AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_mjan_reg_300.orf -o00350_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ0002 300 M. jannaschii predicted coding region MJ0002 #2 MJ0102 300 Phenylacrylic acid decarboxylase #3 MJ0684 68 aspartate aminotransferase (aspB2) #4 MJ0771 88 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #5 MJ0955 48 histidinol-phosphate aminotransferase (hisC) #6 MJ1027 125 formate hydrogenlyase, subunit 5 #7 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #8 MJ1029 47 dimethyladenosine transferase (ksgA) #9 MJ1521 88 Na+/H+ antiporter #10 MJ1522 146 cobalamin biosynthesis precorrin-6Y methylase (cbiE) #11 MJ1530 178 ribosomal protein S18 alanine acetyltransferase #12 MJ1575 300 GMP synthase (guaA) #13 MJ1576 80 LemA protein #14 MJ1577 29 M. jannaschii predicted coding region MJ1577 #15 MJ1578 66 cobalamin biosynthesis precorrin-3 methylase (cbiF) #16 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 CCATGGTTTGTTGATAATGGTTTTCACCAATCCC 1 13 0 TTTAATTTTT 0.944882 -288 ATATAATTTTTTATAATTGGTATTTTGATGCTCT 1 197 0 TTAATTTATT 0.928544 -104 TTATGTAATTTTTTATATAATTTTTTATAATTGG 1 211 0 TTATATTTTT 0.930361 -90 CCAATTAGAATTTCTAATAATTTTGGAGATATTA 1 264 1 TTTAATTTTT 0.944882 -37 TCTGAAAGATTTTGTTTAACTTTTTCTAAAAGTT 2 137 1 TTTTTATTTT 0.683212 -164 TCGGCACCATTTTATTATTTTATTTTAGGTTGTT 2 188 1 TTTTATTATT 0.845213 -113 TTTTAGGTTGTTATATTTATTTTTTTAGATTTAT 2 210 1 TTATTTTTTT 0.950937 -91 GATTAACTATTTTTAAATAGTATTTATTTTTTAA 2 245 1 TTAAATTATT 0.899568 -56 TTATTATTAATTAATAATACTTTTCGTGGTGGCA 3 15 0 TTTAATTTTT 0.944882 -54 TATTAATTAATAATAATTCCTTTTAGTGTTTATA 3 33 1 TAAATTTTTT 0.76051 -36 AAAATTACAATTAAAAACTTTTTTAGATAACTTA 4 52 0 TTAAACTTTT 0.793142 -37 AGAAATCTTATTTAAAATATTTTTGGTTAAAAAT 5 24 1 TTAAATTTTT 0.950937 -25 TAGCTTAACCTTTTATATAGTTTTGTTTTAATAA 6 21 0 TTATATTTTT 0.930361 -105 AATAGTTTAGTTAATTTCTATTTTGTTACATTAT 7 19 1 TTTTTCTTTT 0.772274 -42 TTCTATTTTGTTACATTATTTATTTTACTGATAT 7 34 1 TTATTATATT 0.529822 -27 ATTTTTATTTTCTTTTCTCTTTTTTA 8 3 1 TTATTTTTTT 0.950937 -45 AACTTATATTTTTATATTCTTATTTTATATTCTT 10 42 1 TTTATTTATT 0.919957 -105 TTACCTTATCTTTTTAATTTTATTGATATTTAAA 10 88 1 TTTAATTATT 0.887919 -59 GTCCTTAGTATTTCAAAATGTTTTAAAAGACTCT 11 48 1 TTAAAATTTT 0.709169 -131 TTAGTATTATTTTAAATTCTTTTTATAGAGTCTT 11 74 0 TTAATTTTTT 0.965659 -105 AAATTCTATTTTAATTTTAGTATTATTTTAAATT 11 90 0 TTTTTTTATT 0.887919 -89 TTGTGTAATTTATTAAATTCTATTTTAATTTTAG 11 104 0 TAAAATTATT 0.502863 -75 ACACTATATTTTAAAATTTCTTTTATTATGATTA 12 36 0 TTAATTTTTT 0.965659 -265 ATATCCATTATTAATATTAATTTTAACAACTTTG 12 74 0 TTTATTTTTT 0.961346 -227 AAAAGGTTCTTTCAAAATGTTTTTGAAAGATACT 12 256 1 TTAAATTTTT 0.950937 -45 TCAACTTATATAAATTTTATTATTAG 13 3 0 TATTTTTATT 0.472189 -78 ATCCAAATAATTCAAATTCTTTTTTGTGGTGAAA 13 55 1 TTAATTTTTT 0.965659 -26 TTATTAATTTTAATTTTTAGGGGATTT 14 4 1 TTTTTTTTTT 0.944881 -26 ATTTCTCCTCTTGTTTTTGTTTTTATAGTAGGTC 15 42 0 TTTTTTTTTT 0.944882 -25 GCTATAAGCTTTGGTTTTGATATTGAAGAACTAT 16 81 1 TTTTTTTATT 0.887919 -220 GAACTATCTCTTAATATTGATTTTGAGGAGGAAT 16 108 1 TTTATTTTTT 0.961346 -193 TTTGGGAACTTTAAAATCTCTTTTTTAACAGCTC 16 147 0 TTAATCTTTT 0.847623 -154 ** **** **** Masking position 11 Map Score: 50.2046 Number of sites scoring better than the average of aligned sites = 1806 Number in coding regions = 1253 Number in noncoding regions = 553 Number of orfs with sites within 600 bp upstream = 390 Fraction of orfs with sites within 600 bp upstream = 0.0626405 Motif number 2 TAGGACTTATGTAATTTTTTATATAATTTTTTAT 1 217 0 GTTTTTATAT 0.904742 -84 GCTATTGGATTTTTAATATCTCCAAAATT 1 282 0 TGTTTTATAT 0.825117 -19 TGAAAACTCTTTTAGTTTTCATTTAACCGAAGCG 2 84 1 TTTTTTATTT 0.976083 -217 TTATTTTATTTTAGGTTGTTATATTTATTTTTTT 2 202 1 TTTTGTATAT 0.938528 -99 GTTGTTATATTTATTTTTTTAGATTTATGGATTA 2 216 1 TTTTTTAGAT 0.857276 -85 TTAAATAGTATTTATTTTTTAAATCTTAACTTAA 2 257 1 TTTTTTAAAT 0.942618 -44 TAAAAAAGTTTTTAATTGTAATTTTATAAAATCG 4 61 1 TTTTGTATTT 0.916666 -28 TTTTATATAGTTTTGTTTTAATAAAGTTATCGAG 6 11 0 TTTTTTATAA 0.768841 -115 GATAATTAGCTTAACCTTTTATATAGTTTTGTTT 6 27 0 TTCTTTATAT 0.825117 -99 ATTTTTATTTTCTTTTCTCTTTTTTA 8 3 1 TTTTTTTTTT 0.696374 -45 TGTTTCACTTTTTATTTATTCTAAAAA 8 31 0 TTTTTTATTT 0.976083 -17 CACCAATCTTTTAGTTTTTAATATCTGGATATAC 9 60 0 TTTTTTATAT 0.982652 -29 TTTCAATTTTTAAATTTTTAATTCA 10 2 1 TTTTTTAAAT 0.942618 -145 AAAATATAAGTTAAATTTTGAATTAAAAATTTAA 10 20 0 TTTTTTAATT 0.92209 -127 AAAATTTAACTTATATTTTTATATTCTTATTTTA 10 35 1 TTTTTTATAT 0.982652 -112 TATCTTTACCTTATCTTTTTAATTTTATTGATAT 10 83 1 TTTTTTAATT 0.92209 -64 TTTATTACTATTATGTTTTTAAATATCAATAAAA 10 105 0 TTTTTTAAAT 0.942618 -42 ATTTATTAAATTCTATTTTAATTTTAGTATTATT 11 97 0 TTTTTTATTT 0.976083 -82 TTATTAATTTTAATTTTTAGGGGATT 14 3 1 ATTTTTATTT 0.715 -27 CTCCTCTTGTTTTTGTTTTTATAGTAGGTCTTTC 15 38 0 TTTTTTATAG 0.831354 -29 ACAAATAAAAGTCCATTGTTATATAGATTAGGAT 16 18 0 GTTTGTATAT 0.719101 -283 GGCTATAAGCTTTGGTTTTGATATTGAAGAACTA 16 80 1 TTTTTTATAT 0.982652 -221 TAATGAATCATTAACTTATTATTTAAGAGATTGT 16 193 1 TTTTATATTT 0.829992 -108 ATTTAAGAGATTGTTTTATAATTTTAGAGGACTA 16 213 1 TTTTATATTT 0.829992 -88 ** **** **** Masking position 7 Map Score: 34.0484 Number of sites scoring better than the average of aligned sites = 819 Number in coding regions = 545 Number in noncoding regions = 274 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 3 TTTTTATATAATTTTTTATAATTGGTATTTT 1 205 0 ATTTTTATAA 0.758895 -96 AATTGGTAGTATTTTATAATAGGACTTATGT 1 239 0 ATTTTTAATA 0.930296 -62 TACCAATTAGAATTTCTAATAATTTTGGAGA 1 262 1 AATTTTAATA 0.758548 -39 TGGATTAACTATTTTTAAATAGTATTTATTT 2 243 1 ATTTTAAATA 0.94903 -58 CACGAAAAGTATTATTAATTAATAATAATTC 3 21 1 ATTATAATTA 0.790032 -48 CTTACGATTTTATAAAATTACAATTAA 4 72 0 ATTTTTAAAA 0.789777 -17 AGATTTCTGGATTTTTTATTA 5 1 0 ATTTTTATTA 0.917904 -48 AACCAAAAATATTTTAAATAAGATTTCTGGA 5 21 0 ATTTTAATAA 0.818119 -28 GCTAATTATCATTATTAATTATGATAAATTA 6 51 1 ATTATAATTA 0.790032 -75 ATTATGATAAATTATCTATTCATTACCTTAG 6 68 1 ATTATTATTC 0.327507 -58 TTTCAATTTTTAAATTTTTAATTCAA 10 6 1 ATTTTAAATT 0.525118 -141 TATAAGTTAAATTTTGAATTAAAAATTTAAA 10 19 0 ATTTTAATTA 0.941107 -128 TTATATTCTTATTTTATATTCTTATTCTGAT 10 53 1 ATTTTTATTC 0.674152 -94 TTACTATTATGTTTTTAAATATCAATAAAAT 10 104 0 GTTTTAAATA 0.632747 -43 CTTTTAAAACATTTTGAAATACTAAGGACCA 11 46 0 ATTTTAAATA 0.94903 -133 CTATAAAAAGAATTTAAAATAATACTAAAAT 11 80 1 AATTTAAATA 0.814344 -99 AATAAAAGAAATTTTAAAATATAGTGTCTTT 12 43 1 ATTTTAAATA 0.94903 -258 TTTCAAAAACATTTTGAAAGAACCTTTTAGT 12 253 0 ATTTTAAAGA 0.866379 -48 CTAATAATAAAATTTATATAAGTTGATATCA 13 11 1 AATTTTATAA 0.425586 -70 CACAAAAAAGAATTTGAATTATTTGGATAGT 13 52 0 AATTTAATTA 0.789983 -29 AATTTTATTAATTTTGAAAGACCTACTATAA 15 23 1 ATTTTAAAGA 0.866379 -44 TCATTAACTTATTATTTAAGAGATTGTTTTA 16 200 1 ATTATTAAGA 0.516507 -101 ***** ***** Masking position 5 Map Score: 20.4448 Number of sites scoring better than the average of aligned sites = 1354 Number in coding regions = 957 Number in noncoding regions = 397 Number of orfs with sites within 600 bp upstream = 320 Fraction of orfs with sites within 600 bp upstream = 0.0513974 Motif number 4 AAACAATCCAAATAAACCTTTAATTAACTAAACG 1 104 1 AATAAACTTT 0.773261 -197 CCTTTAATTAACTAAACGCTAAATATTCTCCATA 1 120 1 ACTAAACTAT 0.919159 -181 TTAAATGAAAACTAAAAGAGTTTTCATAGCTGGA 2 76 0 ACTAAAAGTT 0.809277 -225 TTTAACTTTTTCTAAAAGTTTCGTTTGTATCCCT 2 151 1 TCTAAAATTT 0.707728 -150 TTAAATCTTAACTTAACAGTTTTTAATGGTGAAT 2 275 1 ACTTAACTTT 0.8082 -26 GTCACCAAAAATTTATTGTCAATTTAG 4 4 1 ACCAAAATTT 0.82416 -85 TAAAATTACAATTAAAAACTTTTTTAGATAACTT 4 53 0 ATTAAAATTT 0.655613 -36 AATTTTTAACCAAAAATATTTTAAATAAGATT 5 27 0 ACCAAAAATT 0.647413 -22 ATAGAAATTAACTAAACTATTTTTAAACT 7 6 0 ACTAAACTTT 0.96364 -55 ATTACCACCAAAAAATTTATATGCTTTCTA 9 7 1 ACCAAAATTT 0.919183 -82 ATATACAGACACTAAACTTTACATTTAGAAAGCA 9 32 0 ACTAAACTAT 0.917688 -57 GATATTAAAAACTAAAAGATTGGTGGGATT 9 69 1 ACTAAAATTT 0.840307 -20 TTAAAATAATACTAAAATTAAAATAGAATTTAAT 11 93 1 ACTAAAAAAT 0.681853 -86 GTTCTCACTTAACCTTTAGTAAAGCCTTTG 11 159 0 ACTTAACTTT 0.644656 -20 TGAACCTTTTACTAAAAGGTTCTTTCAAAATGTT 12 243 1 ACTAAAATTT 0.96741 -58 CTAATAATAAAATTTATATAAGTTGATAT 13 6 1 AATAAAATAT 0.670681 -75 TTTCAAAATTAATAAAATTTACTTATGAAAA 15 8 0 AATAAAATAT 0.664604 -59 ******* ** * Masking position 6 Map Score: 17.3368 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 169 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 TTTGGATTGTTTGTTGACGCATTGATTGGATATAT 1 81 0 TTTGACATTA 0.939992 -220 GGTTGTCCAATTAGAGAAACATTGAGAACTGATTA 1 152 0 TTGGACATTA 0.726974 -149 TTTCTAATAATTTTGGAGATATTAAAAATCCAATA 1 274 1 TTTGATATTA 0.437204 -27 CTTTCCAGCTATGAAAACTCTTTTAGTTTTCATTT 2 73 1 ATAAACTTTA 0.512843 -228 TATTAATTAATAATAATTCCTTTTAGTGTTTATAA 3 33 1 TATATCTTTA 0.543876 -36 TGAATTTTGAACGCTTTCATAAAGGGGGT 11 5 1 TTTAACTTTA 0.906503 -174 TAAATTCTTTTTATAGAGTCTTTTAAAACATTTTG 11 61 0 TTTGACTTTA 0.893045 -118 ACTTAACCTTTAGTAAAGCCTTTGAATAATTTTAA 11 148 0 TATAACTTTA 0.758428 -31 ACACTATATTTTAAAATTTCTTTTATTATGATTAT 12 35 0 TTAATCTTTA 0.532488 -266 AAATTTTAAAATATAGTGTCTTTCAAAGTTGTTAA 12 51 1 ATTGTCTTTA 0.761868 -250 TGTTAGATTTTTGATGAACCTTTTACTAAAAGGTT 12 229 1 TTAGACTTTA 0.932214 -72 AACCTTTTACTAAAAGGTTCTTTCAAAATGTTTTT 12 245 1 TAAGGCTTTA 0.510768 -56 CCTTATATTTTATTAGTATCTTTCAAAAACATTTT 12 269 0 TATGTCTTTA 0.817458 -32 TTGTGTATTATTTTAGACACTTTTAGAGATGAGGC 16 48 1 TTTGACTTTA 0.972546 -253 CAACCTCTGTTTTTGGGAACTTTAAAATCTCTTTT 16 157 0 TTTGGCTTTA 0.919779 -144 ACAGAGGTTGATAATGAATCATTAACTTATTATTT 16 182 1 ATAGACATTA 0.567926 -119 AGTAGGGGAGTTTTAGATGCATTTAGGGAG 16 281 1 TTTGACATTA 0.939948 -20 ** * ** **** * Masking position 12 Map Score: 10.4185 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 478 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 CATTAATAGAGCATCAAAATACCAATTATA 1 190 1 GCATCAAAAT 0.877047 -111 ATTTTTAATATCTCCAAAATTATTAGAAAT 1 273 0 TCTCCAAAAT 0.64245 -28 GCTTTCCATTTCATCAAAATAGGATGCATT 2 39 0 TCATCAAAAT 0.957588 -262 GTCACCAAAAATTTATTGTCA 4 2 1 TCACCAAAAA 0.907739 -87 ATATAGTAAGTTATCTAAAAAAGTTTTTAA 4 46 1 TTATCTAAAA 0.48253 -43 ATTATGATTATCCTCCAAATTTATTGAAGT 12 16 0 TCCTCCAAAT 0.831464 -285 AGTAAAAGGTTCATCAAAAATCTAACACCT 12 226 0 TCATCAAAAA 0.951195 -75 AAAAATCCCCTAAAAATTAAAATTA 14 15 0 TCCCCTAAAA 0.854641 -15 CATTAATTCCTCCTCAAAATCAATATTAAG 16 117 0 TCCTCAAAAT 0.948913 -184 ATCAACATAGTCCTCTAAAATTATAAAACA 16 224 0 TCCTCTAAAA 0.920928 -77 ATCTAAATAATCATCAACATAGTCCTCTAA 16 236 0 TCATCAACAT 0.780757 -65 TTCATCACCCTCATCTAAATAATCATCAAC 16 248 0 TCATCTAAAT 0.942532 -53 CTCCCTAAATGCATCTAAAACTCCCCTACT 16 281 0 GCATCTAAAA 0.817275 -20 ********** Masking position 7 Map Score: 12.8012 Number of sites scoring better than the average of aligned sites = 635 Number in coding regions = 522 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 7 CCATAATCAGTTCTCAATGTTTCTCTAATT 1 149 1 TTCTCAATGT 0.679157 -152 CTCAATGTTTCTCTAATTGGACAACCACCC 1 161 1 CTCTAATTGG 0.839909 -140 TTTTGATGCTCTATTAATGGGTGGTTGTCC 1 179 0 CTATTAATGG 0.580641 -122 ATATAATTTTTTATAATTGGTATTTTGATG 1 201 0 TTATAATTGG 0.918652 -100 TGGTAGTATTTTATAATAGGACTTATGTAA 1 237 0 TTATAATAGG 0.526395 -64 TTATTAGAAATTCTAATTGGTAGTATTTTA 1 254 0 TTCTAATTGG 0.947575 -47 AACTTAACAGTTTTTAATGGTGAATTT 2 284 1 TTTTTAATGG 0.63609 -17 CTTTTAGTGTTTATAAATGGTGATGTC 3 52 1 TTATAAATGG 0.936996 -17 CTAAAAAAGTTTTTAATTGTAATTTTATAA 4 60 1 TTTTAATTGT 0.661269 -29 ATTATCATGTTTATAATTGTTGG 6 113 1 TTATAATTGT 0.842087 -13 TTTATATGCTTTCTAAATGTAAAGTTTAGT 9 26 1 TTCTAAATGT 0.918303 -63 TCCTTAGTATTTCAAAATGTTTTAAAAGAC 11 49 1 TTCAAAATGT 0.766879 -130 AAAATTAATATTAATAATGGATATTTGAAC 12 84 1 TTAATAATGG 0.582871 -217 AAAAGGTTCTTTCAAAATGTTTTTGAAAGA 12 256 1 TTCAAAATGT 0.766879 -45 ********** Masking position 6 Map Score: 8.11985 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 377 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 CGCTTTCATAAAGGGGGTGTTTATTGGTCCT 11 22 1 AGGGGGTGTT 0.983766 -157 GCTCTCCTATAGGGAGGTGTTCATTAATGCC 12 114 1 AGGAGGTGTT 0.986504 -187 GAGCGTAAGCGAGGAGGTGTTAGATTTTTGA 12 212 1 GGGAGGTGTT 0.991374 -89 TATTGATTTTGAGGAGGAATTAATGGAGCTG 16 122 1 GGGAGGAATT 0.905031 -179 GGAGGAATTAATGGAGCTGTTAAAAAAGAGA 16 134 1 AGGAGCTGTT 0.943692 -167 GATGAATTCAGTAGGGGAGTTTTAGATGCAT 16 272 1 GAGGGGAGTT 0.887647 -29 * ********* Masking position 10 Map Score: 1.88383 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 78 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 GTCAACAAACAATCCAAATAAACCTTTAAT 1 98 1 AATCCAAATA 0.933583 -203 AAAAATAGTTAATCCATAAATCTAAAAAAA 2 229 0 AATCCATAAA 0.899572 -72 TATAGTAAGTTATCTAAAAAAGTTTTTAAT 4 47 1 TATCTAAAAA 0.788074 -42 TAATAAAAAATCCAGAAATCTTATTTAA 5 9 1 AATCCAGAAA 0.952161 -40 AATTTTTAACCAAAAATATTTTAAAT 5 33 0 TAACCAAAAA 0.66433 -16 CTTTTTATTTATTCTAAAAAAGAGAAAAGA 8 21 0 ATTCTAAAAA 0.617243 -27 AGTGTCTGTATATCCAGATATTAAAAACTA 9 53 1 TATCCAGATA 0.842183 -36 TGCCTTAGTTATTCCAGAAACCATAGGGCT 12 141 1 ATTCCAGAAA 0.847907 -160 CATACTAAACTATCCAAATAATTCAAATTC 13 44 1 TATCCAAATA 0.904383 -37 GAAAAATCCTAATCTATATAACAATGGACT 16 13 1 AATCTATATA 0.632294 -288 ********** Masking position 6 Map Score: 3.6497 Number of sites scoring better than the average of aligned sites = 566 Number in coding regions = 500 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 10 TATTTAGCGTTTAGTTAATTAAAGGTTTAT 1 115 0 TTAGTTAATT 0.923374 -186 ATAATAGGACTTATGTAATTTTTTATATAA 1 225 0 TTATGTAATT 0.439203 -76 TATTGTCAATTTAGCTAAATTTATATAGTA 4 24 1 TTAGCTAAAT 0.800928 -65 TATAAAAGGTTAAGCTAATTATCATTATTA 6 38 1 TAAGCTAATT 0.890216 -88 TATGACTCACTAAGGTAATGAATAGATAAT 6 78 0 TAAGGTAATG 0.916986 -48 TAAAAATAGTTTAGTTAATTTCTATTTTGT 7 15 1 TTAGTTAATT 0.923374 -46 TATAAAAATATAAGTTAAATTTTGAATTAA 10 28 0 TAAGTTAAAT 0.894101 -119 ATTAAAAAGATAAGGTAAAGATATCAGAAT 10 76 0 TAAGGTAAAG 0.866894 -71 AAAGAACCTTTTAGTAAAAGGTTCATCAAA 12 238 0 TTAGTAAAAG 0.622449 -63 TTTTCATAAGTAAATTTTATTAATTT 15 7 1 TAAGTAAATT 0.780366 -60 TCTTAAATAATAAGTTAATGATTCATTATC 16 191 0 TAAGTTAATG 0.930516 -110 ********** Masking position 7 Map Score: 4.89618 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 320 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 TATTATTAATTAATAATACTTTTCGTGGTG 3 18 0 TAATAATACT 0.73634 -51 TATTATTAATTAATAATAATTCCTTTTAGT 3 30 1 TAATAATAAT 0.936828 -39 AAAAAGTTTTTAATTGTAATTTTATAAAAT 4 63 1 TAATTGTAAT 0.839608 -26 TCATAATTAATAATGATAATTAGCTTAACC 6 45 0 TAATGATAAT 0.844297 -81 AATAGATAATTTATCATAATTAATAATGAT 6 58 0 TTATCATAAT 0.559076 -68 TTTAAAAACATAATAGTAATAAATTATTTG 10 116 1 TAATAGTAAT 0.893591 -31 AGCCTTTGAATAATTTTAATCAATGAATGT 11 137 0 TAATTTTAAT 0.829036 -42 ATTTGGAGGATAATCATAATAAAAGAAATT 12 26 1 TAATCATAAT 0.908919 -275 TTGTTAAAATTAATATTAATAATGGATATT 12 79 1 TAATATTAAT 0.886095 -222 CTAATAATAAAATTTATATAA 13 2 1 TAATAATAAA 0.653296 -79 TTATTAATTTTAATTTTTAGGGGA 14 5 1 TAATTTTAAT 0.829036 -25 ********** Masking position 3 Map Score: 6.20515 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 159 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 12 ********** No masking Map Score: -1.94446e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: -1.94446e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: -1.94446e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0