AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inarP_ecoli_bsub_300.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 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #2 ccmC 41 heme exporter protein C #3 napF 300 ferredoxin-type protein: electron transfer #4 yhfC 270 putative transport #5 nirB 261 nitrite reductase (NAD(P)H) subunit #6 nirC 300 nitrite reductase activity #7 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #8 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #9 nrfE 79 formate-dependent nitrite reductase; possible assembly function #10 nasF 60 uroporphyrin-III C-methyltransferase #11 nasE 31 assimilatory nitrite reductase (subunit) #12 nasD 121 assimilatory nitrite reductase (subunit) #13 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #14 cysH 300 phosphoadenosine phosphosulfate #15 ylnB 48 similar to sulfate adenylyltransferase #16 ylnD 98 similar to uroporphyrin-III C-methyltransferase #17 citB 227 aconitate hydratase #18 yneN 71 similar to thiol:disulfide interchange protein #19 resC 135 essential protein similar to cytochrome c biogenesis protein #20 resA 131 essential protein similar to cytochrome c biogenesis protein #21 ypuL 91 similar to hypothetical proteins #22 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #23 ypuI 54 similar to hypothetical proteins from B. subtilis #24 ypuG 280 similar to hypothetical proteins #25 spoIIIAC 22 spoIIIAC #26 spoIIIAA 75 spoIIIAA #27 yqhV 144 alternate gene name: yqgE #28 efp 24 elongation factor P #29 yqhS 86 similar to 3-dehydroquinate dehydratase #30 yqhR 226 yqhR #31 gerBA 264 gerBA #32 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter Motif number 1 TCAATAGCGGTAGAAAAACGCACCACTGCCT 1 82 0 TAAAAAACGC 0.714956 -150 CGGGAAGCGTGGCAAAAACGGGCTTTTGCTC 3 124 0 GGAAAAACGG 0.74139 -177 CAAACAGAGCAGAAAAAAAGCAAGTGAAGAG 4 24 1 AGAAAAAAGC 0.788001 -247 AATAGCCTTCAAGAACAAGGCCATCCCTTTA 4 61 1 AAAACAAGGC 0.743936 -210 CGGGGGAAGAGAGGAAAAGGCCGGACGACGA 5 33 0 GAGAAAAGGC 0.967649 -229 CCCGAGACTTAACAACAACGCCAGAAAACCG 9 53 0 AAAACAACGC 0.78784 -27 TATTTTAAGAGGTAAAAAGGCTATCTGTATA 14 195 1 GGAAAAAGGC 0.951583 -106 TCCGGCATCTGAGAAGAACGCAGCAGATCAT 16 13 0 GAAAGAACGC 0.944457 -86 GAATCAATAGGAAGAGAAGGCATTTCGCTTT 18 12 1 GAGAGAAGGC 0.930344 -60 GTCATAAAAAGAAGAGAAAGCGAAATGCCTT 18 28 0 GAGAGAAAGC 0.858068 -44 CGGGAATAAAGATAAAAAGGGCAGGCCAAAC 19 113 1 GAAAAAAGGG 0.772732 -23 GGCGGATCACGGTAAAAACGCTTTCTAAATT 20 27 1 GGAAAAACGC 0.961716 -105 TGCCAAATCTAAAAAAAACGCCGTTT 21 6 0 AAAAAAACGC 0.940867 -86 ATCTTATGATGATGAAAAAGCGCGATTCATT 23 17 0 GAGAAAAAGC 0.93122 -38 GATAAAAGGAAAAAAGAACGCCCGGCCTCTA 24 53 1 AAAAGAACGC 0.876614 -228 CGCAGAAGCGGGAGAAAAAGCCTTTGCTTCT 24 106 0 GGGAAAAAGC 0.899309 -175 ATGAAATGTCAATAAAAAAGCTCACACTTTT 30 177 0 AAAAAAAAGC 0.849277 -50 ATGTTGTCATAGGAAAAAGGCAGCTTATACG 31 77 0 AGAAAAAGGC 0.891443 -188 TTACCCCTTCAAAGAAAACGCTTCCTATCTA 31 131 1 AAGAAAACGC 0.941086 -134 TATTCTTATCGAGGAAAAGGCTGAAACAAAG 31 183 0 GAGAAAAGGC 0.967649 -82 AAAAATAGTTGACGAAAACGCTATCATGATT 32 165 0 GAGAAAACGC 0.97451 -136 ** ******** Masking position 5 Map Score: 27.2292 Number of sites scoring better than the average of aligned sites = 903 Number in coding regions = 781 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 2 TGCTTTCCTCTTTTTTCAGGGGTAT 1 217 0 TCCTCTTTTT 0.895416 -15 ATTTGCACAATTCTACTTTTGCGTGA 7 7 0 TTCTACTTTT 0.6073 -294 GTCAGTATCTTCCTCTTTTTCAACAGCATG 7 106 0 TCCTCTTTTT 0.895416 -195 GTATCTTAAATATTCCTTTTTGCTGTGCTA 12 65 1 TATTCCTTTT 0.553592 -57 AAGATTCCCCTTTCTAGACCCTCA 13 5 1 TTCCCCTTTC 0.791056 -175 CTCGTAAGTTTTCTCCTATTAAAAATTATG 13 137 0 TTCTCCTATT 0.684576 -43 GCTGTTCCTGTCTTTCTTTCCGCCGGATTG 14 156 1 TCTTTCTTTC 0.597094 -145 TTCTTCTTTCCTCCTTTCGGAGACAAAC 14 283 0 TCCTCCTTTC 0.974212 -18 AAATGCCTTCTCTTCCTATTGATTCA 18 7 0 TCTTCCTATT 0.851322 -65 TTTCGCTTTCTCTTCTTTTTATGACACAAT 18 34 1 TCTTCTTTTT 0.819893 -38 ATTTCACATTTCTTACTTTTTGAAGGTTAT 20 62 0 TCTTACTTTT 0.803151 -70 TGCCCCCTTCCCCCTATTGCAGATCCAT 20 114 0 TCCCCCTATT 0.842646 -18 TCAAGTATTATCTTACTTTTTTCAACCTTA 21 62 0 TCTTACTTTT 0.803151 -30 CGTTTACTCTCCCTTTTTCAGGGAGAG 22 8 1 TCTCCCTTTT 0.936462 -115 GATAGCTTCTTCCTTATATCTTATGAT 23 38 0 TCTTCCTTAT 0.60538 -17 GGTGCTTCCTCCTTTAATGTGCTTTT 24 7 1 TCCTCCTTTA 0.881503 -274 GGGCGTTCTTTTTTCCTTTTATCCCTTCTA 24 46 0 TTTTCCTTTT 0.856596 -235 TTGCTTCTGGTTTTCCTTTCTAAGAAGCAC 24 84 0 TTTTCCTTTC 0.801907 -197 CAGAGCCTCCTCCTTTCTACCGATTGG 26 59 0 TCCTCCTTTC 0.974212 -17 AAAAACAGAATCTTTCTTTTATACGGAAAT 27 62 1 TCTTTCTTTT 0.6862 -83 TCTCCCAACCTCCCATTTTTTTATATGATA 27 120 0 TCCCATTTTT 0.369506 -25 GTTTAATGTCCTCCTATATTCCAA 28 7 0 TCCTCCTATA 0.589681 -18 ACAATCTCTCCTTTTCGCGAGGGTTT 29 71 0 TCTCCTTTTC 0.605383 -16 ATAAGAATAATTCTCCTTTTTTGATACAAA 31 205 1 TTCTCCTTTT 0.918263 -60 TATTTCTCCCCCTTTTATTTAAACAA 32 7 1 TCCCCCTTTT 0.965181 -294 TGTCTTTTCCTGCTTTCTTTCATGATT 32 284 0 TCCTGCTTTC 0.700839 -17 ********** Masking position 7 Map Score: 24.5424 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 281 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 3 ATCGTCGTCCGGCCTTTTCCTCTCTTCCCC 5 32 1 GGCCTTTTCC 0.847325 -230 CATGCATAACTGCATGTTCCTCAAAGAATT 7 80 0 TGCATGTTCC 0.673727 -221 AGAGTTAGTCAGTATCTTCCTCTTTTTCAA 7 113 0 AGTATCTTCC 0.591869 -188 TCCATTGTGTTTTCCGCCCCTTGCG 8 24 0 TGTGTTTTCC 0.658142 -15 CCTTATCAAATGTTTTTTCCAGCGTAGCAC 12 89 0 TGTTTTTTCC 0.840388 -33 AACTTACACATGTCTTTTCCAGAAAATAAT 13 70 0 TGTCTTTTCC 0.947653 -110 GAAGCTCGTAAGTTTTCTCCTATTAAAAAT 13 141 0 AGTTTTCTCC 0.668186 -39 GTTTGTAAGGTGCTACTTCCAGCAAAATGA 14 98 1 TGCTACTTCC 0.651473 -203 TTCTGCCGGTTGTCTTTTCCCATGTAATGT 14 242 0 TGTCTTTTCC 0.947653 -59 ATGCCACCTCCGCAGCACATT 18 61 0 TGCCACCTCC 0.791802 -11 GATAGCTTCTTCCTTATATCTTA 23 42 0 AGCTTCTTCC 0.856178 -13 GGTGCTTCCTCCTTTAATGTGC 24 3 1 TGCTTCCTCC 0.844969 -278 CAGAGCCTCCTCCTTTCTACCGA 26 63 0 AGCCTCCTCC 0.923735 -13 GGAAAAAAGAAGTCTGTTCCCAAATGGGAG 27 14 1 AGTCTGTTCC 0.855215 -131 GCACAAAAAAAGCCTGCTCCCATTTGGGAA 27 30 0 AGCCTGCTCC 0.861916 -115 GAAGTAGTCTTGTCATTTCCGTATAAAAGA 27 76 0 TGTCATTTCC 0.786047 -69 CCGTATAAGCTGCCTTTTTCCTATGACAAC 31 76 1 TGCCTTTTTC 0.587966 -189 GCTTTGTTTCAGCCTTTTCCTCGATAAGAA 31 182 1 AGCCTTTTCC 0.954328 -83 TGTCTTTTCCTGCTTTCTTT 32 291 0 TGTCTTTTCC 0.947653 -10 ********** Masking position 8 Map Score: 18.087 Number of sites scoring better than the average of aligned sites = 718 Number in coding regions = 638 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 GCTACAGGTTTTACCCCGATCGGGGTATGCA 3 171 1 TTACCCGATC 0.915231 -130 CCTTCCATCATTAACGCGCTCTGAAAATTGA 3 275 0 TTACGCGCTC 0.892053 -26 ATCACCTAAAATCGCCCGCTCGCGGCATATC 4 214 1 ATCCCCGCTC 0.979262 -57 CGCTCGCGGCATATCCCGCTATGCCATTTTA 4 230 1 ATACCCGCTA 0.889218 -41 TTTTCCTCTCTTCCCCCGCTACGTGCATCTA 5 46 1 TTCCCCGCTA 0.946597 -216 TCTATTTCTATAAACCCGCTCATTTTGTCTA 5 73 1 TAACCCGCTC 0.965069 -189 AACGATTCAGCAACCCCGCTTATTGATGTAA 5 205 0 CAACCCGCTT 0.865409 -57 CTGTCGGCAAATAACCCGCTCGGCTTTTGGG 6 113 1 ATACCCGCTC 0.976055 -188 GGTCCAGTCCCTCAGCCGCTCTTGATAAGTT 14 44 0 CTCGCCGCTC 0.88759 -257 CGTATTTCCCCCGATCTATTCGAGTT 16 83 0 TTCCCCGATC 0.925964 -16 CAAAGGCTTTTTCTCCCGCTTCTGCGCTCCG 24 111 1 TTCCCCGCTT 0.96212 -170 TTACCAGTCACAATCCCGCTTATTCAGATTA 32 115 1 CAACCCGCTT 0.865409 -186 *** ******* Masking position 10 Map Score: 10.9183 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 348 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 TTTTTGCGCGAAATCAAAAAGAACATCTGT 1 151 0 AAATCAAAAA 0.645857 -81 CGAGGAAACTAACAGTAAAATTCTGAATCT 1 180 0 AACAGTAAAA 0.798709 -52 ATTAGAATTTAACACTAAAAGAGCAGGTAA 3 20 0 AACACTAAAA 0.798709 -281 GCCTGCGTTCAAAAATAAAATGGCATAGCG 4 246 0 AAAAATAAAA 0.801061 -25 AATAAAAACAAAAAATAAAACAAAAAGTTT 6 12 0 AAAAATAAAA 0.801061 -289 TTATCCTTTAAAAAATAAAAACAAAAAATA 6 25 0 AAAAATAAAA 0.801061 -276 TGTCGTGAAAAACAATAAAAACCGCCATTG 7 251 1 AACAATAAAA 0.785521 -50 TTGATTCAGAAAATGTAAAATAATGAGGGT 13 28 0 AAATGTAAAA 0.813521 -152 AATTTACTACAAATCTAAAAACTTATCAAG 14 25 1 AAATCTAAAA 0.813521 -276 TTACCTCTTAAAATAAAAAACTTTCAATCC 14 180 0 AAATAAAAAA 0.627327 -121 AGAGAGCGTAAACAGTAAAAATTACCGGTA 17 57 1 AACAGTAAAA 0.798709 -171 TTCCTATGCCAAATCTAAAAAAAACGCCGT 21 13 0 AAATCTAAAA 0.813521 -79 AAATTTGCGTAAATGAAAAAGGATCGCTGT 32 70 0 AAATGAAAAA 0.645857 -231 CAAACTATTTAACTAAAAAAATAGTTGACG 32 182 0 AACTAAAAAA 0.604908 -119 ********** Masking position 7 Map Score: 8.35187 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 140 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 6 TCCGCCTTCGCAAATTGACCTACCTCAATAG 1 106 0 CAAATGACCT 0.935799 -126 CAGACAATTTTACCTGCTCTTTTAG 3 5 1 CAATTTACCT 0.88308 -296 ATTCCGTGATCAAAATCACCTCTTAAAATGC 4 139 1 CAAATCACCT 0.984513 -132 AAACAGATCACAAAATCACCTAAAATCGCCC 4 200 1 CAAATCACCT 0.984513 -71 TGATGTAAATCAAATTCACCTTTATATACTC 5 182 0 CAAATCACCT 0.984513 -80 CATTATCACCTCAATCATAAT 17 1 1 CATTTCACCT 0.910199 -227 ACAATCTCTCCTTTTCGCGAGG 29 75 0 CAATTCTCCT 0.910199 -12 **** ****** Masking position 2 Map Score: 4.50753 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 40 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 7 GTATTACTGCGCGAGGAAACTAACAGTAAA 1 191 0 GCGAGGAAAC 0.946998 -41 ATTCTAATGAGAGAGCAAACCAGCAGAAAT 3 42 1 GAGAGCAAAC 0.969804 -259 CATTTGAAATGTGAGCAAAAGCCCGTTTTT 3 112 1 GTGAGCAAAA 0.92178 -189 AGCGGGGGAAGAGAGGAAAAGGCCGGACGA 5 36 0 GAGAGGAAAA 0.856614 -226 CTGAAAAAGGGAGAGTAAACG 22 2 0 GAGAGTAAAC 0.88018 -121 TTATATTTCTGGAAGCAAACATAAAAAAAC 22 37 0 GGAAGCAAAC 0.799162 -86 CCACAAGGACGTGAGCAAAC 22 113 1 GTGAGCAAAC 0.957282 -10 GCGCAGAAGCGGGAGAAAAAGCCTTTGCTT 24 108 0 GGGAGAAAAA 0.77498 -173 CTTCTGCGCTCCGAGCAAACACCTCTTGTG 24 129 1 CCGAGCAAAC 0.855022 -152 ACGTGAGGGGAGCAAAAATAAA 25 8 1 GGGAGCAAAA 0.963705 -15 TTTGGCAGCTGCGAGTAAAATTTGAAAATA 30 149 0 GCGAGTAAAA 0.858619 -78 ********** Masking position 4 Map Score: 7.89848 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 168 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 8 ATTTGCGAAGGCGGATTATTTTGTGGCAAACA 1 122 1 GCGGTTTTTT 0.840087 -110 CACGCTTCCCGCCACTCTTTTGATCCTGCTAC 3 144 1 GCCATCTTTG 0.89753 -157 TATTAATTATGCGGTTTATTTGGTCGCTCTCA 3 246 1 GCGGTTTTTG 0.974234 -55 CAAAAGCCGAGCGGGTTATTTGCCGACAGGCG 6 110 0 GCGGTTTTTG 0.974234 -191 AAATTACCCTGCCGTTTATTTGCACAATTCTA 7 22 0 GCCGTTTTTG 0.974234 -279 CCTTCCTGAAGTCGGTTTTCTGGCGTTGTTGT 9 41 1 GTCGTTTCTG 0.758612 -39 AGAAAAGTGATCCGGTCTTTTGA 10 2 0 TCCGTCTTTG 0.717288 -59 TTGATAAGGAGCGGATCATCTG 12 110 1 GCGGTCTCTG 0.976169 -12 GTAGCTTTCTGCCGGTTGTCTTTTCCCATGTA 14 246 0 GCCGTTTCTT 0.858868 -55 CATCATCACAGCGAATCTTCTGGAAGAACTCG 16 57 1 GCGATCTCTG 0.910285 -42 ACCGTGATCCGCCAGTGCTCTGAGCCTTT 20 8 0 GCCATGTCTG 0.742379 -124 TAGATAGGAAGCGTTTTCTTTGAAGGGGTAAT 31 130 0 GCGTTTTTTG 0.787539 -135 **** ** **** Masking position 6 Map Score: 6.64503 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 462 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 9 AAGAACATCTGTTTGCCACAAAATAATCCGCC 1 131 0 GTTTCACAAA 0.809319 -101 TTTTGTCTATTTTTTGCACAAACATGAAATAT 5 95 1 TTTTCACAAA 0.834884 -167 CCCTGCCGTTTATTTGCACAATTCTACTTTTG 7 16 0 TATTCACAAT 0.72257 -285 CTATTAAAAATTATGTCACAATGCATTGTTAA 13 120 0 TTATCACAAT 0.948747 -60 TTGTAGTAAATTTTAGCACAATTCTA 14 5 0 TTTTCACAAT 0.94873 -296 ACGCTCTCTCATATAACACAATAAAAGAAGCC 17 34 0 ATATCACAAT 0.793518 -194 TCCATCACAATTTTCTCACAATTTCATATTAA 17 157 0 TTTTCACAAT 0.948747 -71 TCTCTTCTTTTTATGACACAATGTGCTGCGGA 18 42 1 TTATCACAAT 0.948747 -30 ATATTGTGAAGTATTTCACAATTAATTTTTAC 32 235 0 GTATCACAAT 0.938532 -66 ATTGAGCATAGTATGGCACGATATTGTGAAGT 32 255 0 GTATCACGAT 0.761009 -46 **** ****** Masking position 8 Map Score: 4.63319 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 31 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ACGATAGTGCCGTCCGGCATGAGCAA 5 7 0 CGTCCGGCAT 0.976536 -255 GCACTATCGTCGTCCGGCCTTTTCCTCTCT 5 27 1 CGTCCGGCCT 0.991689 -235 GCAAATAACCCGCTCGGCTTTTGGGTCAGC 6 119 1 CGCTCGGCTT 0.905958 -182 CCCACATACGCGCCCGCCATGGCGGAGCTG 6 145 0 CGCCCGCCAT 0.954982 -156 TCGATCCATCCGTACGCCCTTTGGTGATGG 6 213 1 CGTACGCCCT 0.908776 -88 CCCCGTTCCGCCTCGCAAGGGGC 8 4 1 CGTTCCGCCT 0.88893 -35 GAAAAAAGAACGCCCGGCCTCTAGTGCTTC 24 61 1 CGCCCGGCCT 0.993063 -220 ********** Masking position 10 Map Score: 5.69923 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 228 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TATTTGGTCGCTCTCAATTTTCAGAGCGCGTT 3 262 1 CTCCATTTTC 0.96377 -39 TCTTGGGATCATCCTGATTTTCACGCTCGGTA 6 175 1 ATCTATTTTC 0.944782 -126 TTTCTAGACCCTCATTATTTTACATTTTCTGA 13 21 1 CTCTATTTTA 0.751899 -159 AGGATATAGGACCATTATTTTCTGGAAAAGAC 13 57 1 ACCTATTTTC 0.906445 -123 ATTACATTCCATCACAATTTTCTCACAATTTC 17 164 0 ATCCATTTTC 0.943728 -64 CATCTCACCATTTTCAAGTATCACT 24 266 0 CTCCATTTTC 0.96377 -15 ATGCATTATACCCGTTATTTTCAAATTTTACT 30 134 1 CCCTATTTTC 0.938905 -93 TAAATAACTGATCATCATTTTCCCGGTGCGCC 31 30 1 ATCTATTTTC 0.944782 -235 *** * ****** Masking position 7 Map Score: 3.7602 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 113 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 CTTTCCTCTTTTTTCAGGGGTATTACTGCGCG 1 208 0 TTTTAGGGTA 0.955772 -24 ATGGCCTTGTTCTTGAAGGCTATTTAGAATCT 4 53 0 TCTTAAGGTA 0.86073 -218 TGTTTTTATTTTTTAAAGGATAATCAAATGTT 6 32 1 TTTTAAGGTA 0.941531 -269 GCAGGGTAATTTTTGAAGGTCAGCAACAAAAG 7 42 1 TTTTAAGGCA 0.810501 -259 ATGAATTCCATTTTGAAAGATAAGGGCTGCAT 14 124 1 TTTTAAAGTA 0.712712 -177 AAGTTTTTTATTTTAAGAGGTAAAAAGGCTAT 14 187 1 TTTTAGAGTA 0.769012 -114 AATGATCTGATCTGAAGGGGGATTTTGGAGA 17 207 1 TCTGAGGGGA 0.693855 -21 ATTTCTTACTTTTTGAAGGTTATGTGAAATTT 20 53 0 TTTTAAGGTA 0.941531 -79 TACTCTCCCTTTTTCAGGGAGAGTTTTTTTAT 22 15 1 TTTTAGGGGA 0.938973 -108 TCATATCCTGTTTTGAAGGAGTTTGTACAGAA 24 168 0 TTTTAAGGGT 0.592968 -113 AAGCGTTTTCTTTGAAGGGGTAATGAAAAGAT 31 122 0 TTTGAGGGTA 0.892402 -143 **** **** ** Masking position 6 Map Score: 3.10881 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 61 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 TCGCTGTTTTGTCTCTCTTGCCGTTAAAAATTAA 1 13 1 GTCTCTTGCT 0.847999 -219 CAGACAATTTTACCTGCTCTTTTAGTGTTA 3 7 1 ATTTCCTGCT 0.966486 -294 GATTGGCCTGCGTTCAAAAATAAA 4 257 0 GATTCCTGCT 0.965285 -14 GACCTTCAAAAATTACCCTGCCGTTTATTTGCAC 7 29 0 AATTCCTGCT 0.901118 -272 GGAACATGCAGTTATGCATGCTGTTGAAAAAGAG 7 90 1 GTTACATGCT 0.760346 -211 CTAAAGTGGTATTTTACATGCACTTACAATTGAT 7 141 1 ATTTCATGCT 0.868353 -160 CGGTTTGGCCTGCCCTTTTTATCTTT 19 120 0 GTTTCCTGCT 0.988763 -16 AGGGTAGCCAGTTTTTCCGGCAATGAGAGTGATA 24 239 1 GTTTCCGGCT 0.953615 -42 CAAATTTTAGGTCTTGCCTGCTTTACCAGTCACA 32 93 1 GTCTCCTGCT 0.977278 -208 **** ***** * Masking position 14 Map Score: 2.26358 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 279 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 14 AGCGCGTTAATGATGGAAGGTCAAT 3 286 1 TGATGGAAGG 0.963822 -15 TTGCTCATGCCGGACGGCACTATCGTC 5 8 1 TGCCGGACGG 0.971462 -254 TTTTTTACAGTGACGGAAGGATGAC 10 46 1 TGACGGAAGG 0.976685 -15 CAAGAGCGGCTGAGGGACTGGACCTATGAA 14 51 1 TGAGGGACTG 0.835835 -250 GAATTCATTTTGCTGGAAGTAGCACCTTAC 14 102 0 TGCTGGAAGT 0.806687 -199 TCTTCTCAGATGCCGGAATGCAAGCGAGAA 16 27 1 TGCCGGAATG 0.960774 -72 GAGAAAATTGTGATGGAATGTAATGTTCAT 17 172 1 TGATGGAATG 0.928052 -56 ********** Masking position 7 Map Score: 2.47108 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 408 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 GCTCGCTGTTTTGTCTCTCTTGCC 1 5 1 GCTGTTTTGT 0.780104 -227 AGATATTTCTGCTGGTTTGCTCTCTCATTA 3 46 0 GCTGGTTTGC 0.942288 -255 TGGGTATATTGCTGATTTGTATAAATTTTC 5 147 0 GCTGATTTGT 0.921085 -115 AAGCCGAGCGGGTTATTTGCCGACAGGCGT 6 109 0 GGTTATTTGC 0.839001 -192 TTACCCTGCCGTTTATTTGCACAATTCTAC 7 21 0 GTTTATTTGC 0.637798 -280 TTCACAGTGTGGTTATTTGTTACACATAGG 7 186 1 GGTTATTTGT 0.879796 -115 CCAGAAAAGAGGTGGTTTCTGGACGTATTC 9 12 1 GGTGGTTTCT 0.748074 -68 GAAAGCTACTGTTTGTTTGTCTCCGAAAGG 14 269 1 GTTTGTTTGT 0.829323 -32 ATTTGAAAAAGCTTGTTTGTTAAGGTTGAA 21 42 1 GCTTGTTTGT 0.934981 -50 ACGTCCTTGTGGTGGTTTGTACAAGTTTAT 22 95 0 GGTGGTTTGT 0.958215 -28 ********** Masking position 6 Map Score: 4.5744 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 260 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652