121 assimilatory nitrite reductase (subunit) #4 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #5 cysH 300 phosphoadenosine phosphosulfate #6 ylnB 48 similar to sulfate adenylyltransferase #7 ylnD 98 similar to uroporphyrin-III C-methyltransferase #8 citB 227 aconitate hydratase #9 yneN 71 similar to thiol:disulfide interchange protein #10 yoaE 300 similar to formate dehydrogenase #11 resC 135 essential protein similar to cytochrome c biogenesis protein #12 resA 131 essential protein similar to cytochrome c biogenesis protein #13 ypuL 91 similar to hypothetical proteins #14 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #15 ypuI 54 similar to hypothetical proteins from B. subtilis #16 ypuG 280 similar to hypothetical proteins #17 spoIIIAC 22 spoIIIAC #18 spoIIIAA 75 spoIIIAA #19 yqhV 144 alternate gene name: yqgE #20 efp 24 elongation factor P #21 yqhS 86 similar to 3-dehydroquinate dehydratase #22 yqhR 226 yqhR #23 nadB 102 L-aspartate oxidase #24 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #25 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #26 gerBA 264 gerBA #27 narJ 25 nitrate reductase (protein J) #28 narG 195 nitrate reductase (alpha subunit) #29 ywiD 143 ywiD #30 narK 135 nitrite extrusion protein #31 ywiB 300 ywiB #32 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter #33 yyaE 300 similar to formate dehydrogenase Motif number 1 AAGATTCCCCTTTCTAGACCCTCA 4 5 1 TTCCCCTTTC 0.885908 -175 CTCGTAAGTTTTCTCCTATTAAAAATTATG 4 137 0 TTCTCCTATT 0.829085 -43 GTATCAGACCTCCTTTGGCGAAGCTCG 4 163 0 ACCTCCTTTG 0.869871 -17 TTCTTCTTTCCTCCTTTCGGAGACAAAC 5 283 0 TCCTCCTTTC 0.959941 -18 AAATGCCTTCTCTTCCTATTGATTCA 9 7 0 TCTTCCTATT 0.742306 -65 CCATGACATCACTCCCTTTTCGC 11 4 0 ACTCCCTTTT 0.826753 -132 CGGTTTGGCCTGCCCTTTTTATCTTTATT 11 117 0 CTGCCCTTTT 0.603118 -19 TGCCCCCTTCCCCCTATTGCAGATCCAT 12 114 0 TCCCCCTATT 0.890823 -18 CGTTTACTCTCCCTTTTTCAGGGAGAG 14 8 1 TCTCCCTTTT 0.913155 -115 GGTGCTTCCTCCTTTAATGTGCTTTT 16 7 1 TCCTCCTTTA 0.867322 -274 GGGCGTTCTTTTTTCCTTTTATCCCTTCTA 16 46 0 TTTTCCTTTT 0.862091 -235 TTGCTTCTGGTTTTCCTTTCTAAGAAGCAC 16 84 0 TTTTCCTTTC 0.732711 -197 CAGAGCCTCCTCCTTTCTACCGATTGG 18 59 0 TCCTCCTTTC 0.959941 -17 GTTTAATGTCCTCCTATATTCCAA 20 7 0 TCCTCCTATA 0.569361 -18 ACAATCTCTCCTTTTCGCGAGGGTT 21 72 0 CTCTCCTTTT 0.872085 -15 ATTGCTAACCATTTCCTTTCACTCTATTGT 22 37 1 ATTTCCTTTC 0.554392 -190 ATGCCATCCTCCTGTTGTTTACACCT 23 87 0 TCCTCCTGTT 0.946034 -16 CTGTAATCCTCCCCCCTGTTTGAGCTATAA 25 38 0 CCCCCCTGTT 0.786273 -255 CGTTTTCTTGACGCCCTTTTGAGGGAGGAG 25 171 1 ACGCCCTTTT 0.846814 -122 TACTTTACCCCCTGTTTGATAAGTGC 25 277 0 ACCCCCTGTT 0.854519 -16 ATAAGAATAATTCTCCTTTTTTGATACAAA 26 205 1 TTCTCCTTTT 0.959975 -60 GCAGCCTTCCTTCTCCTTTGTGTGAACATT 28 76 1 TTCTCCTTTG 0.866034 -120 CGAAATCCTCCTTTTTTCTTTCATT 29 6 1 TCCTCCTTTT 0.982029 -138 AGGAAAACCTCCTGTGCTAAGGATAG 29 128 0 ACCTCCTGTG 0.681981 -16 CCCGAAGACTTTGTCCTTTTGATCGTGA 30 9 0 TTGTCCTTTT 0.87866 -127 TCTTCGGGCTTTGTCCTTTTTTTATGAGAA 30 31 1 TTGTCCTTTT 0.87866 -105 GAAATCTATCATTTCCTTTTCACATTTTTT 31 93 0 ATTTCCTTTT 0.739385 -208 TCTGACACGTCCTTTTCATCATTCCA 31 285 0 ACGTCCTTTT 0.882184 -16 TATTTCTCCCCCTTTTATTTAAACAA 32 7 1 TCCCCCTTTT 0.975812 -294 ********** Masking position 7 Map Score: 34.1202 Number of sites scoring better than the average of aligned sites = 1232 Number in coding regions = 699 Number in noncoding regions = 533 Number of orfs with sites within 600 bp upstream = 621 Fraction of orfs with sites within 600 bp upstream = 0.099743 Motif number 2 TATTTTAAGAGGTAAAAAGGCTATCTGTATA 5 195 1 GGAAAAAGGC 0.91769 -106 TCCGGCATCTGAGAAGAACGCAGCAGATCAT 7 13 0 GAAAGAACGC 0.9564 -86 GAATCAATAGGAAGAGAAGGCATTTCGCTTT 9 12 1 GAGAGAAGGC 0.955532 -60 GTCATAAAAAGAAGAGAAAGCGAAATGCCTT 9 28 0 GAGAGAAAGC 0.901673 -44 GGCGGATCACGGTAAAAACGCTTTCTAAATT 12 27 1 GGAAAAACGC 0.943029 -105 TGCCAAATCTAAAAAAAACGCCGTTT 13 6 0 AAAAAAACGC 0.901445 -86 ATCTTATGATGATGAAAAAGCGCGATTCATT 15 17 0 GAGAAAAAGC 0.939382 -38 GATAAAAGGAAAAAAGAACGCCCGGCCTCTA 16 53 1 AAAAGAACGC 0.844055 -228 CGCAGAAGCGGGAGAAAAAGCCTTTGCTTCT 16 106 0 GGGAAAAAGC 0.873733 -175 ATGAAATGTCAATAAAAAAGCTCACACTTTT 22 177 0 AAAAAAAAGC 0.724454 -50 AAAAGGGCGTCAAGAAAACGCGTACATAAAT 25 160 0 CAGAAAACGC 0.829466 -133 ATGTTGTCATAGGAAAAAGGCAGCTTATACG 26 77 0 AGAAAAAGGC 0.733402 -188 TTACCCCTTCAAAGAAAACGCTTCCTATCTA 26 131 1 AAGAAAACGC 0.930081 -134 TATTCTTATCGAGGAAAAGGCTGAAACAAAG 26 183 0 GAGAAAAGGC 0.9732 -82 CTTTTTTTATGAGAAAAACGTGTGATGTAAT 30 46 1 GAAAAAACGT 0.633893 -90 AAAGTGGAATGATGAAAAGGACGTGTCAGA 31 281 1 GAGAAAAGGA 0.629092 -20 AAAAATAGTTGACGAAAACGCTATCATGATT 32 165 0 GAGAAAACGC 0.981789 -136 TCGTAGAAATGAAAAAACCGCATCCATGCGG 33 85 1 GAAAAACCGC 0.88442 -216 AGAAGGTAAGGAGAAGACGGCG 33 289 1 GAAAGACGGC 0.753081 -12 ** ******** Masking position 5 Map Score: 21.2036 Number of sites scoring better than the average of aligned sites = 921 Number in coding regions = 820 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 ATTTTTCATAAAATTTTTAGAACTTTTCGTA 3 3 1 TTTTAAATAA 0.966674 -119 TTGTGCTAAAATTTACTACAAATCTAAAAACTTATCAAG 5 16 1 ATTTAAATAA 0.937263 -285 ACTTATTGTATTTAATAAAAACATTGATATTTACTTATG 8 106 1 TTTAAAATAA 0.755325 -122 TAGTTAGATATTTTGTAAGAATTATAACATTTCCGATGA 10 255 0 TTTTAAATAA 0.966671 -46 CGCTTTCTAAATTTCACATAACCTTCAAAAAGTAAGAAA 12 45 1 ATTTAAATAA 0.937266 -87 TTTGAAGGAGTTTGTACAGAATATTCAAAACACAAGAGG 16 150 0 TTTGAAATAA 0.89378 -131 ATAGCCTTGCTTTTCCTACATGCATTATACCCGTTATTT 22 115 1 TTTTAATTAA 0.726449 -112 TTGACACCTATATTTACACAAGGATAAAATAAACTCAAG 23 45 0 TATTAAATAA 0.726445 -58 TTCTTGCTTAATTTTTCATAAGAATTACAGGATCATTCT 25 66 0 ATTTAAATAA 0.937267 -227 CACTCTGCTTTTTTCACAAAATGTTCACACAAAGGAGAA 28 86 0 TTTTAAATAA 0.96667 -110 AATTTGATAGTTTTAAGATAAAAGTACAACATAGATCTG 31 30 0 TTTTAAATCA 0.797213 -271 AATACATATATTTTGAAAAAAATGTGAAAAGGAAATGAT 31 77 1 TTTTAAATAA 0.966676 -224 GAAATGATAGATTTCGGAAAAATGTAACATTTCCTAAAG 31 108 1 ATTTAAATAA 0.937267 -193 GCTCATCAGATTTGAAGATAAACCTCATAAAAAGCATTT 31 182 0 TTTGAAATAA 0.893564 -119 CGAGAAGAGAATTTGAAAGAAAACTAAAAAAAGTACTAG 33 196 1 ATTTAAATAA 0.937267 -105 **** * ** * * * Masking position 10 Map Score: 13.363 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 92 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 CCTTATCAAATGTTTTTTCCAGCGTAGCAC 3 89 0 TGTTTTTTCC 0.780791 -33 AACTTACACATGTCTTTTCCAGAAAATAAT 4 70 0 TGTCTTTTCC 0.949529 -110 GAAGCTCGTAAGTTTTCTCCTATTAAAAAT 4 141 0 AGTTTTCTCC 0.751982 -39 GTTTGTAAGGTGCTACTTCCAGCAAAATGA 5 98 1 TGCTACTTCC 0.713416 -203 TTCTGCCGGTTGTCTTTTCCCATGTAATGT 5 242 0 TGTCTTTTCC 0.949529 -59 AATATCCATCTCCTCCTAGTTAA 6 36 0 ATCCATCTCC 0.648918 -13 ATGCCACCTCCGCAGCACATT 9 61 0 TGCCACCTCC 0.924688 -11 AACATTATTGTGCCAATTCCAGCAAGCGCT 10 88 0 TGCCAATTCC 0.630383 -213 GATAGCTTCTTCCTTATATCTTA 15 42 0 AGCTTCTTCC 0.82617 -13 GGTGCTTCCTCCTTTAATGTGC 16 3 1 TGCTTCCTCC 0.829601 -278 CAGAGCCTCCTCCTTTCTACCGA 18 63 0 AGCCTCCTCC 0.959086 -13 GGAAAAAAGAAGTCTGTTCCCAAATGGGAG 19 14 1 AGTCTGTTCC 0.821556 -131 GCACAAAAAAAGCCTGCTCCCATTTGGGAA 19 30 0 AGCCTGCTCC 0.892398 -115 GAAGTAGTCTTGTCATTTCCGTATAAAAGA 19 76 0 TGTCATTTCC 0.899827 -69 TGTATAATCCTTTTCCAGTATGATAA 21 7 1 ATCCTTTTCC 0.805659 -80 TAGGATTGCTAACCATTTCCTTTCACTCTA 22 33 1 AACCATTTCC 0.66436 -194 AAATGTGCTAAATCTCTTCCCCCACTTCTT 25 246 0 AATCTCTTCC 0.619862 -47 GCTTTGTTTCAGCCTTTTCCTCGATAAGAA 26 182 1 AGCCTTTTCC 0.97066 -83 GAACGCAGCCTTCCTTCTCCTTTGTGTGAA 28 72 1 TTCCTTCTCC 0.809401 -124 TTCCGAAATCTATCATTTCCTTTTCACATT 31 97 0 TATCATTTCC 0.529542 -204 TGTCTTTTCCTGCTTTCTTT 32 291 0 TGTCTTTTCC 0.949529 -10 CGCCGTCTTCTCCTTACCTTCTA 33 288 0 CGTCTTCTCC 0.750987 -13 ********** Masking position 8 Map Score: 18.6292 Number of sites scoring better than the average of aligned sites = 1396 Number in coding regions = 1257 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 5 AACTTATCAAGAGCGGCTGAGGGACTGGACCTA 5 44 1 GAGCGGAGGG 0.978789 -257 TTTCTATCCAGAGAGGTGGAGGGACTGGCCCTA 10 130 0 GAGAGGAGGG 0.989178 -171 TCTAACTAGAGAGAGGAACTGGGCC 10 286 1 GAGAGGTGGG 0.913699 -15 CTCAGAGCACTGGCGGATCACGGTAAAAACGCT 12 16 1 TGGCGGACGG 0.901139 -116 GGATCTGCAATAGGGGGAAGGGGGCA 12 116 1 TAGGGGGGGG 0.873162 -16 TAAGAAGCACTAGAGGCCGGGCGTTCTTTTTTC 16 61 0 TAGAGGGGCG 0.926402 -220 TGTTTGCTCGGAGCGCAGAAGCGGGAGAAAAAG 16 117 0 GAGCGCAGCG 0.710335 -164 ATAAAAAAATGGGAGGTTGGGAGAGTGCT 19 126 1 GGGAGGGGAG 0.856578 -19 CCTGTCAATCTAGAGGTTTAGCGGTGTTTCCTG 22 68 0 TAGAGGAGCG 0.96473 -159 GGAGAACGGATGGAGGAAGACCGG 23 2 0 TGGAGGACCG 0.919628 -101 ACTAGATTACTAGAGGGAGAGGGGCTATC 24 15 1 TAGAGGAGGG 0.977357 -19 TCAAACAGGGGGGAGGATTACAGAATGATCCTG 25 45 1 GGGAGGACAG 0.868596 -248 TTATTTACAGGGGAGGGGTACGGATC 26 4 0 GGGAGGACGG 0.974514 -261 GCGTTTGTAAGAGGGGCGCACCGGGAAAATGAT 26 43 0 GAGGGGACCG 0.91091 -222 AGTTTAGGAAAAGAGGTGAAGGGTCTTGGCGGA 33 29 1 AAGAGGAGGG 0.899609 -272 ****** **** Masking position 5 Map Score: 14.235 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 175 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 AATTCCATTTTGAAAGATAAGGGCTGCATGCTGTTC 5 127 1 TGAAAGAGTG 0.920966 -174 ACGTCAATTCTGAAAAAAAGAGATTGACATCAATCT 10 217 0 TGAAAAAGTG 0.986645 -84 CATAGGAATTTGAAAAAGCTTGTTTGTTAAGGTTGA 13 35 1 TGAAAAAGTG 0.986645 -57 AAACTCTCCCTGAAAAAGGGAGAGTAAACG 14 5 0 TGAAAAAGTA 0.942228 -118 CTTATGATGATGAAAAAGCGCGATTCATTAAACTT 15 10 0 TGAAAAAGTC 0.905363 -45 AAAGGAAAAAAGAAGTCTGTTCCCAAATG 19 4 1 GGAAAAAGTG 0.958917 -141 ATTGACAGGCTGAAAAAATTGCCATAGCCTTGCTTT 22 92 1 TGAAAAACTA 0.761445 -135 GTAATTCTTATGAAAAATTAAGCAAGAAATATATAT 25 77 1 TGAAAAAGAG 0.887162 -216 TGTTGTCATAGGAAAAAGGCAGCTTATACGGGCGTT 26 71 0 GGAAAAAGTA 0.837467 -194 GAACATTTTGTGAAAAAAGCAGAGTGTGTGACATAG 28 99 1 TGAAAAAGTG 0.986645 -97 TTTGCGTAAATGAAAAAGGATCGCTGTGTCCTTTAT 32 61 0 TGAAAAACTG 0.935314 -240 ATTCTTAATCTGAATAAGCGGGATTGTGACTGGTAA 32 115 0 TGAATAAGTG 0.887162 -186 ACCTTCTATATGAAAAAGCATGAGTGTCGGCCTATT 33 260 0 TGAAAAAGTG 0.986645 -41 ******* * ** Masking position 7 Map Score: 16.6539 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 83 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TCTTTTATTGTGTTATATGAGAGAGCGTAA 8 38 1 TGTTATATGA 0.576239 -190 TGATATTTACTTATGTATGATTTTGTTTTA 8 130 1 TTATGTATGA 0.660331 -98 GCTTTCTCTTCTTTTTATGACACAATGTGC 9 38 1 CTTTTTATGA 0.86866 -34 CAGAGCGCGCCTATATATGAATCTCTTTCC 10 11 0 CTATATATGA 0.586283 -290 AATCTGAGTCTTCTTTATGATAAACGTATT 10 192 0 TTCTTTATGA 0.807673 -109 CAGGGAGAGTTTTTTTATGTTTGCTTCCAG 14 29 1 TTTTTTATGT 0.51852 -94 CCTCCCATTTTTTTATATGATATGCTCTAG 19 112 0 TTTTATATGA 0.835121 -33 AACTCAAGAGTTTTTTATGGAGAACGGATG 23 23 0 TTTTTTATGG 0.614812 -80 ATAGAGCCGGTTTTTTTTGATCTTTGAATG 28 11 1 TTTTTTTTGA 0.500418 -185 GCTTTGTCCTTTTTTTATGAGAAAAACGTG 30 38 1 TTTTTTATGA 0.916261 -98 TTTGGCTAGTTTTTGTATGATAAGACTGAT 30 88 1 TTTTGTATGA 0.807673 -48 TAAGGAAATGCTTTTTATGAGGTTTATCTT 31 177 1 CTTTTTATGA 0.86866 -124 AACGCTATCATGATTTATGATGAAAGCGTA 32 150 0 TGATTTATGA 0.576239 -151 GAGTGTCGGCCTATTTATGAAGTAGGCTCC 33 245 0 CTATTTATGA 0.753804 -56 TCTCCTTACCTTCTATATGAAAAAGCATGA 33 273 0 TTCTATATGA 0.660331 -28 ********** Masking position 6 Map Score: 6.62519 Number of sites scoring better than the average of aligned sites = 361 Number in coding regions = 268 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 8 TCAATCCGGCGGAAAGAAAGACAGGAACAG 5 157 0 GGAAAGAAAG 0.961836 -144 TCTTTCCGCCGGATTGAAAGTTTTTTATTT 5 170 1 GGATTGAAAG 0.793215 -131 CTCAGATGCCGGAATGCAAGCGAGAACATC 7 31 1 GGAATGCAAG 0.857787 -68 TTGAAAGATAGGAAAGCAAGGTTTATACCG 10 55 0 GGAAAGCAAG 0.907879 -246 CCACCTCTCTGGATAGAAAATATTGAGTAT 10 144 1 GGATAGAAAA 0.704032 -157 ACGTCAATTCTGAAAAAAAGAGATTGACAT 10 223 0 TGAAAAAAAG 0.530898 -78 CATTTCCGTATAAAAGAAAGATTCTGTTTT 19 63 0 TAAAAGAAAG 0.812537 -82 ATGCATGTAGGAAAAGCAAGGCTATGGCAA 22 110 0 GAAAAGCAAG 0.68109 -117 ATTGATTAGTTGATTGAAAAATTTTATTTT 25 117 0 TGATTGAAAA 0.536048 -176 AGGAAAAGGCTGAAACAAAGCTTGAAAAGC 26 173 0 TGAAACAAAG 0.626498 -92 TTTTGATCTTTGAATGAAAGGCAGCTAATG 28 25 1 TGAATGAAAG 0.92448 -171 GCATTTATAATGAAAGAAAAAAGGAGGATT 29 14 0 TGAAAGAAAA 0.883602 -130 AAAATTTGCGTAAATGAAAAAGGATCGCTG 32 71 0 TAAATGAAAA 0.501696 -230 TGCTCAATCATGAAAGAAAGCAGGAAAAGA 32 279 1 TGAAAGAAAG 0.952384 -22 TGATATCGTAGAAATGAAAAAACCGCATCC 33 80 1 GAAATGAAAA 0.559204 -221 GAAGAGAATTTGAAAGAAAACTAAAAAAAG 33 199 1 TGAAAGAAAA 0.883602 -102 ********** Masking position 3 Map Score: 10.7448 Number of sites scoring better than the average of aligned sites = 984 Number in coding regions = 812 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 9 TGACAAAAACTATCATTGAGGAGG 2 5 1 AAAAACTATC 0.927528 -27 AACGTGTCACAAAAACTTACACATGTCTTT 4 83 0 AAAAACTTAC 0.564925 -97 TCTTAAAATAAAAAACTTTCAATCCGGCGG 5 175 0 AAAAACTTTC 0.852787 -126 TAAGAGGTAAAAAGGCTATCTGTATATCAG 5 200 1 AAAGGCTATC 0.817548 -101 ATCACGGTAAAAACGCTTTCTAAATTTCAC 12 32 1 AAACGCTTTC 0.788685 -100 GCAAACATAAAAAAACTCTCCCTGAAAAAG 14 23 0 AAAAACTCTC 0.901113 -100 GATATAAGGAAGAAGCTATC 15 45 1 AGAAGCTATC 0.789601 -10 TAAGCCACCAAAAAGCTCTCGTCCAATACT 16 203 0 AAAAGCTCTC 0.94417 -78 ATGTCAATAAAAAAGCTCACACTTTTTGGC 22 173 0 AAAAGCTCAC 0.791484 -54 CGAGCTACACTAAAGCTATCCTTAGCACAG 29 113 1 TAAAGCTATC 0.829265 -31 CTTATCATACAAAAACTAGCCAAACAGGAT 30 82 0 AAAAACTAGC 0.706766 -54 ACTTTTATCTTAAAACTATCAAATTACTAA 31 44 1 TAAAACTATC 0.723301 -257 TAGTTGACGAAAACGCTATCATGATTTATG 32 161 0 AAACGCTATC 0.891848 -140 ********** Masking position 3 Map Score: 6.7116 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 246 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 GACCGGATCACTTTTCTAGTGGTCCTTCATT 1 17 1 CTTTTTAGTG 0.88231 -44 GGTCCTTCATTTTTTACAGTGACGGAAGGAT 1 37 1 TTTTTCAGTG 0.841875 -24 TAAATATTCCTTTTTGCTGTGCTACGCTGGA 3 71 1 TTTTTCTGTG 0.900299 -51 AATATGGCTTCTTTTATTGTGTTATATGAGA 8 29 1 CTTTTTTGTG 0.927088 -199 GTACCGGTAATTTTTACTGTTTACGCTCTCT 8 57 0 TTTTTCTGTT 0.803435 -171 CTTTATGCGGCCTTTCTTGTGTATTTAATCG 11 54 1 CCTTTTTGTG 0.815046 -82 TTAGAAAGCGTTTTTACCGTGATCCGCCAGT 12 24 0 TTTTTCCGTG 0.705745 -108 TGGGAGCAGGCTTTTTTTGTGCCCAAAAACA 19 38 1 CTTTTTTGTG 0.927088 -107 CCTTTTTTTGTTTTTCTAGCAG 31 2 1 CTTTTTTGTT 0.851972 -299 GAATTTTAGGTCTTTTTTGTTTAAATAAAAG 32 22 0 TCTTTTTGTT 0.632614 -279 TCGTCAACTATTTTTTTAGTTAAATAGTTTG 32 181 1 TTTTTTAGTT 0.74551 -120 TGACTAGTACTTTTTTTAGTTTTCTTTCAAA 33 207 0 TTTTTTAGTT 0.74551 -94 ***** ***** Masking position 5 Map Score: 5.20833 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 185 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 11 TCTTTTCCCATGTAATGTGATTCGCGGCTGCTGAT 5 225 0 TGTAATTTCC 0.915465 -76 GAAGATTCGCTGTGATGATGTTCTCGCTTGCATTC 7 42 0 TGTGAATTCC 0.945453 -57 CGGCCTTTCTTGTGTATTTAATCGCTGTCCCAATC 11 61 1 TGTGTTATCC 0.882908 -75 AAGCAGAGTGTGTGACATAGTTCACAAGGAAACAC 28 115 1 TGTGATTTCC 0.988164 -81 TCATACAGGCTGTGAAATACATCACTGCTGTACAG 29 71 1 TGTGATATCC 0.973205 -73 GAGAAAAACGTGTGATGTAATTCACAATCCTGTTT 30 56 1 TGTGATTTCC 0.988164 -80 GGCACGATATTGTGAAGTATTTCACAATTAATTTT 32 238 0 TGTGATTTCC 0.988164 -63 ***** * *** * Masking position 12 Map Score: 3.68842 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 17 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 GTCATCCTTCCGTCACTGTAA 1 50 0 TCATCCTTCC 0.816748 -11 TCTCCAAAATCCCCCTTCAGATCAGATCA 8 209 0 TCCCCCTTCA 0.947265 -19 TGCCCCCTTCCCCCTATTGCA 12 121 0 GCCCCCTTCC 0.983883 -11 TTTATTTTTGCTCCCCTCACGT 17 4 0 GCTCCCCTCA 0.82116 -19 CCGGTCTTCCTCCATCCGTTCTCCATA 23 8 1 TCCTCCATCC 0.735357 -95 GATAGCCCCTCTCCCTCTAGTAAT 24 20 0 GCCCCTCTCC 0.907371 -14 CATTCTGTAATCCTCCCCCCTGTTTGAGCT 25 42 0 TCCTCCCCCC 0.757573 -251 TTCATTTTACTCCTCCCTCAAAAGGGCGTC 25 180 0 TCCTCCCTCA 0.930308 -113 GATCCGTACCCCTCCCCTGTAAATA 26 6 1 GTACCCCTCC 0.61491 -259 ATCTTTTCATTACCCCTTCAAAGAAAACGC 26 122 1 TACCCCTTCA 0.541942 -143 CTGCCTGAACGCAGCCTTCCTTCTCCTTTG 28 66 1 GCAGCCTTCC 0.743866 -130 TTGGCTTGCCCCTTTCAATGATTCAAT 30 119 0 GCCCCTTTCA 0.815433 -17 CACTGTGAGAGCATCCCTCACACTTAATTC 33 157 0 GCATCCCTCA 0.89042 -144 AGCATGAGGAGCCTACTTCATAAATAGGCC 33 238 1 GCCTACTTCA 0.554666 -63 ********** Masking position 9 Map Score: 4.85185 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 486 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 13 TAACAAAATATACGAAAAGTTCTAAAAATTTTATG 3 17 0 TGAAAAGTAA 0.866914 -105 AGATACATGTTATAAAATGTAACAAAATATACGAA 3 36 0 TAAAATGTAA 0.748138 -86 TATGAAATTGTGAGAAAATTGTGATGGAATGTAAT 8 161 1 TGAAAATTAT 0.76921 -67 GACGTTATCATCGGAAATGTTATAATTCTTACAAA 10 248 1 TGAAATGTAA 0.911748 -53 TTGAAGGTTATGTGAAATTTAGAAAGCGTTTTTAC 12 38 0 TGAAATTTAA 0.769201 -94 CTTCAAAAAGTAAGAAATGTGAAATGAACGTGCAA 12 67 1 TGAAATGTAT 0.941767 -65 TTGTTAAGGTTGAAAAAAGTAAGATAATACTTGAG 13 58 1 TAAAAAGTAT 0.748138 -34 GATTGGCTTCTTTAAAATGTATGATGTGAGGCAGA 18 30 0 TAAAATGTAT 0.82296 -46 ATTGACAGGCTGAAAAAATTGCCATAGCCTTGCTT 22 92 1 TAAAAATTAT 0.489277 -135 ACTAATCAATTCGGAAAATTATAATTTATGTACGC 25 137 1 TGAAAATTAT 0.76921 -156 GTTTGATAAGTGCGAAATGTGCTAAATCTCTTCCC 25 255 0 TGAAATGTAA 0.911745 -38 GTTACATTTTTCCGAAATCTATCATTTCCTTTTCA 31 101 0 TGAAATCTAT 0.701477 -200 TAATTACCTTTAGGAAATGTTACATTTTTCCGAAA 31 119 0 TGAAATGTAT 0.941766 -182 * ******* ** Masking position 7 Map Score: 5.03019 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 93 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 CTAGAAAAGTGATCCGGTCTTTTGA 1 4 0 GTCCGTCTTT 0.970296 -57 CAGATGATCCGCTCCTTATCAAATGTT 3 105 0 GTCCCTCCTT 0.973122 -17 GGGCTTCATAGGTCCAGTCCCTCAGCCGCTCT 5 53 0 GTCCGTCCCT 0.98308 -248 GCTGCATGCTGTTCCTGTCTTTCTTTCCGCCG 5 149 1 GTCCGTCTTT 0.970296 -152 AGGTTTCATAGGGCCAGTCCCTCCACCTCTCT 10 122 1 GGCCGTCCCT 0.961513 -179 GGCCCAGTTCCTCTCTCTAGTTAGATAT 10 283 0 GTCCCTCTCT 0.946815 -18 GTTTGCTCACGTCCTTGTGGTGGTTT 14 107 0 GTCAGTCCTT 0.830373 -16 ATAAAAGAAAGATTCTGTTTTTGGGCACAAAA 19 52 0 GTTCGTTTTT 0.436711 -93 GATAGCCCCTCTCCCTCTAGTAATCT 24 18 0 GCCCCTCCCT 0.88778 -16 AGTTTCTCTCCTTCTTAAACATA 26 252 0 GTTCCTCCTT 0.847974 -13 ATAGAGCCGGTTTTTTTTGATCTTT 28 4 1 GGCCGTTTTT 0.683928 -192 * *** ****** Masking position 8 Map Score: 6.8876 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 255 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 15 GACAAAAACTATCATTGAGGAGGAATGGAC 2 12 1 AATTGAGGAG 0.926607 -20 AAGCCATATTATGATTGAGGTGATAATG 8 7 0 AATTGAGGTG 0.926607 -221 AAGTAAGATAATACTTGAGGTGAAAGAC 13 74 1 ACTTGAGGTG 0.952439 -18 AATATTCAAAACACAAGAGGTGTTTGCTCGGA 16 138 0 ACAAGAGGTG 0.869614 -143 GCCAATCGGTAGAAAGGAGGAGGCTCTG 18 58 1 AAAGGAGGAG 0.861728 -18 CTTTTGATAAATGAGGTGTAACAAG 27 7 1 AAATGAGGTG 0.95295 -19 AAAAAACCGCATCCATGCGGAGCGAACAGCTG 33 96 1 ACATGCGGAG 0.895099 -205 AGTACTAGTCAAGCATGAGGAGCCTACTTCAT 33 227 1 ACATGAGGAG 0.969812 -74 * ********* Masking position 1 Map Score: 2.05781 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 40 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789