AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inarL_ecoli_bsub_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A #2 narK 300 nitrite extrusion protein #3 narG 300 nitrate reductase 1, alpha subunit #4 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #5 ccmC 41 heme exporter protein C #6 napF 300 ferredoxin-type protein: electron transfer #7 nirB 261 nitrite reductase (NAD(P)H) subunit #8 nirC 300 nitrite reductase activity #9 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #10 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #11 nrfE 79 formate-dependent nitrite reductase; possible assembly function #12 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #13 nasF 60 uroporphyrin-III C-methyltransferase #14 nasE 31 assimilatory nitrite reductase (subunit) #15 nasD 121 assimilatory nitrite reductase (subunit) #16 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #17 cysH 300 phosphoadenosine phosphosulfate #18 ylnB 48 similar to sulfate adenylyltransferase #19 ylnD 98 similar to uroporphyrin-III C-methyltransferase #20 citB 227 aconitate hydratase #21 yneN 71 similar to thiol:disulfide interchange protein #22 yoaE 300 similar to formate dehydrogenase #23 resC 135 essential protein similar to cytochrome c biogenesis protein #24 spoIIIAC 22 spoIIIAC #25 spoIIIAA 75 spoIIIAA #26 yqhV 144 alternate gene name: yqgE #27 nadB 102 L-aspartate oxidase #28 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #29 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #30 gerBA 264 gerBA #31 narJ 25 nitrate reductase (protein J) #32 narG 195 nitrate reductase (alpha subunit) #33 narK 135 nitrite extrusion protein #34 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter #35 yyaE 300 similar to formate dehydrogenase Motif number 1 ACAATAATTACTCCTCACTTACACGTAATA 1 50 1 CTCCTCACTT 0.79032 -251 GAAAGAGTTACTCCTTATTTGCCGTGTGGT 2 81 1 CTCCTTATTT 0.49731 -220 TGCTTTCCTCTTTTTTCAGGGGTA 4 218 0 TTCCTCTTTT 0.899654 -14 ACAATTTTACCTGCTCTTTTAGTGTTAAAT 6 14 1 CTGCTCTTTT 0.935231 -287 TTCTGCTGGTTTGCTCTCTCATTAGAATTT 6 40 0 TTGCTCTCTC 0.634962 -261 GTCCGGCCTTTTCCTCTCTTCCCCCGCTAC 7 38 1 TTCCTCTCTT 0.867428 -224 AGTCAGTATCTTCCTCTTTTTCAACAGCAT 9 107 0 TTCCTCTTTT 0.899654 -194 GTCCAGAAACCACCTCTTTTCTGGC 11 6 0 CACCTCTTTT 0.839172 -74 AGTGATAATTTAGCCCTCTTGCGCACTAAA 12 125 1 TAGCCCTCTT 0.330287 -170 CGCTATTCCACTGCTCCTTTATAGGTACAA 12 201 0 CTGCTCCTTT 0.893895 -94 AAGATTCCCCTTTCTAGACCCTCA 16 5 1 TTCCCCTTTC 0.764907 -175 TTCTTCTTTCCTCCTTTCGGAGACAAA 17 284 0 TTCCTCCTTT 0.83951 -17 GGCCCAGTTCCTCTCTCTAGTTAGATA 22 284 0 TTCCTCTCTC 0.764907 -17 CATGACATCACTCCCTTTTCGC 23 3 0 CTCCCTTTTC 0.652481 -133 CGGTTTGGCCTGCCCTTTTTATCTTTATT 23 117 0 CTGCCCTTTT 0.913329 -19 CAGAGCCTCCTCCTTTCTACCGATTG 25 60 0 CTCCTCCTTT 0.940329 -16 ATCTGTCTCCCCTCTCTCCTGCGTAT 29 7 1 CTCCCCTCTC 0.877351 -286 TTTCATTTTACTCCTCCCTCAAAAGGGCGT 29 181 0 CTCCTCCCTC 0.851164 -112 CCCGTATAAGCTGCCTTTTTCCTATGACAA 30 75 1 CTGCCTTTTT 0.668715 -190 AAGAATAATTCTCCTTTTTTGATACAAATT 30 207 1 CTCCTTTTTT 0.838021 -58 CTTGTTACACCTCATTTATCAAAAG 31 9 0 CACCTCATTT 0.499436 -17 GTCACACACTCTGCTTTTTTCACAAAATGT 32 101 0 CTGCTTTTTT 0.734459 -95 TTGGCTTGCCCCTTTCAATGATTCA 33 121 0 TTGCCCCTTT 0.67115 -15 TATTTCTCCCCCTTTTATTTAAACA 34 6 1 CTCCCCCTTT 0.920003 -295 TGTCTTTTCCTGCTTTCTTTCATGATTGA 34 282 0 CTGCTTTCTT 0.668715 -19 CAAGACCCTTCACCTCTTTTCCTAAACTGC 35 27 0 CACCTCTTTT 0.839172 -274 ********** Masking position 9 Map Score: 25.3045 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 417 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 2 CGGTTTTCTCCTGTGGGAGCCT 3 289 0 GTTTTCTCCT 0.905442 -12 TCGTCGTCCGGCCTTTTCCTCTCTTCCCCC 7 33 1 GCCTTTTCCT 0.966624 -229 CTTATCAAATGTTTTTTCCAGCGTAGCACA 15 88 0 GTTTTTTCCA 0.516883 -34 ACTTACACATGTCTTTTCCAGAAAATAATG 16 69 0 GTCTTTTCCA 0.786261 -111 AAGCTCGTAAGTTTTCTCCTATTAAAAATT 16 140 0 GTTTTCTCCT 0.905442 -40 TCTGCCGGTTGTCTTTTCCCATGTAATGTG 17 241 0 GTCTTTTCCC 0.892339 -60 AAAGCGAAATGCCTTCTCTTCCTATTGATT 21 13 0 GCCTTCTCTT 0.840822 -59 AAGGCATTTCGCTTTCTCTTCTTTTTATGA 21 28 1 GCTTTCTCTT 0.605725 -44 CAGAGCCTCCTCCTTTCTACCGAT 25 62 0 GCCTCCTCCT 0.885358 -14 GAAAAAAGAAGTCTGTTCCCAAATGGGAGC 26 15 1 GTCTGTTCCC 0.689929 -130 CACAAAAAAAGCCTGCTCCCATTTGGGAAC 26 29 0 GCCTGCTCCC 0.867382 -116 CTTTGTTTCAGCCTTTTCCTCGATAAGAAT 30 183 1 GCCTTTTCCT 0.966624 -82 AACGCAGCCTTCCTTCTCCTTTGTGTGAAC 32 73 1 TCCTTCTCCT 0.736729 -123 AAGTCTTCGGGCTTTGTCCTTTTTTTATGA 33 28 1 GCTTTGTCCT 0.691098 -108 TGTCTTTTCCTGCTTTCTTTC 34 290 0 GTCTTTTCCT 0.947398 -11 CGCCGTCTTCTCCTTACCTTCTAT 35 287 0 GTCTTCTCCT 0.970522 -14 ********** Masking position 4 Map Score: 15.6854 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 262 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 AAGGGAGACAAAAAAAGCGCCCGCAGGCGC 1 7 0 AAAAACGCCC 0.971026 -294 CAATAGCGGTAGAAAAACGCACCACTGCCTGACA 4 78 0 AGAAACGCCA 0.722466 -154 TTTGCCACAAAATAATCCGCCTTCGCAAATTGAC 4 118 0 AAAATCGCTC 0.930707 -114 AGAGCGACCAAATAAACCGCATAATTAATAAGCC 6 242 0 AAAAACGCTA 0.89281 -59 CAACAACGCCAGAAAACCGACTTCAGGAAGGAAT 11 38 0 AGAAACGATC 0.880927 -42 TTGCGCACTAAAAAAATCGATCTCGTCAAATTTC 12 143 1 AAAAACGACC 0.880927 -152 TGCTACTTCCAGCAAAATGAATTCCATTTTGAAA 17 108 1 AGAAATGATC 0.506882 -193 AAAGGGCGTCAAGAAAACGCGTACATAAATTATA 29 156 0 AAAAACGCTC 0.983593 -137 AATAAATCTTAATAAAGTGCTTACAATTGAAAGA 29 216 1 AAAAATGCTC 0.89281 -77 TACCCCTTCAAAGAAAACGCTTCCTATCTATTAT 30 132 1 AAAAACGCTC 0.983593 -133 TATTCAGATTAAGAATACGCTTTCATCATAAATC 34 135 1 AAAATCGCTC 0.930707 -166 CGTAGAAATGAAAAAACCGCATCCATGCGGAGCG 35 86 1 AAAAACGCTC 0.983593 -215 ** *** *** * * Masking position 5 Map Score: 9.51626 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 216 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 4 TTACGTGTAAGTGAGGAGTAATTATTGTTC 1 48 0 GTGAGGAGTA 0.892158 -253 CAGATGGGTATTAAGGAGTATTCCCCATGG 3 46 0 TTAAGGAGTA 0.761951 -255 AATATACCCATTAAGGAGTATATAAAGGTG 7 167 1 TTAAGGAGTA 0.761951 -95 ACCGACTTCAGGAAGGAATACGTCCAGAAA 11 27 0 GGAAGGAATA 0.82116 -53 AAAAACAATCTGGAGGAATGTC 12 283 1 TGGAGGAATG 0.413248 -12 TTACAGTGACGGAAGGATGAC 13 50 1 GGAAGGATGA 0.758394 -11 AAAACTATCATTGAGGAGGAATGGAC 14 16 1 TTGAGGAGGA 0.798014 -16 GTTTGTCTCCGAAAGGAGGAAAGAAGAA 17 283 1 GAAAGGAGGA 0.77513 -18 TGATCTGATCTGAAGGGGGATTTTGGAGA 20 209 1 TGAAGGGGGA 0.825469 -19 CCAATCGGTAGAAAGGAGGAGGCTCTG 25 59 1 GAAAGGAGGA 0.77513 -17 GGAGAACGGATGGAGGAAGACCGG 27 5 0 TGGAGGAAGA 0.734256 -98 TCAAACAGGGGGGAGGATTACAGAATGATC 29 45 1 GGGAGGATTA 0.801497 -248 GCCCTTTTGAGGGAGGAGTAAAATGAAATT 29 183 1 GGGAGGAGTA 0.969616 -110 TTATTTACAGGGGAGGGGTACGGATC 30 7 0 GGGAGGGGTA 0.925811 -258 GCGTTTTCTTTGAAGGGGTAATGAAAAGAT 30 122 0 TGAAGGGGTA 0.828421 -143 CACCTGACTCGGAAGGAGTGAACTCTC 32 179 1 GGAAGGAGTG 0.863461 -17 ********** Masking position 4 Map Score: 10.1086 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 178 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 5 TATCGTCGTCCGGCCTTTTCCTCTCTTCCCCCGC 7 31 1 CGCCTCCTCT 0.882411 -231 CATAGGTCCAGTCCCTCAGCCGCTCTTGATAAGT 17 45 0 GCCCTCCGCT 0.988079 -256 TATACAGATAGCCTTTTTACCTCTTAAAATAAAA 17 192 0 GCTTTCCTCT 0.649893 -109 CATAGGGCCAGTCCCTCCACCTCTCTGGATAGAA 22 128 1 GCCCTCCTCT 0.994137 -173 GGCCCAGTTCCTCTCTCTAGTTAG 22 287 0 GCCCACCTCT 0.981679 -14 CAGAGCCTCCTCCTTTCTACCGATTG 25 60 0 GGCCTCCTTT 0.83507 -16 GATAGCCCCTCTCCCTCTAGTAATCTAG 28 16 0 GCCCTCCTCT 0.994137 -18 TGCTTTACCAGTCACAATCCCGCTTATTCAGATT 34 111 1 GCACACCGCT 0.745208 -190 TATCCGCCAAGACCCTTCACCTCTTTTCCTAAAC 35 30 0 GCCCTCCTCT 0.994137 -271 * **** ***** Masking position 14 Map Score: 6.5006 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 27 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 GCGCCTGCGGGCGCTTTTTTTG 1 3 1 GCCTGCGGGC 0.77316 -298 TCCTGTGGGAGCCTGTCGGCCCTCTGATAA 3 273 0 GCCTGTCGGC 0.811379 -28 CGACGATAGTGCCGTCCGGCATGAGCAA 7 9 0 GCCGTCCGGC 0.547265 -253 CGGCACTATCGTCGTCCGGCCTTTTCCTCT 7 25 1 GTCGTCCGGC 0.873528 -237 CGCATTGCACGCCTGTCGGCAAATAACCCG 8 101 1 GCCTGTCGGC 0.811379 -200 GTTCTCGCTTGCATTCCGGCATCTGAGAAG 19 28 0 GCATTCCGGC 0.946726 -71 AAAGGACAAAGTCTTCGGGCTTTGTCCTTT 33 20 1 GTCTTCGGGC 0.944513 -116 ********** Masking position 8 Map Score: 6.17006 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 247 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 CGGGCGCTTTTTTTGTCTCCCTTTGATACCGAA 1 18 1 TTTTGCCCTT 0.975203 -283 GCTCGCTGTTTTGTCTCTCTTGCCGTTAAAA 4 9 1 TTTTGCCCTT 0.975203 -223 AAAAGCCCGTTTTTGCCACGCTTCCCGCCACTC 6 128 1 TTTTGCCCTT 0.975203 -173 CCTTTTCCTCTCTTCCCCCGCTACGTGCATCTA 7 44 1 TCTTCCCCTA 0.718033 -218 TTTTGCCTCGATTTCTTTTCTAT 7 249 0 TTTTGCCATT 0.896709 -13 TCCATTGTGTTTTCCGCCCCTTGCGAGGCGGA 10 17 0 TTTTCGCCTT 0.807032 -22 TTCAGTGATAATTTAGCCCTCTTGCGCACTAAA 12 122 1 ATTTACCCTT 0.706201 -173 TTGTAGTAAATTTTAGCACAATTCTA 17 4 0 TTTTACCATT 0.70311 -297 TCCATCACAATTTTCTCACAATTTCATATTAAA 20 156 0 TTTTCCCATT 0.896709 -72 GTACGCGTTTTCTTGACGCCCTTTTGAGGGAGG 29 166 1 TCTTGCCCTT 0.956494 -127 GTGCTAAATCTCTTCCCCCACTTCTTTCAATTG 29 239 0 TCTTCCCCTT 0.956494 -54 TATTTCTCCCCCTTTTATTTAAAC 34 2 1 ATTTCCCCTT 0.898077 -299 ***** * * *** Masking position 4 Map Score: 7.83652 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 128 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 TGCCAGGCCGCCGATCGCTGTCGTTTTT 1 283 0 CAGCCGCCGC 0.98498 -18 AGGATGATCCCAAGACCCACATACGCGCCCGCCATG 8 154 0 CAGCCCCCGC 0.997077 -147 AGCGTTAAGGCGATACCAAAGGTCGCGCCCATCACC 8 235 0 CATCCAACGC 0.778462 -66 CTTCATAGGTCCAGTCCCTCAGCCGCTCTTGATAAG 17 46 0 CAGCCCCCGC 0.997077 -255 ATTATTGTGCCAATTCCAGCAAGCGCTAGCTTGAAA 22 79 0 CATCCACCGC 0.938886 -222 TTTCATAGGGCCAGTCCCTCCACCTCTCTGGATAGA 22 125 1 CAGCCCCCTC 0.991134 -176 GATAGCCCCTCTCCCTCTAGTAATCTA 28 17 0 AAGCCCCCTC 0.916385 -17 GCCTGCTTTACCAGTCACAATCCCGCTTATTCAGAT 34 108 1 CAGCACACGC 0.884374 -193 CTTTATCCGCCAAGACCCTTCACCTCTTTTCCTAAA 35 31 0 CAGCCCTCTC 0.935487 -270 * ** *** * *** Masking position 3 Map Score: 6.14491 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 194 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 TTACCAAACCACGGCGACTCACCTCAGCAGCCAATA 1 249 0 AGGATACTCA 0.981402 -52 TTACCGATGTAAAGCGACTAACCACACGGCAAATAA 2 95 0 AGGATACACA 0.859394 -206 ATTTTACAGCACCGTGAAAAATCTCATAATTTTTAT 2 139 1 AGGAAATTCA 0.786376 -162 GTTATCTTATCGTTTGATTTACATCAAATTGCCTTT 2 225 1 CTGATACTCA 0.801476 -76 CCGCCTTCGCAAATTGACCTACCTCAATAGCGGTAG 4 100 0 ATGACACTCA 0.892404 -132 TATAAAGGTGAATTTGATTTACATCAATAAGCGGGG 7 187 1 ATGATACTCA 0.920942 -75 CCGGAATGCAAGCGAGAACATCATCACAGCGAATCT 19 39 1 AGGACTCTCA 0.813148 -60 ATTCTGAAAAAAAGAGATTGACATCAATCTGAGTCT 22 211 0 AGGATACTCA 0.981402 -90 GCGAAAAGGGAGTGATGTCATGGCAGAGCT 23 5 1 AGGATATTCA 0.920942 -131 AGCGTGTTTCCTTGTGAACTATGTCACACACTCTGC 32 117 0 CGGACATTCA 0.741901 -79 GCCAAACAGGATTGTGAATTACATCACACGTTTTTC 33 58 0 AGGATACTCA 0.981402 -78 GTAAAAATTAATTGTGAAATACTTCACAATATCGTG 34 235 1 AGGAAACTCA 0.943424 -66 * * ** * ** *** Masking position 7 Map Score: 7.02304 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 69 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 TTCTAAAAATTTTATGAAAAAT 15 2 0 TTTATGAAAA 0.91114 -120 ATAAGTTCGACTTATGAGAAAAATGTACCGG 20 81 0 CTTATGAAAA 0.929191 -147 TTCTCTTCTTTTTATGACACAATGTGCTGCG 21 41 1 TTTATGAACA 0.801221 -31 CTGAGTCTTCTTTATGATAAACGTATTCTTC 22 188 0 TTTATGAAAA 0.755302 -113 TGAGGCAGACTTTATGACAAGCCTCTCT 25 8 0 TTTATGAAAG 0.768251 -68 TCCTGTAATTCTTATGAAAAATTAAGCAAGA 29 73 1 CTTATGAAAA 0.922434 -220 CTTTTGATAAATGAGGTGTAA 31 1 1 CTTTTGAAAA 0.617483 -25 GTGTGAACATTTTGTGAAAAAAGCAGAGTGT 32 95 1 TTTGTGAAAA 0.780713 -101 TTGTCCTTTTTTTATGAGAAAAACGTGTGAT 33 41 1 TTTATGAAAA 0.944441 -95 GCTATCATGATTTATGATGAAAGCGTATTCT 34 146 0 TTTATGAGAA 0.795149 -155 CCTTACCTTCTATATGAAAAAGCATGAGTGT 35 269 0 TATATGAAAA 0.73229 -32 ******* *** Masking position 7 Map Score: 5.8608 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 25 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 ATCTACCTATCTCTTTGATTTTCAAATTAT 1 96 1 CTCTTTGATT 0.715188 -205 AACAGATGTTCTTTTTGATTTCGCGCAAAA 4 150 1 CTTTTTGATT 0.89084 -82 CAGAATTTTACTGTTAGTTTCCTCGCGCAG 4 185 1 CTGTTAGTTT 0.81693 -47 TAAACTTTTTGTTTTATTTTTTGT 8 5 1 CTTTTTGTTT 0.922767 -296 TTTTGTTTTATTTTTTGTTTTTATTTTTTA 8 17 1 TTTTTTGTTT 0.836033 -284 CTGCCCACCGCTGTTTGATTCCTGCGTAAA 12 44 0 CTGTTTGATT 0.870657 -251 TCTTGATAAGTTTTTAGATTTGTAGTAAAT 17 26 0 TTTTTAGATT 0.611948 -275 CAGAAAGCTACTGTTTGTTTGTCTCCGAAA 17 267 1 CTGTTTGTTT 0.907877 -34 ATTTTAGGTCTTTTTTGTTTAAATAAAAGG 34 21 0 TTTTTTGTTT 0.836033 -280 ACTAGTACTTTTTTTAGTTTTCTTTCAAAT 35 206 0 TTTTTAGTTT 0.697771 -95 ********** Masking position 5 Map Score: 2.7956 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 91 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 TCGTTATCAATTCCCACGCTGTTTCAGAGCGTT 3 210 1 TTCCGCTGTT 0.886801 -91 TTTCAGAGCGTTACCTTGCCCTTAAACATTAGC 3 231 1 TTCTGCCCTT 0.974889 -70 GCTGTTTTGTCTCTCTTGCCGTTAAAAATTAAG 4 15 1 CTCTGCCGTT 0.869531 -217 CAGACAATTTTACCTGCTCTTTTAGTGTTAA 6 9 1 TTCTGCTCTT 0.953297 -292 CCTTCAAAAATTACCCTGCCGTTTATTTGCACA 9 28 0 TTCTGCCGTT 0.974889 -273 AACATGCAGTTATGCATGCTGTTGAAAAAGAGG 9 92 1 TACTGCTGTT 0.702756 -209 AAAGTGGTATTTTACATGCACTTACAATTGATT 9 143 1 TTCTGCACTT 0.834319 -158 TGCGTAAAATTTGTCTCGCCGTCGCGTTGCGAG 12 19 0 TTCCGCCGTC 0.718934 -276 GAGAAGGCATTTCGCTTTCTCTTCTTTTTATGA 21 25 1 TTCTTCTCTT 0.594252 -47 CGGTTTGGCCTGCCCTTTTTATCTTTA 23 119 0 TTCTGCCCTT 0.974889 -17 TTGGCTTGCCCCTTTCAATGATT 33 123 0 TTCTGCCCCT 0.869531 -13 ATGCGTATAATTTTCCAGCTGTTCGCTCCGCAT 35 110 0 TTCAGCTGTT 0.741744 -191 ** * ******* Masking position 5 Map Score: 4.61641 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 172 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 CACGGCGACTCACCTCAGCAGCCAATACCG 1 246 0 CACCTCAGCA 0.899704 -55 GGTATGGGTATACTTCAGCCAATAGCCGAG 2 49 0 TACTTCAGCC 0.741044 -252 TAGAAAAACGCACCACTGCCTGACAGGCCA 4 73 0 CACCACTGCC 0.795449 -159 GCTTTTGGGTCAGCTCCGCCATGGCGGGCG 8 135 1 CAGCTCCGCC 0.950489 -166 CCCCGTTCCGCCTCGCAAGGGG 10 3 1 CCGTTCCGCC 0.808793 -36 ATTGTTTTTATCCCACAGCCACGTACTTCA 12 262 0 TCCCACAGCC 0.848811 -33 TTTTCCAGCGTAGCACAGCAAAAAGGAATA 15 75 0 TAGCACAGCA 0.480217 -47 ATAGGTCCAGTCCCTCAGCCGCTCTTGATA 17 48 0 TCCCTCAGCC 0.950454 -253 ATGCCACCTCCGCAGCACATTGTG 21 58 0 CACCTCCGCA 0.923303 -14 ATAGGGCCAGTCCCTCCACCTCTCTGGATA 22 129 1 TCCCTCCACC 0.629029 -172 AATTTCCGCTCAGCTCTGCCATGACATCAC 23 22 0 CAGCTCTGCC 0.882409 -114 ATGACAAGACTACTTCAGCAAGCTAGAGCA 26 90 1 TACTTCAGCA 0.503332 -55 GATAGCCCCTCTCCCTCTAGTAATC 28 19 0 CCCCTCTCCC 0.611873 -15 TTCCAGCTGTTCGCTCCGCATGGATGCGGT 35 101 0 TCGCTCCGCA 0.837363 -200 ********** Masking position 6 Map Score: 4.90757 Number of sites scoring better than the average of aligned sites = 1586 Number in coding regions = 1512 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 14 TTTTATTTTTTGTTTTTATTTTTTAAAGGA 8 22 1 TGTTTTTATT 0.859669 -279 TTGCAATGGCGGTTTTTATTGTTTTTCACG 9 254 0 GGTTTTTATT 0.923288 -47 CATCAGATCGTGCTTTTTTTAGTCACTGCC 12 69 0 TGCTTTTTTT 0.726073 -226 CGGATTGAAAGTTTTTTATTTTAAGAGGTA 17 179 1 GTTTTTTATT 0.703265 -122 ATAATATGGCTTCTTTTATTGTGTTATATG 20 27 1 TTCTTTTATT 0.498746 -201 TAAATATCAATGTTTTTATTAAATACAATA 20 109 0 TGTTTTTATT 0.859669 -119 AATGGGAGCAGGCTTTTTTTGTGCCCAAAA 26 36 1 GGCTTTTTTT 0.838909 -109 ACATATTGACGGTTTTTATTAATTTGTATC 30 227 0 GGTTTTTATT 0.923288 -38 ATAGAGCCGGTTTTTTTTGATCTTTGAA 32 9 1 GGTTTTTTTT 0.863268 -187 ********** Masking position 5 Map Score: 2.69547 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 96 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 15 CGACAGGCTCCCACAGGAGAAAACCG 3 285 1 CCACAGGAGA 0.769456 -16 GCGCCCATCACCAAAGGGCGTACGGATGGA 8 217 0 CCAAAGGGCG 0.912548 -84 TAAGGCGATACCAAAGGTCGCGCCCATCAC 8 236 0 CCAAAGGTCG 0.5751 -65 ACGAGCTTCGCCAAAGGAGGTCTGATAC 16 162 1 CCAAAGGAGG 0.9406 -18 TGTTTGTCTCCGAAAGGAGGAAAGAAGAA 17 282 1 CGAAAGGAGG 0.869823 -19 GAATAAAGATAAAAAGGGCAGGCCAAACCG 23 116 1 AAAAAGGGCA 0.704312 -20 GCCAATCGGTAGAAAGGAGGAGGCTCTG 25 58 1 AGAAAGGAGG 0.785191 -18 CAGGTGTAAACAACAGGAGGATGGCAT 27 86 1 CAACAGGAGG 0.906266 -17 ATTATAGCTCAAACAGGGGGGAGGATTACA 29 37 1 AAACAGGGGG 0.85158 -256 ACTCCTCCCTCAAAAGGGCGTCAAGAAAAC 29 172 0 CAAAAGGGCG 0.919824 -121 CGCACTTATCAAACAGGGGGTAAAGTA 29 276 1 AAACAGGGGG 0.85158 -17 ATTTGTATCAAAAAAGGAGAATTATTCTTA 30 206 0 AAAAAGGAGA 0.783299 -59 AAATGTTCACACAAAGGAGAAGGAAGGCTG 32 77 0 ACAAAGGAGA 0.766775 -119 TCACGATCAAAAGGACAAAGTCTTCGG 33 8 1 CAAAAGGACA 0.800551 -128 TTTCTCATAAAAAAAGGACAAAGCCCGAAG 33 32 0 AAAAAGGACA 0.687084 -104 TTTGTTTAAATAAAAGGGGGAGAAATA 34 8 0 TAAAAGGGGG 0.649307 -293 ********** Masking position 5 Map Score: 11.6822 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 211 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223