AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_mjan_reg_100.orf -o00790_mjan_100.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 Purged sequences: MJ0086 36 unspecified methyltransferase MJ1169 26 formylmethanofuran dehydrogenase, subunit A (tungsten) (fwdA) Input sequences: #1 MJ0030 300 coenzyme F420-reducing hydrogenase, delta subunit (frcD) #2 MJ0081 300 methyl coenzyme M reductase II, subunit beta (mrtB) #3 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #4 MJ0087 23 hemin permease (hemU) #5 MJ0090 80 collagenase (prtC) #6 MJ0091 95 Na+/Ca+ exchanger protein, putative #7 MJ0318 171 formylmethanofuran:tetrahydromethanopterin formyltransferase (ftr) #8 MJ0448 130 conserved hypothetical protein #9 MJ0511 300 thymidylate synthase (thyA) #10 MJ0658 134 M. jannaschii predicted coding region MJ0658 #11 MJ0822 300 S-layer structural protein #12 MJ0842 219 methyl coenzyme M reductase I, subunit beta (mcrB) #13 MJ0846 131 methyl coenzyme M reductase I, subunit alpha (mcrA) #14 MJ0847 219 N5-methyl-tetrahydromethanopterin:coenzyme M methyltransferase, subunit E (mtrE) #15 MJ0849 29 N5-methyl-tetrahydromethanopterin:coenzyme M methyltransferase, subunit C (mrtC) #16 MJ0869 119 DNA repair protein RAD51 (radA) #17 MJ0870 176 coenzyme F420-reducing hydrogenase, beta subunit (frhB) #18 MJ0968 55 copper transporting P type ATPase (copA) #19 MJ1035 300 N5,N10-methylene-tetrahydromethanopterin dehydrogenase (mtd) #20 MJ1149 59 mutator MutT protein, putative (mutT) #21 MJ1165 238 formylmethanofuran dehydrogenase, subunit E (tungsten) (fwdE) #22 MJ1167 47 formylmethanofuran dehydrogenase, subunit G (tungsten) (fwdG) #23 MJ1170 32 conserved hypothetical protein #24 MJ1171 25 formylmethanofuran dehydrogenase, subunit C (tungsten) (fwdC) #25 MJ1243 91 conserved hypothetical protein #26 MJ1245 148 M. jannaschii predicted coding region MJ1245 #27 MJ1337 238 M. jannaschii predicted coding region MJ1337 #28 MJ1338 76 H(2)-dependent methylenetetrahydromethanopterin dehydrogenase related protein #29 MJ1349 232 coenzyme F420-reducing hydrogenase, beta subunit #30 MJ1505 178 ATP dependent RNA helicase, putative #31 MJ1534 275 N5,N10-methylene-tetrahydromethanopterin reductase (mer) #32 MJ1574 300 ATP-dependent RNA helicase, eIF-4A family, putative #33 MJ1635 199 M. jannaschii predicted coding region MJ1635 #34 MJ1636 63 N5,N10-methenyl-tetrahydromethanopterin cyclohydrolase (mch) #35 MJ1662 94 methyl coenzyme M reductase system, component A2-like Motif number 1 TTTAAAATCTTTAAAAAAATTTTGAATTCC 2 139 0 TTAAAAAAAT 0.609384 -162 AATGATAAAATTAAAAAAATCTTTAAAATC 2 160 0 TTAAAAAAAT 0.609384 -141 ATTTTATCATTTTAATATTATTATTTTAAC 2 179 1 TTTAATATTA 0.614271 -122 AGTAATAGGTATATAAAATTTTCTATTTTA 2 230 0 ATATAAAATT 0.645237 -71 TAAAAATTATATAAAAAATAGAAAAAAG 3 9 0 ATAAAAAATA 0.751626 -126 ATCAATATTCATAAAAATTATATAAAAAAT 3 20 0 ATAAAAATTA 0.87278 -115 TTAATATCTAATATATATTTTTCGGTAGTT 3 75 0 ATATATATTT 0.712247 -60 ATATTAGATATTAAAAATTTTTGTTCATAT 3 91 1 TTAAAAATTT 0.920381 -44 TCAAATATAATTTAAAATTTAAAAAAATTT 5 57 1 TTTAAAATTT 0.792759 -24 TTGCTTAAGTTTAAATATTATTGCAGAATA 6 36 1 TTAAATATTA 0.827947 -60 ACTTAGATTATTTAAAATTATTGTTGATAT 7 51 1 TTTAAAATTA 0.723872 -121 AAATCCATAAATAAAAATATATCAACAATA 7 69 0 ATAAAAATAT 0.753849 -103 TTTGTTATAGATTAAAAATTGGTGAATATT 8 12 0 ATTAAAAATT 0.593702 -119 TAATCATCAAATAAATATTTTGTTATAGAT 8 30 0 ATAAATATTT 0.85877 -101 GTAGCATCAGATTTATATTTTCCCGCATTT 8 74 0 ATTTATATTT 0.452531 -57 CATAACTGCTATAAAAAATATTTGGTGACA 8 109 1 ATAAAAAATA 0.751626 -22 CCCTCTATGGTTATATATAATTGAAATGGA 9 190 1 TTATATATAA 0.306251 -111 TTTAAATCTTTTTTATATTTCATCAAATTT 9 225 1 TTTTATATTT 0.488544 -76 TACAACAAGTATAAAAATTTGATGAAATAT 9 239 0 ATAAAAATTT 0.909179 -62 TTTAATTATGATAAAAAATAGATACAACAA 9 261 0 ATAAAAAATA 0.751626 -40 TAGTTTCAAAATAAAAATAAAAAAGAAGAA 10 24 0 ATAAAAATAA 0.677294 -111 ATATTTGTAAATTTAAATTTACAAATATAG 10 53 1 ATTTAAATTT 0.577062 -82 GTAGAAACTTATAAAAATATGTGGGGGTTT 11 39 0 ATAAAAATAT 0.753849 -262 TTTTAAATGGATAAAAATTAATTTTGATAT 11 82 0 ATAAAAATTA 0.87278 -219 TATCGCTCTATTAAAAAATAAAAAAAGTTA 11 128 0 TTAAAAAATA 0.777506 -173 TAGAGCGATATTATAAATTAAATTTTGTAT 11 148 1 TTATAAATTA 0.765412 -153 GTTATTTTTAATAAAAAATTTCAGATAGAA 12 28 1 ATAAAAAATT 0.815356 -192 AAAAAATCCCTTATAAAATTTTCTATCTGA 12 48 0 TTATAAAATT 0.677445 -172 CAGGCAAAGTTTTAAAATTAAAATAACATA 12 98 0 TTTAAAATTA 0.723872 -122 TTATCGCAGTTTATATATATCCAGTTTTTC 12 176 0 TTATATATAT 0.376217 -44 ACTTAGAAAAATAAAAAATAAAAATCAAAA 13 91 1 ATAAAAAATA 0.751626 -41 TAATAAAAAATTAAAAAATTTAGAAT 14 7 0 TTAAAAAATT 0.836043 -213 AAAAAGTTAAATAAAAATTAAGTGAATTTT 14 129 1 ATAAAAATTA 0.87278 -91 ATAGAAAACCTTATATATTAACCTAATAAA 14 170 1 TTATATATTA 0.662885 -50 ACCTCCTCAATTATATATTTACTATTCTTA 16 17 1 TTATATATTT 0.741354 -103 CTAATATTATTAAAATAACATTCAATTC 17 9 1 ATTAAAATAA 0.409872 -168 CCAAATGTGTATTTATATTTTTTGATATTT 17 49 0 ATTTATATTT 0.452531 -128 AATTACACACATATAAATTTCCCCCAAATG 17 72 0 ATATAAATTT 0.804799 -105 ACCCCATTAATTAAATATATACGTTCAGAT 18 32 0 TTAAATATAT 0.680793 -24 TATAATTAATTAATATTTGTAGAATATA 19 9 1 ATTAATATTT 0.668032 -292 TTTATTTAAGTTATATATTAGAAAATCTAA 19 142 0 TTATATATTA 0.662885 -159 TATAACTTAAATAAAAATAATAGTTATTAT 19 157 1 ATAAAAATAA 0.677294 -144 GATTTTGTTATTAAAAAATAATAACTATTA 19 174 0 TTAAAAAATA 0.777506 -127 TATTCACCTGATATATAATATCTTTAGATT 19 200 0 ATATATAATA 0.430347 -101 GGGAGAGATATTTAAAATTT 20 1 0 TTTAAAATTT 0.792759 -59 AAAAACTTCATTAAAAATATAGGGAGAGAT 20 22 0 TTAAAAATAT 0.779567 -38 AATGAAGTTTTTATATATATAAGTGAGAGC 20 40 1 TTATATATAT 0.376217 -20 ACCATAAAAAATAAATATTATAATGATTTA 21 28 0 ATAAATATTA 0.806471 -211 AAAGCTAATAATATAAAAATACAACCATAA 21 51 0 ATATAAAAAT 0.357111 -188 GTTGAACTATTTATAAATATGTGAGCAAGA 21 128 1 TTATAAATAT 0.591568 -111 TTAAAAATTAAATTTTAGAA 23 23 0 TTAAAAATTA 0.887918 -10 ATCCTATTATTTAAAAATTTGAAAATTATA 26 12 1 TTAAAAATTT 0.920381 -137 AATTTAACTGTTAAAAATATAGAATATAAA 26 102 0 TTAAAAATAT 0.779567 -47 AATAAGAAAAATAAATAATAAAGTATTTAT 28 34 1 ATAAATAATA 0.647679 -43 AATAAAGTATTTATATAATAATCATCAGAA 28 50 1 TTATATAATA 0.466068 -27 TTAAAAATTGATAAAAATTTCTATTAAATT 29 179 0 ATAAAAATTT 0.909179 -54 TCTAAATAGTTTTAAAAATTGATAAAAATT 29 190 0 TTTAAAAATT 0.62789 -43 CTCGTAATGAATAAATAATTTATTGGCAAT 30 19 1 ATAAATAATT 0.728444 -160 TTTTGTAAAGTTATAAATTTAATATTCTAA 30 65 1 TTATAAATTT 0.82642 -114 CAATTGTTCTTTAAAAATTATAAAAGTAGC 30 144 0 TTAAAAATTA 0.887918 -35 GCCAAATCATTTAAATAATATAAATAATAA 31 84 0 TTAAATAATA 0.679776 -192 TTTCTTGAAATTAAATATTTTTTTAGATAA 31 126 1 TTAAATATTT 0.87534 -150 CTTTACTCCTATAAATATTTTTCGATTTGC 31 177 1 ATAAATATTT 0.85877 -99 AGTTGTTAAAATTAATATTAATAATGGATA 32 26 0 ATTAATATTA 0.579668 -275 GACACTATATTTTAAAATTTCTTTTATTAT 32 62 1 TTTAAAATTT 0.792759 -239 GGTGAAATCATTTAAAATTTAAATAACCAT 32 166 0 TTTAAAATTT 0.792759 -135 GCATTAATCATTAAAAATTTATTTCCCAGT 32 238 1 TTAAAAATTT 0.920381 -63 TGGAAGGTAGATAAATATATCTTATATAAC 33 87 0 ATAAATATAT 0.648208 -113 TATTAACATATTTAATAATTATTACTGCAA 35 45 1 TTTAATAATT 0.506184 -50 ********** Masking position 5 Map Score: 57.0256 Number of sites scoring better than the average of aligned sites = 3089 Number in coding regions = 1991 Number in noncoding regions = 1098 Number of orfs with sites within 600 bp upstream = 669 Fraction of orfs with sites within 600 bp upstream = 0.107453 Motif number 2 GCTTATAACATTTTTCTAACTTCTATAATCTCTTTT 1 108 0 TTTTTTTTAT 0.942818 -193 TTTAAGTTTTTTAAGGGTTTAATTTAAGCTTCC 1 278 0 TTTTTTTAAT 0.839673 -23 CCTCTGTGAGGAATTCAAAATTTTTTTAAAGATTTT 2 130 1 GAATTTTTTT 0.419142 -171 TTAATATTATTATTTTAACATTTTTTAGTAATTTTT 2 190 1 TATTTTTTTT 0.863739 -111 CTTTTTTCTATTTTTTATATAATTTTTA 3 3 1 TTTTTTTTAT 0.942818 -132 TATTGATGTATTTTTAACGATTATTTTTGATAAACT 3 43 1 TTTTTTTTTT 0.896595 -92 CTAATATATATTTTTCGGTAGTTTATCAAAAATAAT 3 62 0 TTTTTGTTAT 0.766642 -73 TTAGAAATTTTTTTAAATTTTAAATTATATTTGAA 5 56 0 TTTTTTTAAT 0.839673 -25 CCTACTAAATTAATTAAAGTTTGTTTTTGAATATAT 6 63 0 TAATTTTTTT 0.697748 -33 CCTCTAAATCTTTTTAATTGTTATATTACCTATACT 7 18 1 TTTTTTTTAT 0.942818 -154 AAATGGAAGATATTTAAATCTTTTTTATATTTCATC 9 213 1 TATTTTTTTT 0.863739 -88 TATTTTCTTCTTTTTTATTTTTATTTTGAAACTATA 10 20 1 TTTTTTTTTT 0.896595 -115 TTTAAATTGTTATTTAAAGTTTCTATATTTGTAAAT 10 69 0 TATTTTTTAT 0.923394 -66 TGTTCAATCTTATTTTTGTTTTAAATTGTTATTTAA 10 88 0 TATTTTTAAT 0.792907 -47 GGTTTATAATGAATTAGAAATTTTTTCTTTAAA 11 8 0 GAATTTTTTT 0.419142 -293 ATTTGTAACTTTTTTTATTTTTTAATAGAGCGATAT 11 123 1 TTTTTTTAAT 0.839673 -178 ATCACCTAAGTTTTTGTATTGTTATTTGATTGACGG 11 270 0 TTTTTGTATT 0.354327 -31 ATATTTTTGAGATTTATAATTTATTTTTGTAGTTTT 13 54 0 GATTTTTTTT 0.664587 -78 TTATTTTTTATTTTTCTAAGTTATATTTTTGAGATT 13 76 0 TTTTTTTTAT 0.942818 -56 CCTCTGTGAGGAATTTTGATTTTTATTTTTTATTTT 13 98 0 GAATTTTTAT 0.578443 -34 ATTCTAAATTTTTTAATTTTTTATTATGTTGATA 14 9 1 TTTTTTTTAT 0.942818 -211 TAAGTTTTTGTATTTTACGTTTTAATATGCTTAACA 14 46 0 TATTTTTAAT 0.792907 -174 ACTTAATTTTTATTTAACTTTTTTTTAGTTATAGGA 14 116 0 TATTTTTTTT 0.863739 -104 TTTGAATTGAGAATTGAATGTTATTTTAATAATATT 17 13 0 GAATTTTTTT 0.419142 -164 TGTATTTATATTTTTTGATATTTTTTGAATTGAGAA 17 36 0 TTTTTTTTTT 0.896595 -141 TGTGATTGATTTATTCACACTTTAATGCTATTTAAT 17 134 0 TTATTTTAAT 0.65604 -43 AATAACCAAAGTTTTAGCTTTTGTATAATTGCTTCA 19 60 0 GTTTTTTTAT 0.8375 -241 ATAATATTTATTTTTTATGGTTGTATTTTTATATTA 21 37 1 TTTTTTTTAT 0.942818 -202 AAATAGAAGTTTTTTGCGTTTTTTATTTGAGGAATT 25 50 0 TTTTTTTTAT 0.942818 -42 ATATTCTATATTTTTAACAGTTAAATTGTAACTTTT 26 105 1 TTTTTTTAAT 0.839673 -44 AAATTCCTTGTTATTTATTATTTTATCTCCTTTTAA 27 188 0 TTATTTTTAT 0.857238 -51 TAAAAACTATTTTTTGCTACTTTTATAATTTTTAAA 30 129 1 TTTTTTTTAT 0.942818 -50 ATAAACTTCCTAATTATTATTTATATTATTTAAATG 31 71 1 TAATTTTTAT 0.814464 -205 TTTATGGTAGTAATTAAGTTTTCTATTTACCGCAAA 31 202 0 TAATTTTTAT 0.814464 -74 AGCTTATGGTTATTTAAATTTTAAATGATTTCACCA 32 161 1 TATTTTTAAT 0.792907 -140 ATATAACTTGTATTTGTATTGTTTTTATAGTTTATG 33 58 0 TATTTGTTTT 0.558113 -142 ATTAATCGTTATTGTATTTTGTATGATATTATAC 33 176 0 TTATTTTTAT 0.857238 -24 AACCTAAAACTTTTTGCTAAGTTTATAAGTTATTAA 35 15 1 TTTTTGTTAT 0.766642 -80 ***** ** *** Masking position 5 Map Score: 48.7791 Number of sites scoring better than the average of aligned sites = 1510 Number in coding regions = 1089 Number in noncoding regions = 421 Number of orfs with sites within 600 bp upstream = 316 Fraction of orfs with sites within 600 bp upstream = 0.0507549 Motif number 3 AATCTTTAAAATCTTTAAAAAAATTTTGAATTCCTCA 2 136 0 ATAAAAATTT 0.785054 -165 TTATCCTAAAAATTACTAAAAAATGTTAAAATAATAA 2 196 0 AATAAAAGTT 0.923204 -105 CTGTAGTAATATATTAACAAAAAGGTTGGTGTTGGTA 2 274 1 ATAAAAAGTT 0.847876 -27 AAATATATATTAGATATTAAAAATTTTTGTTCATATC 3 85 1 TTTAAAATTT 0.479729 -50 AATATAATTTAAAATTTAAAAAAATTTCTAA 5 60 1 ATTAAAATTT 0.719267 -21 TGCAGAATATATTCAAAAACAAACTTTAATTAATTTA 6 57 1 AAAAAAATTT 0.911073 -39 ATAGTGCCTTATTTAATTAAAAACTTTGATAATTGGT 9 20 0 AATAAAATTT 0.887358 -281 ATTTAAATTTACAAATATAGAAACTTTAAATAACAAT 10 63 1 AAAAAAATTT 0.911073 -72 AAAAATAAGATTGAACAAATAAAATTTTGGTGGGGTT 10 107 1 TAAAAAATTT 0.770841 -28 GGGGGTTTATAATGAATTAGAAATTTTTTCTTTAAA 11 10 0 AATAAAATTT 0.887358 -291 ATTAATTTTTATCCATTTAAAAAAGTTGCAAACATTT 11 90 1 AATAAAAGTT 0.92319 -211 TAAAAAATAAAAAAAGTTACAAATGTTTGCAACTTTT 11 110 0 AATAAAAGTT 0.923194 -191 TTATTATATCTTTGTTATACAAAATTTAATTTATAAT 11 157 0 TTAAAAATTT 0.545286 -144 AACAATAGTTTCTGAATGAAAAATTTTATTATATCTT 11 182 0 TATAAAATTT 0.721175 -119 TAATAAAAAATTTCAGATAGAAAATTTTATAAGGGAT 12 36 1 TAAAAAATTT 0.770841 -184 TCCAAATCCATCCACTATATAAATGTTACGATTTTGT 12 133 1 TCAAAAAGTT 0.440358 -87 TTTTAGTGGGAGAAAGTTATAAAGGTTAAATGGGCAA 13 21 0 AATAAAAGTT 0.923204 -111 TCAACATAATAAAAAATTAAAAAATTTAGAAT 14 6 0 AATAAAATTT 0.88732 -214 ATGGATTCCTATAACTAAAAAAAAGTTAAATAAAAAT 14 110 1 ACAAAAAGTT 0.705583 -110 TTACCCCATTAATTAAATATATACGTTCAGATATAAA 18 27 0 AAAAATAGTT 0.387962 -29 TATATAACTTAAATAAAAATAATAGTTATTATTTTTT 19 155 1 AAAAAATGTT 0.387961 -146 TATCCCTATTAAGTAATAAAAAAGGTGATAAC 19 279 1 AATAAAAGTG 0.427088 -22 ATAGTTCAACATATATGAATAAAAGTTCTATTTTTGG 21 101 0 AAGAAAAGTT 0.824588 -138 CAAGACACACACCTATATAAAAAAGTTTCTACTTAAA 21 153 1 AAAAAAAGTT 0.939883 -86 TAATATGTTATTAAAAAAAGAAATTTTAACAATTATC 26 46 0 TAAAAAATTT 0.770841 -103 TATTAAGGAAACTAAATGAAAAACTTTATATTCTATA 26 78 1 AATAAAATTT 0.887358 -71 GACTTAATGTAATTTAATAGAAATTTTTATCAATTTT 29 169 1 ATAAAAATTT 0.785057 -64 CTAATGTCATATGCAAACACAAAAGTTCTATTAGATA 30 91 1 AAAAAAAGTT 0.939883 -88 AAATATTTAATTTCAAGAAAAAACGTTTAAATGCCAA 31 109 0 TAGAAAAGTT 0.60683 -167 GAGGATAATCATAATAAAAGAAATTTTAAAATATAGT 32 65 0 ATAAAAATTT 0.785057 -236 AAACTGTTTAATCTATAAACAAATGTAACATAGAGGA 33 117 1 AAAAAAAGTA 0.395453 -83 TTATACTGTTATATACTCAAAAAAGTTTTCCTCTATG 33 145 0 AATAAAAGTT 0.923204 -55 ATAACTTATAAACTTAGCAAAAAGTTTTAGGTTTTAG 35 11 0 ATGAAAATTT 0.523392 -84 * * * * *** *** Masking position 9 Map Score: 31.5559 Number of sites scoring better than the average of aligned sites = 697 Number in coding regions = 535 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 4 AATAATATTAAAATGATAAAATTAAAAAAATC 2 169 0 AAATGTAAAT 0.919226 -132 AATTACTAAAAAATGTTAAAATAATAATATTA 2 191 0 AAATGTAAAT 0.919226 -110 AATAATTCAAAAAATGTGATAGT 4 4 1 AATTCAAAAT 0.868788 -20 AATATTCGATAAATCCATAAATAAAAATATAT 7 77 0 AAATCATAAT 0.815198 -95 ATTAAAAACCAAATGATAAGATATTAATAGCC 7 106 1 AAATGTAAAT 0.919226 -66 GATAAACTATAATTGTTAAAATCTTAATGGAG 7 143 1 AATTGTAAAT 0.86857 -29 AAACTTTGATAATTGGTTAAATGGAC 9 5 0 AATTGTTAAT 0.718844 -296 CATTTGAACAAAATCGTAACATTTATATAGTG 12 145 0 AAATCTAAAT 0.931572 -75 GATTTTGTTCAAATGAAAAACTGGATATATAT 12 162 1 AAATGAAACT 0.823403 -58 TTATAAACCAAAATCTTTATATAGTCAAATAT 16 86 1 AAATCTTAAT 0.840431 -34 TTCAATTCTCAATTCAAAAAATATCAAAAAAT 17 31 1 AATTCAAAAT 0.868788 -146 CTCCCACAATAATTCTTTATATCTGAACGTAT 18 12 1 AATTCTTAAT 0.753607 -44 TTTAATAACAAAATCTAAAGATATTATATATC 19 189 1 AAATCAAAAT 0.919368 -112 ATAATACGATAATTGTTAAAATTTCTTTTTTT 26 39 1 AATTGTAAAT 0.86857 -110 TAAGGAAACTAAATGAAAAACTTTATATTCTA 26 81 1 AAATGAAACT 0.823403 -68 TTAATACTCAAAATGAATAAATTGTAGGGATT 27 92 1 AAATGATAAT 0.786664 -147 TCCAATAGTTAAATCTAAACCTTTTATTGGCA 27 147 0 AAATCAAACT 0.847973 -92 CATTATCTTAAATTCTAAACATATTATAAGTT 31 15 0 AATTCAAAAT 0.868789 -261 GTAATTCTTCAAATCATTATCTTAAATTCTAA 31 29 0 AAATCTTACT 0.720398 -247 TATTTACCGCAAATCGAAAAATATTTATAGGA 31 183 0 AAATCAAAAT 0.919368 -93 TACTACCATAAATTGATAATATAATAATTGTT 31 226 1 AATTGTAAAT 0.86857 -50 AAATCAACCTAAATCATAAACTATAAAAACAA 33 44 1 AAATCTAACT 0.869447 -156 ***** *** ** Masking position 4 Map Score: 23.954 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 304 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 ACAAAAGAGATTATAGAAGTTAGAAAAATGT 1 106 1 TTATAGAATT 0.47086 -195 CCCTCGAGGCTTATAACATTTTTCTAACTTC 1 121 0 TTATAACATT 0.815222 -180 TTTCGGTAGTTTATCAAAAATAATCGTTAAA 3 55 0 TTATCAAAAT 0.676543 -80 ATTGTCACCATTTTAGGCTATA 3 123 0 TTGTCACCTT 0.653398 -12 ATTTATGGATTTATCGAATATTAAAAACCAA 7 87 1 TTATCGAAAT 0.589959 -85 CAAATATTTTTTATAGCAGTTATGTTTGTGT 8 102 0 TTATAGCATT 0.752162 -29 ATTTAACCAATTATCAAAGTTTTTAATTAAA 9 15 1 TTATCAAATT 0.815222 -286 AAGCCCCAACTTATAACCAATTATCAAAGAA 9 98 0 TTATAACCAT 0.711915 -203 GAAACTATTGTTATAACCGTTTCATATCGTA 11 207 1 TTATAACCTT 0.839037 -94 AAAAAATCCCTTATAAAATTTTCTATCTGAA 12 47 0 TTATAAAATT 0.564006 -173 TCGATATTAGTTATCGCAGTTTATATATATC 12 185 0 TTATCGCATT 0.911899 -35 GTTATCACCTTTTTTATTACTT 19 289 0 TTATCACCTT 0.946746 -12 GGAGATACATTTATCGCAGTTTTGGGCTATG 27 24 1 TTATCGCATT 0.911899 -215 ATTTATTATTTTATCTCCTTTTAAAATGGGT 27 181 0 TTATCTCCTT 0.769376 -58 ATTAGGAAGTTTATCACAAATATTGTAATTC 31 54 0 TTATCACAAT 0.877051 -222 ATTATCACATTTAGTTATTTGA 33 2 1 TTATCACATT 0.937683 -198 TAAGATATATTTATCTACCTTCCAAAACTGT 33 93 1 TTATCTACTT 0.49448 -107 CTTATCACCAATGGAACATGTA 34 52 0 TTATCACCAT 0.893934 -12 GGTTATCACCCATAACTGTGATG 35 82 0 TTATCACCAT 0.893934 -13 ******** ** Masking position 4 Map Score: 14.5892 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 219 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 TTGGATGTCTATATTCCATTGAATATTTATT 1 195 0 ATTTCCATTG 0.884895 -106 GCCTCTGCGTAAGTTCCATTGTGGGAGTGAT 2 17 0 AATTCCATTG 0.816997 -284 GCTATACTCTATTTGCTATTGATGATACTTT 2 46 1 ATTGCTATTG 0.600373 -255 AAAAATGCGTAAGTTCTATTGAATAGGGCTC 2 98 1 AATTCTATTG 0.901245 -203 GGTATATAAAATTTTCTATTTTATCCTAAAA 2 222 0 ATTTCTATTT 0.922202 -79 TATTACTATCATTTTCTATAGCTGTAGTAAT 2 253 1 ATTTCTATAG 0.739647 -48 CTTTTTTCTATTTTTTATATAAT 3 3 1 TTTTCTATTT 0.445729 -132 TTGGGCTTCTAAATTCCATAGTAAATAATAT 9 66 1 AATTCCATAG 0.446611 -235 AGATTTAAATATCTTCCATTTCAATTATATA 9 203 0 ATTTCCATTT 0.852915 -98 TTAAAGAAAAAATTTCTAATTCATTATAAAC 11 12 1 AATTCTAATT 0.439125 -289 CCCTTATAAAATTTTCTATCTGAAATTTTTT 12 40 0 ATTTCTATCT 0.556929 -180 AATATATAAGGTTTTCTATTTGATTCTGTTA 14 158 0 GTTTCTATTT 0.68686 -62 ATATGAATAAAAGTTCTATTTTTGGTAGAAA 21 95 0 AATTCTATTT 0.873156 -144 AAACGCAAAAAACTTCTATTTAAAATGAGGA 25 65 1 AATTCTATTT 0.873156 -27 GAAAAACTTTATATTCTATATTTTTAACAGT 26 95 1 ATTTCTATAT 0.681818 -54 ATAACAAGGAATTTCCTATTTCTATGGAGGG 27 210 1 ATTCCTATTT 0.53122 -29 AATTGATAAAAATTTCTATTAAATTACATTA 29 173 0 AATTCTATTA 0.584364 -60 TATAAATTTAATATTCTAATGTCATATGCAA 30 76 1 ATTTCTAATG 0.641244 -103 GCAAACACAAAAGTTCTATTAGATACTAAAA 30 103 1 AATTCTATTA 0.584365 -76 TAGTAATTAAGTTTTCTATTTACCGCAAATC 31 200 0 GTTTCTATTT 0.68686 -76 GACAATCATCTTCTATTGAATCTTTTCC 32 283 0 ATTTCTATTG 0.940174 -18 ATAAAGCTACATGTTCCATTGGTGATAAG 34 45 1 ATTTCCATTG 0.884896 -19 ** ******** Masking position 4 Map Score: 13.8774 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 227 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 ACAATTAAAAAGATTTAGAGGGATAGAA 7 8 0 AATTTAGAGG 0.743618 -164 GCTATAAAAAATATTTGGTGACATC 8 116 1 AATTTGGTGA 0.900342 -15 TGTCCAAGCAAGATTTGGGGGAGTATCCCAA 9 143 1 AATTTGGGGG 0.95464 -158 ACAAGTATAAAAATTTGATGAAATATAAAAA 9 234 0 AATTTGATGA 0.581508 -67 GAACAAATAAAATTTTGGTGGGGTTT 10 119 1 ATTTTGGTGG 0.970356 -16 ACTTATAAAAATATGTGGGGGTTTATAATGA 11 32 0 AATGTGGGGG 0.727446 -269 ATATATCCAAATATTTAGTAGAAACTTATAA 11 55 0 AATTTAGTAG 0.581508 -246 AAATCCAATAATTTTTGGTGAAAAAATCCCT 12 67 0 ATTTTGGTGA 0.876444 -153 TTATTTTTGTAGTTTTAGTGGGAGAAAGTTA 13 39 0 ATTTTAGTGG 0.876444 -93 ATATAAATACACATTTGGGGGAAATTTATAT 17 61 1 AATTTGGGGG 0.95464 -116 AATCAATCACACATTTAGTGGTGAAAAA 17 159 1 AATTTAGTGG 0.900342 -18 TAAAAGTTCTATTTTTGGTAGAAAAGCTTTA 21 88 0 ATTTTGGTAG 0.834291 -151 TTAATGGACGAGTTTTGATGAAACTTTTACT 29 18 0 ATTTTGATGA 0.521767 -215 AGGAGTAAAGATTTTTGATGGGGGTATTAAT 31 156 0 ATTTTGATGG 0.834291 -120 TGACTTCAATAAATTTGGAGGATAATCATAA 32 88 0 AATTTGGAGG 0.93048 -213 TAGATTAAACAGTTTTGGAAGGTAGATAAAT 33 101 0 ATTTTGGAAG 0.617791 -99 * ********* Masking position 6 Map Score: 11.1713 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 339 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 8 AAAAATTTTTAATATCTAATATATATTTTT 3 83 0 AATATCTAAT 0.551056 -52 ATAAAATAGCAATAACCAATATGACCTCAT 5 24 0 AATAACCAAT 0.851193 -57 ATCGAATATTAAAAACCAAATGATAAGATA 7 99 1 AAAAACCAAA 0.781391 -73 AGAAACTTTAAATAACAATTTAAAACAAAA 10 81 1 AATAACAATT 0.762951 -54 CCGTCAATCAAATAACAATACAAAAACTTA 11 270 1 AATAACAATA 0.844242 -31 AAAATAACATAAAATCCAATAATTTTTGGT 12 79 0 AAAATCCAAT 0.50156 -141 ATAAAAAATAAAAATCAAAATTCCTCACAG 13 101 1 AAAATCAAAA 0.5136 -31 CAATTCAAAAAATATCAAAAAATATAAATA 17 40 1 AATATCAAAA 0.739964 -137 AATTAACATTAATAACCAAAGTTTTAGCTT 19 76 0 AATAACCAAA 0.90595 -225 TAGAAAATCTAATAACTATAAATGACTATA 19 124 0 AATAACTATA 0.797451 -177 ATTAAAAAATAATAACTATTATTTTTATTT 19 165 0 AATAACTATT 0.700046 -136 ATTATTTTTTAATAACAAAATCTAAAGATA 19 182 1 AATAACAAAA 0.857192 -119 ATTAGATACTAAAAACTATTTTTTGCTACT 30 120 1 AAAAACTATT 0.464542 -59 ATTGTTGTTAAATAACAAAATTGAGGGTGA 31 252 1 AATAACAAAA 0.857192 -24 AGAGCGTTCAAATATCCATTATTAATATTA 32 14 1 AATATCCATT 0.710034 -287 ACCGCTCTATAATATCCATAAAAGGAAATA 32 131 0 AATATCCATA 0.804828 -170 TTAAAATTTAAATAACCATAAGCTACCGCT 32 155 0 AATAACCATA 0.896889 -146 AGAGTAATCAAATAACTAAATGTGATAAT 33 10 0 AATAACTAAA 0.813438 -190 CATAAACTATAAAAACAATACAAATACAAG 33 58 1 AAAAACAATA 0.667914 -142 ********** Masking position 4 Map Score: 11.8143 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 397 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 9 ATTTTATCATTTTAATATTATTATTTTAAC 2 179 1 TTTAATATTA 0.690558 -122 TCATTTGGTTTTTAATATTCGATAAATCCA 7 92 0 TTTAATATTC 0.952345 -80 GAAAATATTATTTACTATGGAATTTAGAAG 9 71 0 TTTACTATGG 0.650779 -230 TATTTTACGTTTTAATATGCTTAACAATAT 14 42 0 TTTAATATGC 0.934335 -178 TGACATTGTTTTTAATATTCTGGATGGATT 14 87 1 TTTAATATTC 0.952345 -133 CAATTATATATTTACTATTCTTAGGTTTTT 16 24 1 TTTACTATTC 0.895756 -96 TTTAATGATTTTTAATATTCTTTAAGGTAT 22 18 0 TTTAATATTC 0.952345 -30 GTGGTGTTTCTTTAATATGCTAAAATTCCT 25 27 1 TTTAATATGC 0.934335 -65 AAGTTATAAATTTAATATTCTAATGTCATA 30 72 1 TTTAATATTC 0.952345 -107 ATCTTGGATATTTAATATTGGGTAAACTGG 32 194 0 TTTAATATTG 0.858896 -107 ********** Masking position 6 Map Score: 11.0475 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 35 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 AAAAAATCTTTAAAATCTTTAAAAAAATTTT 2 146 0 TAAATCTTTA 0.818159 -155 TAAAAAATGTTAAAATAATAATATTAAAATG 2 186 0 TAAATAATAA 0.503984 -115 ATAGCTGTAGTAATATATTAACAAAAAGGTT 2 270 1 TAAATATTAA 0.885971 -31 AAAATATATATTAGATATTAAAAATTTTTGT 3 84 1 TTAATATTAA 0.514085 -51 AACCAAATGATAAGATATTAATAGCCCCTAA 7 112 1 TAAATATTAA 0.885977 -60 CTATAATTGTTAAAATCTTAATGGAGGGAAA 7 149 1 TAAATCTTAA 0.746727 -23 TAATCTATAACAAAATATTTATTTGATGATT 8 28 1 CAAATATTTA 0.655724 -103 AATTGAAATGGAAGATATTTAAATCTTTTTT 9 208 1 GAAATATTTA 0.508589 -93 AATAAAAAATTAAAAAATTTAGAAT 14 5 0 TAAAAATTTA 0.36034 -215 ATAGAAAACCTTATATATTAACCTAATAAAA 14 170 1 TTAATATTAA 0.514083 -50 ACCTCCTCAATTATATATTTACTATTCTTAG 16 17 1 TTAATATTTA 0.618189 -103 AGTTATAAACCAAAATCTTTATATAGTCAAA 16 84 1 CAAATCTTTA 0.41959 -36 ACCTGATATATAATATCTTTAGATTTTGTTA 19 194 0 TAAATCTTTA 0.818575 -107 AAATAAGTAGTAAGATATTTATTGGATAAGC 19 234 1 TAAATATTTA 0.92243 -67 TCTAAATCATTATAATATTTATTTTTTATGG 21 26 1 TATATATTTA 0.381005 -213 TGTGTCTTGCTCACATATTTATAAATAGTTC 21 131 0 TCAATATTTA 0.48713 -108 TGAGGAATTTTAGCATATTAAAGAAACACCA 25 28 0 TAGATATTAA 0.52312 -64 CTTTTTTTAATAACATATTAAGGAAACTAAA 26 63 1 TAAATATTAA 0.885977 -86 TAAAAGGAGATAAAATAATAAATAACAAGGA 27 189 1 TAAATAATAA 0.503984 -50 AAATAAATAATAAAGTATTTATATAATAATC 28 42 1 TAAGTATTTA 0.462534 -35 ATATTGCCAATAAATTATTTATTCATTACGA 30 20 0 TAATTATTTA 0.362349 -159 CATATGACATTAGAATATTAAATTTATAACT 30 73 0 TAGATATTAA 0.52312 -106 ATTAAACTTATAATATGTTTAGAATTTAAGA 31 11 1 TAAATGTTTA 0.508583 -265 ATTTATCTAAAAAAATATTTAATTTCAAGAA 31 127 0 AAAATATTTA 0.638254 -149 TACCCCCATCAAAAATCTTTACTCCTATAAA 31 161 1 AAAATCTTTA 0.401083 -115 CCGCAAATCGAAAAATATTTATAGGAGTAAA 31 178 0 AAAATATTTA 0.638254 -98 CATAAATTGATAATATAATAATTGTTGTTAA 31 232 1 TAAATAATAA 0.504008 -44 TATAAGTTATTAACATATTTAATAATTATTA 35 38 1 TAAATATTTA 0.92243 -57 *** ******* Masking position 9 Map Score: 13.4856 Number of sites scoring better than the average of aligned sites = 496 Number in coding regions = 370 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 11 TGATGATACTTTTAGGCTTTCTTTATGATT 2 65 1 TTTAGGCTTT 0.883438 -236 TTGTCACCATTTTAGGCTATATGATATGAA 3 114 0 TTTAGGCTAT 0.883438 -21 TAGTTTATCTTAGGGGCTATTAATATCTTA 7 122 0 TAGGGGCTAT 0.799836 -50 ATAGAAGCCCTTTGGGCTTCTAAATTCCAT 9 55 1 TTTGGGCTTC 0.897972 -246 TGGTTATAAGTTGGGGCTTTCAGCCCCAAT 9 110 1 TTGGGGCTTT 0.957077 -191 GATTTGGGCTTTGCCCATTTAA 13 3 1 TTTGGGCTTT 0.970706 -129 CATAAATGAGTTAGGGCTATATTCTACAAA 19 26 0 TTAGGGCTAT 0.891001 -275 TTATCGCAGTTTTGGGCTATGCGTTAGAGA 27 34 1 TTTGGGCTAT 0.970705 -205 ********** Masking position 8 Map Score: 5.07279 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 79 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ATAGGAATCACTCCCACAATGGAACTTACG 2 11 1 CTCCCACAAT 0.952375 -290 GGGGGCGTAGCCCCCTCTATTGGGATACTC 9 163 0 CCCCCTCTAT 0.973443 -138 GGGGGCTACGCCCCCTCTATGGTTATATAT 9 178 1 CCCCCTCTAT 0.973443 -123 ATTCCAAATCCATCCACTATATAAATGTTA 12 131 1 CATCCACTAT 0.722233 -89 TTATAACTTTCTCCCACTAAAACTACAAAA 13 36 1 CTCCCACTAA 0.795242 -96 GCTTACACCTCCTCAATTATATATTTA 16 8 1 CCTCCTCAAT 0.854195 -112 GCTCCCACAATAATTCTTTAT 18 2 1 CTCCCACAAT 0.952375 -54 TTAAATATCTCTCCCTATATTTTTAATGAA 20 16 1 CTCCCTATAT 0.74847 -44 AATCTCACCCTCAATTTTGTTATTT 31 261 0 CACCCTCAAT 0.9296 -15 ********** Masking position 9 Map Score: 5.03558 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 84 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 TTCCATTGAATATTTATTCCTGCGAAAGTCCTGTTA 1 177 0 TATTTTCTAA 0.826661 -124 TTTAAGGGTTTAATTTAAGCTTCCAAAGAAACAGGA 1 266 0 TATTAACTAA 0.826661 -35 CTTTTAGGCTTTCTTTATGATTCAAAAAAATGCGTA 2 73 1 TTTTATATAA 0.495744 -228 TAAAATTTTCTATTTTATCCTAAAAATTACTAAAAA 2 211 0 TATTATCTAA 0.946627 -90 TGGTTATTGCTATTTTATACTTCAAATATAATTTAA 5 36 1 TATTATCTAA 0.946627 -45 ACTTCAAATATAATTTAAAATTTAAAAAAATTTCTA 5 54 1 TATTAAATAA 0.60367 -27 GATGATTAACTAATTTATCCTCAAATGCGGGAAAAT 8 52 1 TATTATCTAT 0.618852 -79 TTTGTAATTGTATTTAATTATGATAAAAAATAGATA 9 267 0 TATTATATAA 0.849953 -34 TAAGGTTTTCTATTTGATTCTGTTAAAATTCACTTA 14 147 0 TATTATCTAA 0.946627 -73 TAATAGTTATTATTTTTTAATAACAAAATCTAAAGA 19 174 1 TATTTTATAA 0.603605 -127 TATCCTATTATTTAAAAATTTGAAAATTATAATA 26 9 1 TATTAAATAA 0.60367 -140 GCTAAGGAGTTAGTTAATACTCAAAATGAATAAATT 27 79 1 TATTATCTAA 0.946627 -160 ACAAAAGTTCTATTAGATACTAAAAACTATTTTTTG 30 109 1 TATAATCTAA 0.618851 -70 TCCATAAACGTTATTTATACTGGGAAATAAATTTTT 32 250 0 TTTTATCTAA 0.754793 -51 ACATATTTAATAATTATTACTGCAAATATTATCATC 35 50 1 TATTTTCTAA 0.826661 -45 ** ** ** ** ** Masking position 15 Map Score: 8.88009 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 87 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 GGTCCCTTTCGGGTTCCCCTCGAGGCTTATA 1 137 0 GGGTTCCCTC 0.980418 -164 CTATTGAATAGGGCTCACCTCTGTGAGGAAT 2 113 1 GGGCTCCCTC 0.965881 -188 CCCTCTATTGGGATACTCCCCCAAATCTTGC 9 150 0 GGATACCCCC 0.847814 -151 CAATAGAGGGGGCTACGCCCCCTCTATGGTT 9 171 1 GGCTACCCCC 0.956776 -130 GATTTGGGCTTTGCCCATTTAACCTTT 13 7 1 GGCTTTCCCA 0.725235 -125 CGGGCTCACCTCTGTGAGGAAT 13 120 0 GGGCTCCCTC 0.965881 -12 GCAACCATAGGGCTTCGCCTATTGGAATACT 29 120 0 GGCTTCCCTA 0.937114 -113 GCTTTATATGGGGTTCTCCCAACATGGTCAA 34 21 0 GGGTTCCCCA 0.968775 -43 ****** **** Masking position 8 Map Score: 3.93093 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 5 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 AATATTTATTTGATGATTAACTAATTTATC 8 41 1 TGATGATTAA 0.871335 -90 ATAAATATTATAATGATTTAGATTAGAAGA 21 18 0 TAATGATTTA 0.744654 -221 TTATGTTAGTTGATGATTTTCATTTATAAA 21 204 0 TGATGATTTT 0.871335 -35 CCTCACCTTTTAATGATTTTTAATATTCTT 22 26 0 TAATGATTTT 0.81023 -22 TAGGGATTACTAATGATTATAGCAGGAACT 27 116 1 TAATGATTAT 0.862083 -123 TTAGAGTTTCTGATGATTATTATATAAATA 28 57 0 TGATGATTAT 0.90838 -20 ATTTCTTTTATTATGATTATCCTCCAAATT 32 78 1 TTATGATTAT 0.770124 -223 AATAAATTTTTAATGATTAATGCTAAATAG 32 231 0 TAATGATTAA 0.810229 -70 TTTTTATAGTTTATGATTTAGGTTGATTTA 33 43 0 TTATGATTTA 0.609833 -157 CCCATAACTGTGATGATAATATTTGCAGTA 35 67 0 TGATGATAAT 0.582477 -28 ********** Masking position 6 Map Score: 3.62466 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 128 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172