AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iarcA_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 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #2 gltA_sdhC 600 gltA: citrate synthase, sdhC: succinate dehydrogenase, cytochrome b556 #3 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #4 focA 300 probable formate transporter (formate channel 1) #5 icdA 201 isocitrate dehydrogenase, specific for NADP+ #6 aldA 196 aldehyde dehydrogenase, NAD-linked #7 glcD_glcC 250 glcD: glycolate oxidase subunit D, glcC: transcriptional activator for glc operon #8 lldP 300 L-lactate permease #9 sodA 284 superoxide dismutase, manganese #10 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #11 ycbD 29 similar to aldehyde dehydrogenase #12 lctE 176 L-lactate dehydrogenase #13 lctP 31 L-lactate permease #14 ycgM 190 similar to proline oxidase #15 yfmT 249 similar to benzaldehyde dehydrogenase #16 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #17 citA 108 citrate synthase I #18 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #19 mmgD 33 citrate synthase III #20 mmgC 27 acyl-CoA dehydrogenase #21 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #22 sodA 178 superoxide dismutase #23 yrhG 262 similar to formate dehydrogenase #24 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #25 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #26 ysfC 102 similar to glycolate oxidase subunit #27 citC 163 isocitrate dehydrogenase #28 citZ 300 citrate synthase II #29 gbsA 198 glycine betaine aldehyde dehydrogenase #30 yvfH 300 similar to L-lactate permease #31 rocA 226 pyrroline-5 carboxylate dehydrogenase #32 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter #33 cydA 300 cytochrome bd ubiquinol oxidase (subunit I) Motif number 1 GTTTGCAACCTTTCTTTACGCCGTTTTTGTGTGCATT 3 169 1 TTTTTTTTTT 0.866477 -132 GACTCCTGACTTTTATTTCTGCCTTTTATTCCTTTTA 6 51 1 TTTATTTTTT 0.79886 -146 GTCAGACCATTTTTTTTCCAGCTCTGTGACCTTGTCT 7 117 0 TTTTTTCTGT 0.810875 -134 GGGCTTTTCGTTTTCGTCTATCTCTTTAGCTACCGGT 7 152 0 TTTCGTCTTT 0.84168 -99 TGATGTGAGTTTTAATTGGGAAATTGTGAACCAGAGG 8 127 0 TTTATTTTGT 0.660199 -174 TGTTTTTTGTCGCTTCCTTTTCTCCTTTAT 14 4 1 TTTTGTCTTT 0.84441 -187 GACGTATTTATTTCCTTGGAAATCTTT 16 1 0 TTTCTTCTTT 0.895676 -231 ATATCCGGTCTTTTTTTTGCATGCTGTAAAACGAGAC 16 60 1 TTTTTTCTGT 0.810875 -172 GATTAATATTTTTAATTAATTCCCTTTAAAATATTGA 17 26 1 TTTATTCTTT 0.842868 -83 GACCTCCTAGTTTGATTAAGCAATTTTAAAGTTTACA 18 81 0 TTTATTTTTT 0.79886 -34 ACACAGGTTATTTGAGTGCTGCCTTTTTTATTGCCTT 23 190 1 TTTAGTTTTT 0.710927 -73 TATGTACGCGTTTTCTTGACGCCCTTTTGAGGGAGGA 25 163 1 TTTCTTCTTT 0.895676 -130 AGAGAGTTTCAGTTTCATTTTTTGTATGTTTCT 26 7 1 TTTAGTTTTT 0.710927 -96 CATGGAAGGCTTTGCTTTTTTTCTTTTACAATAGATT 26 45 1 TTTCTTTTTT 0.864072 -58 AAAAAACGCCTTTATTTGCGGGTTTTTG 28 2 0 TTTTTTTTTT 0.866477 -299 ACCTATAATTTTTTTTTTCCATTCTGTGATTTCCCCG 28 39 0 TTTTTTCTGT 0.810875 -262 CCATTTTGATTTTTCTTTTTGACTTTTCCTCATGTTT 29 78 0 TTTCTTTTTT 0.864072 -121 ACATTAAATTTTTATTTAACAAACTTTATTTACGTCA 29 161 1 TTTTTTCTTT 0.897588 -38 TTCATATATTTTTTTGTTTTAATCTGTTTATATTTCA 30 46 1 TTTTGTCTGT 0.726395 -255 TGAACGCAAATTTATTTTGCGTTTTTTGCTCTTTACG 31 52 0 TTTTTTTTTT 0.866477 -175 CATGATAGCGTTTTCGTCAACTATTTTTTTAGTTAAA 32 168 1 TTTCGTTTTT 0.797418 -133 TTGAGCAATATTTTTTTCGTCTATTTTGTGAATTACT 33 202 1 TTTTTTTTTT 0.866477 -99 *** *** **** Masking position 7 Map Score: 19.5854 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 110 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 2 CCGTTTGTTGTTTAAAAATTGTTAACAATTTTGTAAAA 1 71 1 TTATTTACAA 0.959269 -230 TGTAACAACTTTGTTGAATGATTGTCAAATTAGATGAT 2 237 0 TTATTTTCAA 0.746921 -364 TGACAAGCCAATTACAAATCATTAACAAAAAATTGCTC 5 91 1 ATATTTACAA 0.920362 -111 ATTAAATGATATTGAAAATGATTATCAATGCCGTACTT 9 190 0 ATATTTTCAA 0.741912 -95 CACATTTATATTGTGCAACACTTCACAAACTTTTGCAA 12 93 0 TTACTTACAA 0.692279 -84 CACAATATAAATGTGAAATACTTCACAAACAAAAAGAC 12 116 1 ATATTTACAA 0.702445 -61 TTTCCCTCTATTATATATCTGTTTTCAATGCTTACGAT 18 44 1 TTACTTTCAA 0.705023 -71 TATATATTTCTTGCTTAATTTTTCATAAGAATTACAGG 25 74 0 TTATTTATAA 0.565387 -219 TAAGCACTTTATTAAGATTTATTGACAATTTCATTTTA 25 201 0 ATATTTACAA 0.920393 -92 AAAAAAATTATAGGTAAACATTTAACAAATGTCTGATT 28 61 1 TAACTTACAA 0.602083 -240 AAAATCAAAGTACAAGACTTTTTGACAAAATAGTCAAA 30 159 0 TAATTTACAA 0.799004 -142 TAAAAATTAATTGTGAAATACTTCACAATATCGTGCCA 32 236 1 TTATTTACAA 0.499239 -65 TGACTGGTTCATATTAAGTACTTTACAACGATTCATTT 33 92 0 ATATTTACAA 0.89874 -209 GAAAAAAATATTGCTCAATATTTCACAAATGTGTCAAA 33 182 0 TTATTTACAA 0.950729 -119 AACCGAGACTTTGATCAGTAATTCACAAAATAGACGAA 33 217 0 TTATTTACAA 0.870589 -84 AACTGTTAATTTGCTCACTACTTCACAAATAGAACCGA 33 249 0 TTATTTACAA 0.950729 -52 ** * * ** **** Masking position 7 Map Score: 14.6304 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 25 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 3 CCCAGAGCTCTGTACCCAGGTTTTCCCCTCTTTC 2 473 1 TGTACCCTTT 0.933866 -128 TCAACCTGGCTTTACCCGTTTTTTATTTGGCTCG 2 516 0 TTTACCCTTT 0.76924 -85 GCAACCTTTCTTTACGCCGTTTTTGTGTGCATTC 3 173 1 TTTACGCTTT 0.927211 -128 GGCCTCTATCTGTAAGCGCTTTTATTAATTTTTC 10 174 0 TGTAAGCTTA 0.868252 -53 GAGGATATTGTGAACGCTGGTTTTGTCCATTTAC 14 118 1 TGAACGCTTT 0.953621 -73 TTATAATTTATGTACGCGTTTTCTTGACGCCCTT 25 155 1 TGTACGCTTT 0.981789 -138 TTCTTTCAATTGTAAGCACTTTATTAAGATTTAT 25 217 0 TGTAAGCTTT 0.974503 -76 TACAATAGATTGAAAGCGTTTTTTGACAGGGGGA 26 71 1 TGAAAGCTTT 0.935747 -32 CAATTTAAAGTGTAACCCAATTTTGATGTCTGAA 27 55 0 TGTAACCTTT 0.909115 -109 CTTATTTAAGTTTAAGCCTATTCTCATTATAAAC 28 102 0 TTTAAGCTTT 0.900235 -199 GCCAGTAAAATGTAAGCATTTTCTTTTTGGGGGA 28 188 1 TGTAAGCTTT 0.974505 -113 TGGCGCCATATGTAAGCGGTTTCTATAGATGATA 30 251 0 TGTAAGCTTT 0.974241 -50 TTTCCGATCTTGAACGCAAATTTATTTTGCGTTT 31 65 0 TGAACGCTTA 0.781124 -162 TCCTTTTTCATTTACGCAAATTTTAGGTCTTGCC 32 77 1 TTTACGCTTT 0.927211 -224 TGATTTATGATGAAAGCGTATTCTTAATCTGAAT 32 136 0 TGAAAGCTTT 0.935731 -165 ******* ** * Masking position 4 Map Score: 18.7514 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 80 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 GTACCCAGGTTTTCCCCTCTTTCACAGAGC 2 484 1 TTTCCCCTCT 0.892545 -117 TTACCAGACATCTCCCCCCACAAGAATTGG 8 72 1 TCTCCCCCCA 0.922291 -229 TTCGACAGAATCCCCCCCCGACTTTCTAAC 14 40 1 TCCCCCCCCG 0.85294 -151 TTCTATTCTCCCTCTGATTAATATT 17 6 1 TTCTCCCTCT 0.916463 -103 TTGTATTCCCCCTATCCTTTTCT 17 96 0 TATTCCCCCT 0.788021 -13 AAAACGTTCATCTTCCCTCTCGATTATGCA 18 17 0 TCTTCCCTCT 0.948683 -98 AAGATGAACGTTTTCCCTCTATTATATATC 18 33 1 TTTTCCCTCT 0.910016 -82 GATAGCCCCTCTCCCTCTAGTAATCTAG 24 16 0 CTCTCCCTCT 0.859007 -18 ATCTGTCTCCCCTCTCTCCTGCGTA 25 6 1 TCTCCCCTCT 0.938209 -287 ATTCTGTAATCCTCCCCCCTGTTTGAGCTA 25 41 0 CCTCCCCCCT 0.945343 -252 TTCATTTTACTCCTCCCTCAAAAGGGCGTC 25 180 0 TCCTCCCTCA 0.88429 -113 GTGCTAAATCTCTTCCCCCACTTCTTTCAA 25 242 0 TCTTCCCCCA 0.935277 -51 TACTTTACCCCCTGTTTGATAAG 25 280 0 TTTACCCCCT 0.724954 -13 TTCACCCATCCCCCTGTCAAAAAAC 26 88 0 CCATCCCCCT 0.747675 -15 GCAAGTATTTCTCTCCCCCAAAAAGAAAAT 28 205 0 CTCTCCCCCA 0.826459 -96 TATTTCTCCCCCTTTTATTTAAA 32 4 1 TTCTCCCCCT 0.957452 -297 ********** Masking position 5 Map Score: 16.1121 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 75 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 TATCCGTCGGTATTTTACAAAATTGTTAAC 1 91 0 TATTTTACAA 0.485541 -210 GTTAGGGTATTACTTCACATACCCTATGGA 1 137 1 TACTTCACAT 0.885439 -164 TGCAAACAAGTGGTTCACAAACGGGCAATT 6 12 0 TGGTTCACAA 0.854521 -185 ATCTGACCTCTGGTTCACAATTTCCCAATT 8 121 1 TGGTTCACAA 0.854521 -180 GTGGGTGATTTGCTTCACATCTCGGGCATT 9 134 1 TGCTTCACAT 0.812061 -151 TATTGTGCAACACTTCACAAACTTTTGCAA 12 93 0 CACTTCACAA 0.855532 -84 AAATGTGAAATACTTCACAAACAAAAAGAC 12 124 1 TACTTCACAA 0.971828 -53 AATTGTGAAATACTTCACAATATCGTGCCA 32 244 1 TACTTCACAA 0.971828 -57 TCATATTAAGTACTTTACAACGATTCATTT 33 92 0 TACTTTACAA 0.827375 -209 TATTGCTCAATATTTCACAAATGTGTCAAA 33 182 0 TATTTCACAA 0.871675 -119 CTTTGATCAGTAATTCACAAAATAGACGAA 33 217 0 TAATTCACAA 0.793906 -84 ATTTGCTCACTACTTCACAAATAGAACCGA 33 249 0 TACTTCACAA 0.971828 -52 ********** Masking position 7 Map Score: 10.5742 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 38 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 TGAATGCACACAAAAACGGCGTAAAGAAAG 3 178 0 CAAAAACGGC 0.832625 -123 TCTTAACTCGCAAAACACGCACATCACGTA 7 49 1 CAAAACACGC 0.834439 -202 CCAGAAAAAACACGAAAGGGGCA 11 4 1 GAAAAAACAC 0.77629 -26 TAGACAAAAAACGCAAAAACGGAG 19 5 1 CAAAAAACGC 0.967061 -29 TACATTGAATGAAGAAAGGCTCGCTGTGAA 22 121 1 GAAGAAAGGC 0.818614 -58 AGAAAGGCAATAAAAAAGGCAGCACTCAAA 23 200 0 TAAAAAAGGC 0.748707 -63 CACAGTTATGCAAGAAAGGCAATAAAAAAG 23 212 0 CAAGAAAGGC 0.908246 -51 TATTGTAAAAGAAAAAAAGCAAAGCCTTCC 26 48 0 GAAAAAAAGC 0.634538 -55 ATCCCCCTGTCAAAAAACGCTTTCAATCTA 26 76 0 CAAAAAACGC 0.967061 -27 TGATTTCCCCGAAAAAACGCCTTTATTTGC 28 20 0 GAAAAAACGC 0.930487 -281 GCGTAAAGAGCAAAAAACGCAAAATAAATT 31 51 1 CAAAAAACGC 0.967061 -176 TTTATTTAAACAAAAAAGACCTAAAATTCG 32 24 1 CAAAAAAGAC 0.898379 -277 AAATAAGCAACAAAATAGACAAAAATCCGT 33 19 1 CAAAATAGAC 0.643573 -282 CAGTAATTCACAAAATAGACGAAAAAAATA 33 210 0 CAAAATAGAC 0.643573 -91 ********** Masking position 5 Map Score: 10.0289 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 349 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 7 CGAATAGACAAATCGGTTGCCGTTTGTTGTT 1 52 1 AATCGTTGCC 0.728489 -249 TGAACAGCCTATACTGCCGCCAGGTCTCCGG 2 115 0 ATACGCCGCC 0.954839 -486 AGCGCGCAAAAATCAGCTGCCACACAACACA 7 212 1 AATCGCTGCC 0.931627 -39 CGGCATTAACAATCGGCCGCCCGACAATACT 9 254 1 AATCGCCGCC 0.987472 -31 ACCAAACAGCCGGCTGACCAGGCT 10 4 1 AAACGCCGGC 0.951117 -223 CACACGTCTCAAACTGTCTCCAAAGTGAAGA 16 125 1 AAACGTCTCC 0.836465 -107 GGAATTGCTCAAACAGCCGCCGACGCGGCTT 21 83 1 AAACGCCGCC 0.993389 -67 TGCCCCATTAAACCTGCCGCCAGCATTTC 22 9 0 AACCGCCGCC 0.978829 -170 AATAAAACGCCTCCATTACTTCTT 23 249 0 AAAAGCCTCC 0.694132 -14 CTTGAAACATAAACTGGCGCCATATGTAAGC 30 268 0 AAACGGCGCC 0.961344 -33 **** ****** Masking position 1 Map Score: 8.11409 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 399 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 8 AGCGTTGTAACGTGTCGTTTTCGCATCTGGAA 2 58 0 CTTCGTTTTC 0.919457 -543 ATTAAGCGGGCTTTTCGTTTTCGTCTATCTCT 7 164 0 CTTCGTTTTC 0.919457 -87 TGAGGATTGCCCTTTTCTTTACCAGACATCTC 8 54 1 CTTTCTTTAC 0.901698 -247 GTCTGTTGCTCATCTCCTTGTCACACGTTGTG 8 242 0 CTTCCTTGTC 0.964048 -59 TGTTTTTTGTCGCTTCCTTTTCTCCTTTATTC 14 11 1 CCTCCTTTTC 0.893366 -180 GGTCAGCATCTCCTTTATAACCGCAAAT 15 232 0 CTTCCTTTAT 0.683308 -18 TTGTATTCCCCCTATCCTTTTCTGTTATTATA 17 87 0 CTTCCTTTTC 0.981522 -22 GCCTCCATTACTTCTTCTTTTCTCACAGTTAT 23 233 0 CTTTCTTTTC 0.966183 -30 TTTATGTACGCGTTTTCTTGACGCCCTTTTGA 25 161 1 CTTTCTTGAC 0.822399 -132 TAGGAAAAATCATTTTATTTTCTATATAAGAA 27 94 1 CTTTATTTTC 0.692423 -70 AAAATGTAAGCATTTTCTTTTTGGGGGAGAGA 28 194 1 CTTTCTTTTT 0.783313 -107 ATATAACATCTCCTTTTCAATAAATTTC 28 283 0 CTTCCTTTTC 0.981522 -18 AGAATCATGCCATTTTCTTGTCTTTTGCTGAA 31 152 0 CTTTCTTGTC 0.935164 -75 * * ******** Masking position 5 Map Score: 9.83809 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 58 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 TTTTCGCATCTGGAAGCAGTGTTTTGCATG 2 43 0 TGGAAGCAGT 0.822527 -558 TCCGGAGACCTGGCGGCAGTATAGGCTGTT 2 114 1 TGGCGGCAGT 0.975069 -487 ATATGCAACGTGGTGGCAGACGAGCAAACC 5 159 1 TGGTGGCAGA 0.770132 -43 TTGTGTTGTGTGGCAGCTGATTTTTGCGCG 7 214 0 TGGCAGCTGA 0.778105 -37 TCGACAACGGCGGCAACAGGCGAAAGGTTA 9 81 0 CGGCAACAGG 0.627266 -204 ATCTTCACTTTGGAGACAGTTTGAGACGTG 16 127 0 TGGAGACAGT 0.666274 -105 AAACAAATCATGGTAGCTGGCGCAGGTCAG 21 44 1 TGGTAGCTGG 0.751177 -106 AAAGCCGCGTCGGCGGCTGTTTGAGCAATT 21 85 0 CGGCGGCTGT 0.926558 -65 CCAGAGGCCGCGGAGGCAGGA 21 139 1 CGGAGGCAGG 0.932418 -11 GAAATGCTGGCGGCAGGTTTAATGGGG 22 8 1 TGGCGGCAGG 0.986735 -171 AGAACCATTGGAGGCTGGCTTGCGTCAA 27 9 1 TGGAGGCTGG 0.945839 -155 TACATTTTACTGGCTGCTGGAACTAAAACC 28 172 0 TGGCTGCTGG 0.823316 -129 CGCTTACATATGGCGCCAGTTTATGTTTCA 30 267 1 TGGCGCCAGT 0.820382 -34 ********** Masking position 7 Map Score: 8.91169 Number of sites scoring better than the average of aligned sites = 1426 Number in coding regions = 1387 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 GTTCAGGATAAAACCCGACAAACTATATGTAG 2 165 0 AAACCGCAAA 0.937862 -436 TTTTGTTCATAAATCAGACAAAACTTTTCTCT 12 62 1 AAATCGCAAA 0.954951 -115 GCATGCTGTAAAACGAGACAAATGAATCAGTT 16 78 1 AAACGGCAAA 0.957077 -154 GTTTGAGACAAAACGAGACACACGTCTCAAAC 16 107 1 AAACGGCACA 0.90555 -125 ATTTGAATGGAAATCAAACAAATCATGGTAGC 21 29 1 AAATCACAAA 0.649372 -121 ATGTCCGCTGAAATGAGCCAAATCGTGAGCTT 22 61 1 AAATGGCAAA 0.969056 -118 ACATCATATCAAATGTGACAAATTTGTGTCAA 23 22 0 AAATGGCAAA 0.969056 -241 GATAAGTGCGAAATGTGCTAAATCTCTTCCCC 25 254 0 AAATGGTAAA 0.732338 -39 AAATAGACAAAAATCCGTCACATAGTGCGGGA 33 31 1 AAATCGCACA 0.901136 -270 AATATTTCACAAATGTGTCAAAAAGTCATCCA 33 172 0 AAATGGCAAA 0.969056 -129 ***** * **** Masking position 3 Map Score: 7.10062 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 80 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 GTCAAATTAGATGATTAAAAATTAAATAAATGTTGT 2 216 0 ATAAAATAAA 0.851409 -385 TGCAAACATGTTAATAAAAACTCAAATTGATCCCAC 3 140 0 TTAAAATAAA 0.726223 -161 TGTCTGATTTATGAACAAAAAAGAAACCATCATTGA 12 46 0 ATAAAAAAAA 0.869075 -131 CGTTCACAATATCCTCAAAATACAAAGATTCTGATT 14 98 0 ATAAAAAAAA 0.869075 -93 TCGGTTCATCTTGCATAAAATTGAATATACGATTAG 15 168 0 TTAAAATAAT 0.628941 -82 AGTAAATATAATATTTAAAAAATAATCAATATTTTA 17 52 0 ATAAAAAAAT 0.809218 -57 AGAAATATATATTGATAAAATAAAATTTTTCAATCA 25 101 1 ATAAAAAAAT 0.809217 -192 TATTTTTCTTATATAGAAAATAAAATGATTTTTCCT 27 95 0 ATAAAAAAAT 0.809218 -69 TTAACGAAACATGAGGAAAAGTCAAAAAGAAAAATC 29 72 1 ATAAAATAAA 0.851409 -127 AGCATTATATTTTGAAAAAAATCAAAGTACAAGACT 30 178 0 TTAAAATAAA 0.726222 -123 TTTTTGCTCTTTACGCAAAAAACAAATGCAAAATTA 31 31 0 TTAAAAAAAA 0.75448 -196 TGCGTTCAAGATCGGAAAAAGAGAAAGGTGATCACC 31 81 1 ATAAAAAAAA 0.869075 -146 GTAGACAAAAATTCGTAAAAATTAATTGTGAAATAC 32 221 1 ATAAAATAAT 0.785469 -80 ** **** * *** Masking position 8 Map Score: 3.90284 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 62 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 12 TTGAATTTTTTCCGCATCCTCCGCTAAAACAG 4 100 0 TCCGCCCTCC 0.987421 -201 TTCTTTCACATCCGCTCCTTCCCATATATCCT 10 145 0 TCCGCCTTCC 0.976344 -82 AGTTCTCGACCTCCTAGTTTGATT 18 101 0 TTCTCCCTCC 0.903787 -14 ATCCTCAACCTCCGTTTTTGCGT 19 21 0 TCCTCCCTCC 0.983864 -13 TCCTGCCTCCGCGGCCTCTGGATTCACAT 21 131 0 TCCGCCCTCT 0.966489 -19 GATAGCCCCTCTCCCTCTAGTAATCTAG 24 16 0 CCCTCCCTCT 0.808382 -18 ATCTGTCTCCCCTCTCTCCTGCGTATATT 25 8 1 TCCCCTCTCC 0.910421 -285 CTAAATCTCTTCCCCCACTTCTTTCAATTGTA 25 237 0 TCCCCCTTCT 0.887964 -56 TAATAGGGCATCCGCTACTTCTTCATATATTT 30 25 1 TCCGCCTTCT 0.938133 -276 GTGATCACCTTTCTCTTTTTCCGATCTTGAAC 31 84 0 TTCTCTTTCC 0.550236 -143 GCTTTCTCCTCCATTTCCGGTTAAAACT 33 283 0 TCCTCTTTCC 0.888156 -18 ***** ***** Masking position 10 Map Score: 9.1813 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 223 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 GGGCGACTCCTGTGATTTATATGTTTGTTTT 6 176 0 CCGTGTTATA 0.742089 -21 GCTTATCTGACCTCTGGTTCACAATTTCCCAAT 8 117 1 CCCTGTTACA 0.890409 -184 CAGTGATTTACCGCTTTTTTATAAAATATCAGA 10 65 1 CCCTTTTATA 0.890875 -162 TTCTATTCTCCCTCTGATTAATATTTTTAATTA 17 11 1 CCCTGTTATA 0.956935 -98 CCATTCAAATCCCCTTTTTCATCATGTT 21 6 0 CCCTTTTATC 0.88419 -144 GCCGCGTCGGCGGCTGTTTGAGCAATTCCGCTC 21 79 0 CGCTGTTAGC 0.794662 -71 TGCATACATTCCATTGCTTTAGCCTTCTATAAC 23 61 0 CCTTGTTAGC 0.743278 -202 GTAATCCTCCCCCCTGTTTGAGCTATAATATAC 25 33 0 CCCTGTTAGC 0.970708 -260 TACTTTACCCCCTGTTTGATAAGTGCGAAAT 25 272 0 CCCTGTTATA 0.956935 -21 ATGAGGTTAGCCTCTTGTTCAGACATCAAAATT 27 38 1 CCCTTTTAGA 0.928668 -126 AGTCACAATCCCGCTTATTCAGATTAAGAATAC 32 120 1 CCCTTTTAGA 0.928668 -181 ** *** ** *** Masking position 11 Map Score: 5.73912 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 144 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 TTACCCGTTTTTTATTTGGCTCGCCGCTCTG 2 508 0 TTATTTGGCT 0.670157 -93 ATTTTTAAAATTTATTTTTATTTGGATAATC 4 143 1 TTATTTTTAT 0.576088 -158 TGACTTATTGTTTATTTGTCTTACAATTAAA 10 110 1 TTATTTGTCT 0.906911 -117 AGCGCTTTTATTAATTTTTCTTTCACATCCG 10 163 0 TTATTTTTCT 0.939595 -64 CTCAAACTGATTCATTTGTCTCGTTTTACAG 16 83 0 TTATTTGTCT 0.906911 -149 TATTTCTTGCTTAATTTTTCATAAGAATTAC 25 77 0 TTATTTTTCA 0.664025 -216 TATTGACAATTTCATTTTACTCCTCCCTCAA 25 189 0 TTATTTTACT 0.686393 -104 TAGAAAACATTTTATTTTTCTTATATAGAAA 27 112 0 TTATTTTTCT 0.939595 -52 ACTTAACGAATTTAATTTTCTAAAGGAAAAG 29 20 0 TTAATTTTCT 0.664026 -179 AAGTCCCATTTTGATTTTTCTTTTTGACTTT 29 89 0 TTATTTTTCT 0.939595 -110 GTCTTGTACTTTGATTTTTTTCAAAATATAA 30 179 1 TTATTTTTTT 0.576089 -122 ** ******** Masking position 4 Map Score: 3.65142 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 28 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 15 GACCGCCGGAGATAAATATATAGAGGTCATG 1 280 1 GAAAATATTG 0.493321 -21 ATTTGATCGAGAACAATTTATCT 3 1 0 GACAATTTTT 0.944607 -300 TTTCGACGGTGATCAATTTATAGCTAAATTACC 3 46 0 GACAATTTTG 0.914387 -255 ATATACGTGGGATCAATTTGAGTTTTTATTAAC 3 134 1 GACAATTTAT 0.808836 -167 GGATGCTTTAGAGCAATTTTTTGTTAATGATTT 5 106 0 GACAATTTTG 0.914384 -96 GCACAGGTAGGACCAATTTTTCTGTTCTTAACT 7 24 1 GACAATTTTT 0.944607 -227 CTACCGGTCAGACCATTTTTTTTCCAGCTCTGT 7 127 0 GACATTTTTT 0.684218 -124 TATCAAATGTGACAAATTTGTGTCAATGACAAA 23 15 0 GAAAATTTTT 0.862358 -248 TTAGTTGATTGAAAAATTTTATTTTATCAATAT 25 109 0 GAAAATTTAT 0.608472 -184 TCACCTGTTAGACAAATTTCTGTTCGATTCAAC 31 112 1 GAAAATTTTT 0.862358 -115 GTGAAATATTGAGCAATATTTTTTTCGTCTATT 33 194 1 GACAATATTT 0.808837 -107 ** ****** * * Masking position 5 Map Score: 3.33701 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 29 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493