AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_ecoli_reg_100.orf -o00650_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ilvI 227 acetolactate synthase III, valine sensitive, large subunit #2 aceE 160 pyruvate dehydrogenase (decarboxylase component) #3 hlpA 121 histone-like protein, located in outer membrane or nucleoid #4 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #5 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #6 ybaC 151 putative lipase (EC 3.1.1.-) #7 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #8 ybeX 89 putative transport protein #9 ybeZ 113 putative ATP-binding protein in pho regulon #10 sdhC 300 succinate dehydrogenase, cytochrome b556 #11 ybiY 31 putative pyruvate formate-lyase 2 activating enzyme #12 pflB 54 formate acetyltransferase 1 #13 focA 300 probable formate transporter (formate channel 1) #14 htrB 224 heat shock protein #15 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #16 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #17 goaG 37 4-aminobutyrate aminotransferase #18 ydbO 284 orf, hypothetical protein #19 ydcH 72 orf, hypothetical protein #20 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #21 gadB 300 glutamate decarboxylase isozyme #22 rspA 205 starvation sensing protein #23 msbB 119 suppressor of htrB, heat shock protein #24 wcaA 34 putative regulator #25 BIME92 24 BIME #26 wza 300 putative polysaccharide export protein #27 gatD 47 galactitol-1-phosphate dehydrogenase #28 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #29 gatZ 28 putative tagatose 6-phosphate kinase 1 #30 gatY 197 tagatose-bisphosphate aldolase 1 #31 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #32 atoB 30 acetyl-CoA acetyltransferase #33 pdxB 98 erythronate-4-phosphate dehyrogenase #34 b2659 230 orf, hypothetical protein #35 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #36 yqeF 251 putative acyltransferase #37 tdcE 33 probable formate acetyltransferase 3 #38 tdcC 21 anaerobically inducible L-threonine, L-serine permease #39 tdcB 98 threonine dehydratase, catabolic #40 tdcA 188 transcriptional activator of tdc operon #41 gadA 210 glutamate decarboxylase isozyme #42 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #43 ilvG_1 139 acetolactate synthase II, large subunit, cryptic, interrupted #44 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #45 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #46 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase #47 frwC 300 PTS system, fructose-like enzyme II component #48 pflD 50 formate acetyltransferase 2 #49 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit Motif number 1 CTCCTTACCATCCCATTTGCACCGGAGGGTGCAGT 3 91 0 TCCCTGCCGG 0.497753 -31 TCTTTTGTTCGCCAAACTTTACGGCCTGTCTCATT 4 18 1 GCCACTCGGC 0.739535 -87 GCATTTGACTGGCAGACGTCCCCGCCGTTGGTGAT 8 19 1 GGCACTCCGC 0.922137 -71 TTCTCAGGCCTGCCGTTCCGGTGGGCCTTGT 9 7 1 GGCCCGCCGG 0.987486 -107 GGCTCGGGATTGCAGGGTGTTCCGGAGACCTGGCG 10 85 0 TGCAGGCCGG 0.874669 -216 CTGTCTGACCCGCAAGCAGACCGGAGGAAGGAAAT 10 193 1 CGCACGCGGA 0.811672 -108 GCCGGGTAAGCGCAATGCGCCCGGCAATCTATACA 16 27 1 CGCAGGCGGC 0.942636 -248 GAAATAAACGGGCATACGGCCCGGGGATCTCTGCG 16 198 1 GGCACGCGGG 0.990015 -77 TTAAAAAAGCCGCCTGGCTGGCGGCTTAGGAAAGT 20 11 0 CGCCGTCGGC 0.798755 -52 GCAGCCGGTACGCAGTCAGTACCGGCTTTTTTTAT 23 24 1 CGCACGCCGG 0.986711 -96 TTTGGTGCGGGGCAAGTTGCGCCGCTACACTATCA 23 58 1 GGCATGCCGC 0.931401 -62 CATCAACGACTGCATGCTGAGAGGGTGTGAAAAAT 26 49 1 TGCACGAGGG 0.712464 -252 TGGTCTTTCAGGCATCCAGACACGCTACCGCCCCT 26 118 0 GGCACGACGC 0.854886 -183 TAAAAACACGCGCACTTTGCTACGGCTTCCCTATC 30 47 1 CGCATGACGG 0.764311 -151 GCAAAAAAACGGCCTCCCGATAGGGAAGCCGTAGC 30 65 0 GGCCCGAGGG 0.922641 -133 CTGAAATCTTCGCAAGTATGCCTGGCCGCGAGATT 33 26 1 CGCATTCTGG 0.475284 -73 GCGAGATTATGGCACACTTGTCCGGTTAACTCTCG 33 53 1 GGCACTCCGG 0.961569 -46 ATATTATCTGCCCCGTTTTATCGGGGCAGATATAA 34 18 0 CCCCTTCGGG 0.577042 -213 ACCCCGCCGGCGCAAACCGGGCGGGGTTTTTCGTT 42 37 1 CGCACGCGGG 0.987856 -69 TTTTCTTCTGGGCCGACTTTCCGGGAGGTGCTTAA 42 71 0 GGCCCTCGGG 0.95997 -35 GAGAACGTCTGGCCGCTGGTGCCGCCTGGCGCCAG 44 249 1 GGCCTGCCGC 0.922182 -52 CTCCTGAATCCGCAAGGTGATCTGGTCGTACCAGA 46 159 0 CGCAGGCTGG 0.814557 -31 AAGCGAACCCGCCCTTGCGAGCGGGAGAAGAAC 48 9 0 GCCCGGCGGG 0.889556 -42 **** * * **** Masking position 3 Map Score: 22.6106 Number of sites scoring better than the average of aligned sites = 3102 Number in coding regions = 2916 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 2 ACAGGTTCTACGTTTAGTTGCCGCGCTTTTATATGC 2 56 0 CGTGTTGCGC 0.922741 -105 CCGGAGGGTGCAGTTCTTTGCGTGGCCCGGCGATCT 3 69 0 CATTTTGCGC 0.983213 -53 TTTGGATAATCAAATATTTACTCCGTATTTGCATAA 13 163 1 CATTTTACGT 0.455175 -138 GCAAAGCTGACACCTTTCAGCATCGCTTTTCGCCAT 15 32 0 CATTCAGCGC 0.858733 -269 TGATCCAAATCAAATTTTTGCAAAGCTGACACCTTT 15 51 0 CATTTTGCGC 0.983213 -250 CAAAAAAAGGCGTATATTTGCGCTGTGAATGGTTGA 22 84 0 CGTTTTGCGT 0.903815 -122 GTTCGATTCCTTGCATCGCTTGTCGTGAT 22 187 0 CGTCTTGCGC 0.922741 -19 AGCACTGCCACGTATGTTTACACCGCATCCGGCATA 30 13 1 CGTTTTACGC 0.930865 -185 ATCGGGAGGCCGTTTTTTTGCCTTTCACTCCTCGAA 30 79 1 CGTTTTGCTC 0.89773 -119 GCGCACTGTGCAAATTTCTGCATAGCAAGTTTTGGT 31 12 0 CATTCTGCGC 0.97578 -184 GCACAGTGCGCAATTTTCTGCATAGCCGCTCATTCT 31 37 1 CATTCTGCGC 0.97578 -159 ATAAATAATCCACCTGTCTGTCTTGCAGGTGTCGGT 39 31 1 CATTCTGTGC 0.666444 -68 TATAAAAAGTCGTTTTTCTGCTTAGGATTTTGTTAT 41 101 1 CGTTCTGCGG 0.84455 -110 CCAAAAACGCCACGTGTTTACGTGGCGTTTTGCTTT 45 23 1 CATTTTACGC 0.893315 -217 CTTAAGTCTCCGCATCTTAGCACATCGTTCATCCAG 46 35 1 CGTTTAGCTC 0.569791 -155 GTAATGTAACCGTCAATTTGCGACGCGTCTCACAAG 47 94 1 CGATTTGCGC 0.883237 -207 GCCTTTTTATCCACTGTTTGCTCCGCCTGCGATTGC 47 217 1 CCTTTTGCGC 0.931899 -84 ** * ***** ** Masking position 1 Map Score: 14.5036 Number of sites scoring better than the average of aligned sites = 600 Number in coding regions = 564 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 TATAAGATCGCCGGGCCACGCAAAGAACTG 3 65 1 CCGGGCCACG 0.888059 -57 TACGATTGCGGCAGGCCGTGTTATTATTGT 4 55 1 GCAGGCCGTG 0.878801 -50 TTCAATATCAGCAGGCGGGATCGCATTTTC 6 86 1 GCAGGCGGGA 0.876431 -66 GTTCCGGAGACCTGGCGGCAGTATAGGCTG 10 72 0 CCTGGCGGCA 0.8861 -229 CTTTCTGTTACCTGGAGACGTCGGGATTTC 10 223 0 CCTGGAGACG 0.548522 -78 GGCCTATAAGCCAGGCGAGATATGATCTAT 13 216 1 CCAGGCGAGA 0.742364 -85 AATTTTGGTTGCGGGCGAAAAAATGCGACA 14 164 1 GCGGGCGAAA 0.570312 -61 TGCGTCACTTCCAGGTGGCGTAAGCAAGAT 15 112 0 CCAGGTGGCG 0.895355 -189 GCAGAGATCCCCGGGCCGTATGCCCGTTTA 16 202 0 CCGGGCCGTA 0.729024 -73 AAGCCGCCAGCCAGGCGGCTTTTTTAACAA 20 19 1 CCAGGCGGCT 0.872004 -44 CGGTGCGAATGCAGGCGTCG 25 1 0 GCAGGCGTCG 0.859683 -24 CGCAAGTATGCCTGGCCGCGAGATTATGGC 33 36 1 CCTGGCCGCG 0.891466 -63 TGTCTGTCTTGCAGGTGTCGGTTACGGTTA 39 45 1 GCAGGTGTCG 0.434301 -54 CCCGGTTTGCGCCGGCGGGGTTTTGGAATC 42 28 0 GCCGGCGGGG 0.830363 -78 CCGGCGCAAACCGGGCGGGGTTTTTCGTTT 42 43 1 CCGGGCGGGG 0.972332 -63 GGCCGACTTTCCGGGAGGTGCTTAAACGAA 42 66 0 CCGGGAGGTG 0.803804 -40 CCTGGTCTTTCCGGGTGATGTGTTGGCCAT 44 148 0 CCGGGTGATG 0.581875 -153 ATTACTGGCGCCAGGCGGCACCAGCGGCCA 44 258 0 CCAGGCGGCA 0.949005 -43 TTAATGCCGCGCTGGCGATGTTAGGAAAAT 45 72 1 GCTGGCGATG 0.773285 -168 TTGTCACATGGCAGGCCGTTGCCGTGCGCT 47 42 0 GCAGGCCGTT 0.419815 -259 ATAGGCAATCGCAGGCGGAGCAAACAGTGG 47 227 0 GCAGGCGGAG 0.926471 -74 GCCCTTGCGAGCGGGAGAAGAAC 48 4 0 GCGGGAGAAG 0.37897 -47 ********** Masking position 5 Map Score: 14.3233 Number of sites scoring better than the average of aligned sites = 4812 Number in coding regions = 4619 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 4 GGTTTATTCTGCATTTTTTATTGAATGTAGAATTTTAT 1 43 1 GTTTTTTATT 0.84194 -185 ATTGAATGTAGAATTTTATTCTGAATGTGTGGGCTCTC 1 62 1 GTTTTTTATT 0.84194 -166 CTGTAATGGAGGATTTTATCGTTTCTTTTCACCTTTCC 1 178 1 GTTTTTTTTT 0.84194 -50 TGATTTTTCTGGTAAAAATTATCCAGAAG 2 2 1 GTTTTTTAAT 0.896943 -159 GGTGGGCCTTGTTTTTTCTCTCTTTATCCCCATCTTTA 9 30 1 GTTTTTCTAC 0.718162 -84 CTTCTTAAGTGGATTTTTTATTTACTGCGTACTTCGAC 12 16 0 GTTTTTTATC 0.799525 -39 CCAGCCAGGCGGCTTTTTTAACAACTGCATGGATTGAC 20 25 1 GTTTTTCATC 0.609302 -38 TGGTGGTAAGGTGTTTTATGCTGTTATTTTTATGCGCA 21 102 0 GTTTTTTTAT 0.896943 -199 AATAACATTAGGATTTTGTTATTTAAACACGAGTCCTT 21 205 1 GTTTTTTTAC 0.866956 -96 GGTTTATGCTGATTTTTATACTTTAACTTGTTGATATT 40 30 1 GTTTTTTTAT 0.896943 -159 ATGTTTGGGCGATTTTTATTACGATAATAAAGTCTGTT 41 34 1 GTTTTTCAAT 0.772901 -177 TTTCTGCTTAGGATTTTGTTATTTAAATTAAGCCTGTA 41 115 1 GTTTTTTTAT 0.896943 -96 TTGAGAAACAGAATTTTGTGCTGTTATTCATTGTCTGC 43 90 0 GTTTTTTTAT 0.896943 -50 GTCGAAGTGTGTATTTTGTGTTAAAAATATGCAAACAA 46 118 0 GTTTTTTAAT 0.896943 -72 CCATTTACTGGACTTTTGTAATATCAGTACAAAAATGC 47 180 0 GTTTTTTTAT 0.896943 -121 ATCAGATCGTGCTTTTTTTAGTCACTGCCCACCGCTGT 49 60 0 GTTTTTTATC 0.799524 -235 * **** * * * * * Masking position 9 Map Score: 12.4561 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 47 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 5 TTTCACCTTTCCTCCTGTTTATTCTTATTA 1 204 1 CCTCCTGTTT 0.972134 -24 ATCAATCCTGTTTTTCAACCTAT 14 212 0 AATCCTGTTT 0.898761 -13 TATGACTCCTGTTTCACGTCTATC 16 261 0 ACTCCTGTTT 0.964408 -14 AGTGCAAAGGACTCGTGTTTAAATAACAAA 21 219 0 ACTCGTGTTT 0.797453 -82 AAAAACTCCTGATTGTTAAGGGGG 27 34 0 ACTCCTGATT 0.810275 -14 TTTATATTCCTTCTGTTTGTAGGGGTGC 32 13 0 CCTTCTGTTT 0.919572 -18 CGCTACATCCTGTTTTCAAAGG 35 8 0 CATCCTGTTT 0.919571 -15 AACAGCACAAAATTCTGTTTCTCAAGATTC 43 103 1 AATTCTGTTT 0.744282 -37 TTTTTACCCTTCTGTTTTTTTGACCTT 46 8 1 CCTTCTGTTT 0.919572 -182 ********** Masking position 6 Map Score: 7.00611 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 53 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 GTTTTTTCTCTCTTTATCCCCATCTTTATT 9 40 1 TCTTTATCCC 0.738213 -74 ACTCGCATGGTTTTTATGCAAATACGGAGT 13 182 0 TTTTTATGCA 0.754947 -119 AACAAATAATTTTTAATGCGCAAATGTAGC 14 95 0 TTTTAATGCG 0.708482 -130 TATGCTGTTATTTTTATGCGCATTCTGTGT 21 94 0 TTTTTATGCG 0.874077 -207 AATCCTACTTTTTTAATGCGATCCAATCAT 21 266 1 TTTTAATGCG 0.708482 -35 AGTGCGCGTGTTTTTATGCCGGATGCGGTG 30 33 0 TTTTTATGCC 0.960551 -165 CGGGAGGCCGTTTTTTTGCCTTTCACTCCT 30 81 1 TTTTTTTGCC 0.919561 -117 TTTTTATCCCTCTTGCATAC 31 186 0 TTTTTATCCC 0.918655 -10 AAAAAAGTGATTTTTATCACAAAGGAAATA 36 168 0 TTTTTATCAC 0.709917 -84 TTTTTTTGACAAAAATCAGG 40 1 1 TTTTTTTGAC 0.712421 -188 AATCCTACTTTTTTATTGCCTTCAAATAAA 41 176 1 TTTTATTGCC 0.800101 -35 GTCCGGGGGTTTTTTTTGACCTTAAAAACA 43 50 1 TTTTTTTGAC 0.712421 -90 ATATCTGTAATCTTAATGCCGCGCTGGCGA 45 60 1 TCTTAATGCC 0.680379 -180 TACCCTTCTGTTTTTTTGACCTTAAGTCTC 46 15 1 TTTTTTTGAC 0.712421 -175 GTAAATGGCCTTTTTATCCACTGTTTGCTC 47 210 1 TTTTTATCCA 0.588287 -91 CTCCAGATTGTTTTTATCCCACAGCCACGT 49 268 0 TTTTTATCCC 0.918655 -27 ********** Masking position 4 Map Score: 9.93512 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 506 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 162 Fraction of orfs with sites within 600 bp upstream = 0.0260199 Motif number 7 GTAAGTTGTGGGATTCAGCCGATTTATTATCA 1 136 1 GATTCGCCGA 0.945923 -92 GTCTTATTGAGCTTTCCGGCGAGAGTTCAATG 2 90 1 GTTTCGGCGA 0.981377 -71 GGATTGCAGGGTGTTCCGGAGACCTGGCGGCA 10 82 0 GGTTCGGAGA 0.933736 -219 CACAAATTTTGGTTGCGGGCGAAAAAATGCGA 14 160 1 GTTGCGGCGA 0.892607 -65 GTTTTTCAACCTATTCGGGCAATTGTATGTAT 14 194 0 CATTCGGCAA 0.774998 -31 CTCAGGTAAGTGATTCGGGGGAGCGAACGCAG 16 116 1 TATTCGGGGA 0.826726 -159 TATGCCCGTTTATTTCTGGCGACATTCTTTAT 16 182 0 TTTTCGGCGA 0.950886 -93 TTAAATCTCGGTATTCTGGAAACATACGCACT 19 19 0 GATTCGGAAA 0.784826 -54 TTTTACGTGATAATTCAGGAGACACAGAATGC 21 73 1 TATTCGGAGA 0.913729 -228 CCTACATATTTAATTCAGGCGAAGAGGTTTTA 39 75 1 TATTCGGCGA 0.970447 -24 CCAAACATTGCTGTTCGGGCGATCAAATTAA 41 10 0 CGTTCGGCGA 0.930103 -201 TCCAGAGCGTGATTTCTGCCGAGCGTGATCAG 46 66 1 GTTTCGCCGA 0.911609 -124 ATCACCTTGCGGATTCAGGAGACTGAC 46 173 1 GATTCGGAGA 0.966474 -17 * **** ***** Masking position 12 Map Score: 7.77349 Number of sites scoring better than the average of aligned sites = 630 Number in coding regions = 583 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 GCATATAAAAGCGCGGCAACTAAACGTAGA 2 56 1 GCGCGGCAAC 0.955856 -105 TCTTTGCGTGGCCCGGCGATCTTATATTGA 3 61 0 GCCCGGCGAT 0.937619 -61 TTTGCCAGGCATTTGACTGGCAG 8 4 1 GCCAGGCATT 0.954563 -86 TTATTTACAAGCGCGGCAATTTCGCCCAGT 14 123 1 GCGCGGCAAT 0.977924 -102 AGCGCAATGCGCCCGGCAATCTATACACAA 16 35 1 GCCCGGCAAT 0.986315 -240 TGTGGGTACAGTCAGGCAATAGCAAGGGGA 31 151 0 GTCAGGCAAT 0.728788 -45 TAATCTCGCGGCCAGGCATACTTGCGAAGA 33 32 0 GCCAGGCATA 0.790129 -67 CGCAATGGAAGCAAGGCATTACAGGCTTAA 41 142 0 GCAAGGCATT 0.851433 -69 AACATCGCCAGCGCGGCATTAAGATTACAG 45 64 0 GCGCGGCATT 0.968008 -176 GGATAAGAGCGCACGGCAACGGCCTGCCAT 47 35 1 GCACGGCAAC 0.905752 -266 ********** Masking position 7 Map Score: 9.16311 Number of sites scoring better than the average of aligned sites = 600 Number in coding regions = 570 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 TACGTGATCCAAATCAAATTTTTGCAAAGCTGAC 15 57 0 AAATCTTTTG 0.727569 -244 CTATTTTTATAAATCATTATTTATCAGTGCATTA 18 131 0 AAATCTTTAT 0.794239 -154 TAGTTAAGTAAAATCACAAATTTTGTATGTTTGA 18 185 0 AAATCATTTT 0.643099 -100 CTTTATCGATAAATCCTACTTTTTTAATGCGATC 21 255 1 AAATCTTTTT 0.939584 -46 CCTGCGGATGAAATCAATTTTTTTAGGACTGATG 26 175 1 AAATCTTTTT 0.939584 -126 AAATAGTCCTTTTTATTGTTACAG 28 17 0 AAATATTTTT 0.527092 -14 TTTGTGATAAAAATCACTTTTTTTAAACAATTAA 36 175 1 AAATCTTTTT 0.939584 -77 TTTTTGACAAAAATCAGGGTTTATGCTGATTTTT 40 13 1 AAATCTTTAT 0.794239 -176 CATTGCGGATAAATCCTACTTTTTTATTGCCTTC 41 165 1 AAATCTTTTT 0.939584 -46 GAGCGTGATCAGATCGGCATTTCTTTAATCTTTT 46 86 1 AGATCTTTCT 0.644603 -104 CTAAACCATCAGATCGTGCTTTTTTTAGTCACTG 49 71 0 AGATCTTTTT 0.896873 -224 AAATTTGACGAGATCGATTTTTTTAGTGCGCAAG 49 142 0 AGATCTTTTT 0.896873 -153 ***** ***** Masking position 3 Map Score: 5.86171 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 35 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 CTGCCATGAAAATGCGATCCCGCCTGCTGA 6 93 0 AATGCGATCC 0.972468 -59 ATAATGGCGAAAAGCGATGCTGAAAGGTGT 15 29 1 AAAGCGATGC 0.948617 -272 CTACTTTTTTAATGCGATCCAATCATTTTA 21 270 1 AATGCGATCC 0.972468 -31 TGCATCACGACAAGCGATGCAAGGAATCGA 22 184 1 CAAGCGATGC 0.870975 -22 TCAGTACAAAAATGCGATCCGCCTCATAAC 47 165 0 AATGCGATCC 0.972468 -136 CTCCTGTGGGAAAGCGAACCCGCCCTTGCG 48 25 0 AAAGCGAACC 0.897056 -26 ********** Masking position 7 Map Score: 3.38819 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 39 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 CTGTTCACAAAATCATTACAATTAACCTACATATAGTT 10 37 0 ATAATTAACT 0.953059 -264 TTAAATACAAATTACCGATATTTAACCTTATAATTAC 13 10 0 ATAATTAACT 0.953059 -291 AATAAAAATAAATTTTAAAAATTAACAAATGAGTTGAA 13 127 0 ATAATTAACA 0.701643 -174 TGATATAGCAATTATCGATAATTAACATCCACACATTT 14 54 1 ATAATTAACT 0.953059 -171 CAGATGATTTACTAAAAAAGTTTAACATTATCAGGAGA 15 268 1 ATAGTTAACT 0.87557 -33 GTTGCTATACAGATCGCATAGTTAACATTTCGTTAAAA 18 81 0 AAAATTAACT 0.720654 -204 ATGTTTCCAGAATACCGAGATTTAATATCCCGTCTGAA 19 26 1 ATAATTAATT 0.817586 -47 AAAGCAACAAATTAGTAACATTTAACGTAGGGTATTAA 34 182 0 ATAATTAACT 0.953059 -49 TAGGGCGTTAATCTCCCATACTTAACCTGGTTTATGGT 36 57 0 ACAATTAACT 0.792684 -195 TACTCTGGAAAGTATTGAAAGTTAATTTGTGAGTGGTC 40 93 1 ATAATTAATT 0.817586 -96 GACTTTTTATAATATAAACATTTAACATGATAATATTA 41 74 0 ATAATTAACT 0.952954 -137 CTAAATTATCACTGAAGATGATTAATTTAATTACTAAA 49 100 0 ATAGTTAATT 0.608357 -195 * * * * ***** * Masking position 8 Map Score: 5.06779 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 3 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 CGATCAATATAAGATCGCCGGGCCACGCAA 3 58 1 AAGATCGCCG 0.588334 -64 GTTAGTTAATCAAAACGCCGTCGTTAATCA 8 50 0 CAAAACGCCG 0.9469 -40 ACTGTTCAGGATAAAACCCGACAAACTATA 10 14 1 ATAAAACCCG 0.57648 -287 TGCAGTTGTTAAAAAAGCCGCCTGGCTGGC 20 24 0 AAAAAAGCCG 0.948182 -39 AGTGATCACAAAAAAAGGCGTATATTTGCG 22 98 0 AAAAAAGGCG 0.766757 -108 ATAAAGATCGAAAAAAGCCGGAGTGATCAC 22 119 0 AAAAAAGCCG 0.948182 -87 GCACCAAATAAAAAAAGCCGGTACTGACTG 23 36 0 AAAAAAGCCG 0.948182 -84 ATCCGGCATAAAAACACGCGCACTTTGCTA 30 39 1 AAAACACGCG 0.556401 -159 CACACGATTCCAAAACCCCGCCGGCGCAAA 42 23 1 CAAAACCCCG 0.930928 -83 TGCTTAAACGAAAAACCCCGCCCGGTTTGC 42 48 0 AAAAACCCCG 0.966983 -58 TTAACGAACTAAGACCCCCGCACCGAAAGG 43 21 1 AAGACCCCCG 0.811019 -119 AAGGTCAAAAAAAACCCCCGGACCTTTCGG 43 43 0 AAAACCCCCG 0.936648 -97 GTCTTATGCCAAAAACGCCACGTGTTTACG 45 15 1 AAAAACGCCA 0.818202 -225 GATATAAAAGCAAAACGCCACGTAAACACG 45 35 0 CAAAACGCCA 0.674388 -205 ********** Masking position 4 Map Score: 9.41211 Number of sites scoring better than the average of aligned sites = 981 Number in coding regions = 791 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 13 GCAGTATAGGCTGTTCACAAAATCATTACAATT 10 52 0 CTTTCAAAAT 0.91305 -249 AAGGTGTCAGCTTTGCAAAAATTTGATTTGGAT 15 52 1 CTTGCAAAAT 0.982079 -249 GCCCGGCAATCTATACACAAAATCATTCAAGTT 16 45 1 CTTACAAAAT 0.913051 -230 CCAAAACTTGCTATGCAGAAATTTGCACAGTGC 31 13 1 CTTGCAAAAT 0.982079 -183 GAATGAGCGGCTATGCAGAAAATTGCGCACTGT 31 39 0 CTTGCAAAAT 0.982077 -157 CCCACCAGTCCTGTGCAAAAATTAACCATTTGA 45 138 0 CTTGCAAAAT 0.982079 -102 ** **** *** * Masking position 7 Map Score: 2.23046 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 8 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 GACTGGCAGACGTCCCCGCCGTTGGTGATTAA 8 25 1 CGTCCCGCCT 0.959747 -65 GTTAGTATCTCGTCGCCGACTTAATAAAGAGA 13 271 1 CGTCCCGACT 0.866743 -30 TCCTTCAAGCCGCCTCTGCCTTGGCTGCGTTC 16 140 0 CGCCCTGCCT 0.980648 -135 ATGAAATCTACGCAACTGAGCTACTACCATAC 22 153 0 CGCACTGAGT 0.664225 -53 GACACGCTACCGCCCCTGGCTTTTTAGCTACC 26 103 0 CGCCCTGGCT 0.976139 -198 CGCACCTGCCATTTAACAAGGA 29 1 1 CGCACTGCCT 0.949025 -28 ATGTTTACACCGCATCCGGCATAAAAACACGC 30 26 1 CGCACCGGCT 0.976139 -172 GCCCGGTTTGCGCCGGCGGGGTTTTGGAATCG 42 27 0 CGCCGCGGGT 0.863045 -79 TGTTAGCCAGCGCCTTCGGCATCCATGGCCAA 44 124 1 CGCCTCGGCT 0.950615 -177 TGTGGGAAAGCGAACCCGCCCTTGCGAGCGGG 48 19 0 CGAACCGCCT 0.832434 -32 AAATTTGTCTCGCCGTCGCGTTGCGAGTAGAC 49 14 0 CGCCTCGCGT 0.902789 -281 **** ***** * Masking position 12 Map Score: 6.09668 Number of sites scoring better than the average of aligned sites = 1347 Number in coding regions = 1185 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 15 AAACGTAGAACCTGTCTTATTGAGCTTTCCG 2 77 1 CCTGTCTATT 0.941471 -84 TTTTCTGGAACCTGTCCCATTGAACTCTCGC 2 108 0 CCTGTCCATT 0.831918 -53 AACTTTACGGCCTGTCTCATTCTTACGATTG 4 32 1 CCTGTCTATT 0.941471 -73 GATACTCTTCCTGTCAAAATATAAGAAACG 4 85 0 CCTGTCAAAT 0.888654 -20 CTCGCGCGCTCCCGTCAGATTGTGTTAACAT 6 44 0 CCCGTCAATT 0.947823 -108 ACAAAAACTCCTTTCAAATTACGTCATTGT 6 132 0 CCTTTCAATT 0.749258 -20 GATTTAATATCCCGTCTGAAAAACGAAAATC 19 44 1 CCCGTCTAAA 0.595825 -29 GCCTGAAAGACCAGTCTGAATTATTCTGTCA 26 140 1 CCAGTCTAAT 0.663181 -161 TCCAATTTATCCCTTCATATTCAATTAGTTA 31 88 1 CCCTTCAATT 0.800401 -108 TTATTCATTTCCTGTCTCACTTTGCCTTAAT 34 156 1 CCTGTCTACT 0.810333 -75 AACGGACTTTCCCTTCTGAATAAAGGTCTTC 45 176 1 CCCTTCTAAT 0.737505 -64 AAAAATCGATCTCGTCAAATTTCAGACTTAT 49 154 1 CTCGTCAATT 0.56586 -141 ******* *** Masking position 9 Map Score: 2.76495 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 96 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097