AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00650_mjan_reg_300.orf -o00650_mjan_300.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 MJ0266 27 pyruvate ferredoxin oxidoreductase, subunit beta (porB) MJ0538 24 M. jannaschii predicted coding region MJ0538 Input sequences: #1 MJ0030 300 coenzyme F420-reducing hydrogenase, delta subunit (frcD) #2 MJ0033 254 succinate dehydrogenase, flavoprotein subunit (sdhA) #3 MJ0050 109 group II decarboxylase #4 MJ0081 300 methyl coenzyme M reductase II, subunit beta (mrtB) #5 MJ0084 261 CODH nickel-insertion accessory protein (cooC) #6 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #7 MJ0087 23 hemin permease (hemU) #8 MJ0090 80 collagenase (prtC) #9 MJ0091 95 Na+/Ca+ exchanger protein, putative #10 MJ0161 300 acetolactate synthase small subunit (ilvN) #11 MJ0267 21 pyruvate ferredoxin oxidoreductase, subunit alpha (porA) #12 MJ0269 283 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #13 MJ0270 300 M. jannaschii predicted coding region MJ0270 #14 MJ0276 119 2-ketoglutarate ferredoxin oxidoreductase, subunit alpha (korA) #15 MJ0277 183 acetolactate synthase large subunit (ilvB) #16 MJ0278 82 peptidyl-prolyl cis-trans isomerase, FKBP-type rotamase (slyD) #17 MJ0537 276 2-ketoglutarate ferredoxin oxidoreductase, subunit beta (korB) #18 MJ0539 267 tRNA synthetase, putative #19 MJ0541 89 conserved hypothetical protein #20 MJ0542 127 phosphoenolpyruvate synthase #21 MJ0543 132 ubiquinol-cytochrome C reductase complex, subunitVI requiring protein #22 MJ0544 103 dolichyl-phosphate mannose synthase #23 MJ0547 165 cell division inhibitor minD #24 MJ0548 111 conserved hypothetical protein #25 MJ0663 27 acetolactate synthase large subunit (ilvB) #26 MJ1530 178 ribosomal protein S18 alanine acetyltransferase Motif number 1 TTTCTTGTTCTTTTTTTATTTATACTATGCCAAT 2 139 1 TTTTTATTTA 0.946615 -116 TCATCAAAGCTATTTTGATTTATAAGTTTTAAAT 2 196 1 TATTTATTTA 0.839629 -59 CCTTTAATTTTTTTAGTTGATAAACATCATG 3 89 0 TTTTTATTAT 0.936217 -21 GGCTATACTCTATTTGCTATTGATGATACTTTTA 4 45 1 TATTTTTTAT 0.428141 -256 ATTCAAAATTTTTTTAAAGATTTTAAAGATTTTT 4 142 1 TTTTTAATTT 0.904755 -159 ATTTTAAAGATTTTTTTAATTTTATCATTTTAAT 4 161 1 TTTTTATTTA 0.946621 -140 TAATTTTATCATTTTAATATTATTATTTTAACAT 4 177 1 ATTTTTTTTT 0.673694 -124 TTTTAACATTTTTTAGTAATTTTTAGGATAAAAT 4 202 1 TTTTAATTTT 0.914475 -99 GGTATATAAAATTTTCTATTTTATCCTAAAAATT 4 219 0 ATTTTATTAT 0.828852 -82 AACACCAACCTTTTTGTTAATATATTACTACAGC 4 273 0 TTTTTTATTA 0.445544 -28 TTTATTATCTTATTTTAAGTTTTATTTTTTGGAC 5 13 1 TATTTATTTA 0.839629 -249 TAAGTTTTATTTTTTGGACTTTATTTTTAATTTT 5 28 1 TTTTTATTAT 0.936217 -234 TTTATTTTTAATTTTAAAATTTTAATTGGAGGGC 5 47 1 ATTTTATTTA 0.85404 -215 CTTTTTTCTATTTTTTATATAATTTT 6 3 1 TTTTTATTTT 0.973132 -132 ATATATTAGATATTAAAAATTTTTGTTCATATCA 6 89 1 TATTAATTTT 0.759424 -46 ACTATCACATTTTTTGAATTATT 7 1 0 TTTTTATTTT 0.973132 -23 GGTTATTGCTATTTTATACTTCAAATATAATTTA 8 37 1 ATTTTATTAA 0.703378 -44 TTAGAAATTTTTTTAAATTTTAAATTATATTT 8 59 0 TTTTTATTTA 0.946622 -22 ACTTAAGCAAAATTTTCAGTTCATCCATATTGTA 9 12 0 AATTTATTAT 0.588433 -84 TTAAAGTTTGTTTTTGAATATATTCTGCAATAAT 9 52 0 TTTTTAATTT 0.904753 -44 AAATTATTGGTTTTTGCAAATATTCTAAAGATAA 10 128 0 TTTTTAATTT 0.904755 -173 ACAAGGCTTAATTTTTCTTTTGTTAATTAATTGG 10 167 0 ATTTTTTTTT 0.673694 -134 TAAATATCTATTTTATTATTTTTAAATCTTACTA 10 268 1 TTTTAATTTA 0.839629 -33 TGTAAATTAATTTTATTTTTTCTTATGCCTAAAC 12 171 1 TTTTATTTTT 0.6488 -113 TATATATTACTTTTAATAATTGTTAATGATTGAT 12 238 1 TTTTAATTTT 0.914475 -46 ATGTTTAACATTTTTGTATATAAAATTTTTCATA 13 131 1 TTTTTAATAA 0.653329 -170 TAATTCTAAGTATTTAAATATTTTTATGAAAAAT 13 155 0 TATTTAATTT 0.737145 -146 AGTCCTATTTTATTTCCAATTATTTATAATTCTA 13 181 0 TATTTATTTT 0.914475 -120 TGAGGAAATATTTTATTATATAATAACACTCTTT 13 221 1 TTTTAAATAT 0.5319 -80 TTATATATTGAATTTGGAATTTAAATACTCAAAG 13 251 0 AATTTATTAA 0.411786 -50 ATGCTTCTATTTTTTTAAATTGTTATTTTCTTCT 14 23 1 TTTTTATTTT 0.973132 -97 CTTTAATTCTATTTTTTATTTTTAGTCTTTAAGA 15 18 1 ATTTTATTTA 0.85404 -166 AAGTGTTGGTATTTAATATTTAATTACTAATCTT 15 48 0 ATTTAATTAT 0.5884 -136 TATATCAAACTTTTTAAAGTTCTTCAAATGCTAA 15 85 1 TTTTTATTTT 0.973132 -99 AGTATAAAAATTTTTATATATGATTTCAATTTTA 15 125 1 TTTTTAATAT 0.793802 -59 TATAAATAGTTTTTTGTTATTATTTTTTATGGAC 16 24 0 TTTTTTTTTT 0.862211 -59 ACCTCAAATAATTTTTAATTTATAATGGATACCC 17 247 0 ATTTTATTTA 0.854038 -30 TCATCAAAAGTTTTTATAGTTATATAATAAACTT 18 76 0 TTTTTATTTA 0.946615 -192 GTAGTTAATATTTTAACAAATTATTATGTAACCT 18 162 1 TTTTAAATAT 0.53195 -106 GAAATTTGGATTTTTTGATTTTTATATTTTAAAT 18 199 1 TTTTTATTTA 0.946622 -69 TACCTTTAACTTTTAAGTTTTGTTTTTATGACTA 19 12 1 TTTTATTTTT 0.6488 -78 TTATGAAACTTTTTTTAATTTTTTATAACATTT 20 10 1 TTTTTATTTT 0.973132 -118 ATCATTCAAATATTTAAATTTATTTTAAAATAAA 20 81 1 TATTTATTTT 0.914475 -47 TGATGCTAATATTTTTAACTTAATATTTAAAGCT 21 24 0 ATTTTATTAT 0.82885 -109 CCAATTCCTATTTTTCTACTTTTTCTTATTACCA 22 22 1 TTTTTATTTT 0.973132 -82 TTTTAACAAAATTTTAAAATTTTATGGTAATAAG 22 46 0 ATTTTATTTA 0.85404 -58 AACTAACAAATATTACTATTTAATAACTAATATA 24 32 1 TATTAATTAT 0.561231 -80 TTATAGAGTCTTTTAAAACATTTTGAAATACTAA 26 52 0 TTTTAAATTT 0.737145 -127 ATTTTAGTATTATTTTAAATTCTTTTTATAGAGT 26 77 0 TATTTATTTT 0.914475 -102 ***** * ** ** Masking position 4 Map Score: 59.3474 Number of sites scoring better than the average of aligned sites = 3412 Number in coding regions = 2585 Number in noncoding regions = 827 Number of orfs with sites within 600 bp upstream = 518 Fraction of orfs with sites within 600 bp upstream = 0.0831995 Motif number 2 ACCAGTGCCTTATTAAAAATATTACTATTTT 2 111 1 TATAAAAATA 0.939123 -144 TTTTTATCACCAAAAATAGGATACCCTC 2 237 0 CACAAAAATA 0.788325 -18 AAAATAATAATATTAAAATGATAAAATTAAA 4 175 0 TATAAAATGA 0.650588 -126 TAGTAATAGGTATATAAAATTTTCTATTTTA 4 230 0 TATTAAAATT 0.815297 -71 CAAAAAATAAAACTTAAAATAAGATAATAAA 5 13 0 AACTAAAATA 0.509135 -249 AAAATTTTAAAATTAAAAATAAAGTCCAAAA 5 39 0 AATAAAAATA 0.886882 -223 TATGCCCTCCAATTAAAATTTTAAAATTAAA 5 53 0 AATAAAATTT 0.740687 -209 ATAAAAATTATATAAAAAATAGAAAAAAG 6 9 0 TATAAAAATA 0.939391 -126 CATCAATATTCATAAAAATTATATAAAAAAT 6 20 0 CATAAAATTA 0.795879 -115 CAAAAATAATCGTTAAAAATACATCAATATT 6 41 0 CGTAAAAATA 0.557768 -94 TTCGGTAGTTTATCAAAAATAATCGTTAAAA 6 54 0 TATAAAAATA 0.939391 -81 ATATATTAGATATTAAAAATTTTTGTTCATA 6 89 1 TATAAAAATT 0.930495 -46 GACCTCATTATATAAAAAAGA 8 1 0 TATAAAAAGA 0.815949 -80 CTTCAAATATAATTTAAAATTTAAAAAAATT 8 55 1 AATTAAAATT 0.680149 -26 TAGGAAACCAAAAATTAAGTTAAGAT 10 6 1 AACAAAAATT 0.731779 -295 TACGAAAAACTATGAAAATTTTCTTTTAATC 10 34 0 TATAAAATTT 0.849271 -267 TAAATTTAGTTATGAAAAATTGAACACCCTC 10 72 1 TATAAAAATT 0.930629 -229 AATTAATTGGCATCTAAATTATTGGTTTTTG 10 146 0 CATTAAATTA 0.562155 -155 TGTCATATCCTATCAAAAATATGCAAATCAA 10 198 1 TATAAAAATA 0.939391 -103 AAAATATGCAAATCAAAAATTTCAGGTATCA 10 213 1 AATAAAAATT 0.87181 -88 CTATGTAATCCATGTAAATTAATTTTATTTT 12 159 1 CATTAAATTA 0.562155 -125 AAATTTTATATACAAAAATGTTAAACATACT 13 128 0 TACAAAATGT 0.392651 -173 TAAATATTTTTATGAAAAATTTTATATACAA 13 144 0 TATAAAAATT 0.930629 -157 AAGGTTATATTATATAAAAGTAGCTTAGAAG 14 88 1 TATTAAAAGT 0.558211 -32 AAAGACTAAAAATAAAAAATAGAATTAAAGA 15 17 0 AATAAAAATA 0.887101 -167 AAAAGTTTGATATAAAAAAGTGTTGGTATTT 15 68 0 TATAAAAAGT 0.793267 -116 AAATCCTTAGTATAAAAATTTTTATATATGA 15 117 1 TATAAAATTT 0.849271 -67 CGCTTTTGTCCATAAAAAATAATAACAAAAA 16 17 1 CATAAAAATA 0.902758 -66 ATCCATTATAAATTAAAAATTATTTGAGGTG 17 251 1 AATAAAAATT 0.871701 -26 TCAATCATCAAAAATAGATAACATTT 18 6 1 CATAAAAATA 0.902758 -262 AAATATTAACTACCAAAATGATATAAATAAC 18 144 0 TACAAAATGA 0.42757 -124 TTGTCTATATTATTTAAAATATAAAAATCAA 18 213 0 TATTAAAATA 0.806629 -55 AAATAGAAGAAACAAAAATTTTGAGGGAAAT 18 246 1 AACAAAATTT 0.533986 -22 TGTATCACCAAAAATAGTGAAGATTT 19 74 0 CACAAAAATA 0.788325 -16 GTGAAAATGTTATAAAAAATTAAAAAAAGTT 20 17 0 TATAAAAATT 0.930629 -111 ATCATTCAAATATTTAAATTTATTTTAAAAT 20 81 1 TATTAAATTT 0.649663 -47 TTAAATATTAAGTTAAAAATATTAGCATCAC 21 28 1 AGTAAAAATA 0.516327 -105 CAATTCCCAATATATAAAATTTATTGTGATG 21 53 0 TATTAAAATT 0.815297 -80 TTTAAAATTTTGTTAAAAATTTACTAGCATC 22 62 1 TGTAAAAATT 0.645717 -42 CTATAAAAAGAATTTAAAATAATACTAAAAT 26 80 1 AATTAAAATA 0.69909 -99 TTTAAAATAATACTAAAATTAAAATAGAATT 26 92 1 TACAAAATTA 0.723104 -87 *** ******* Masking position 6 Map Score: 42.4517 Number of sites scoring better than the average of aligned sites = 1636 Number in coding regions = 1100 Number in noncoding regions = 536 Number of orfs with sites within 600 bp upstream = 425 Fraction of orfs with sites within 600 bp upstream = 0.0682621 Motif number 3 CAGATATTTAAAACTTATAAATCAAAATAGCTTT 2 201 0 AATATAATCA 0.779354 -54 ATGCGTTCTTAGGTATAAATATAATACAATATAC 3 35 0 AGTAAAATAA 0.812132 -75 AATTACTAAAAAATGTTAAAATAATAATATTAAA 4 189 0 AATTAAATAA 0.818866 -112 TCCAAAAAATAAAACTTAAAATAAGATAATAAAG 5 12 0 AATTAAATAA 0.818868 -250 TTAAAATTTTAAAATTAAAAATAAAGTCCAAAAA 5 38 0 AATAAAATAA 0.915494 -224 CATTTTATCAAAAGTTTTAGATAAAATAATATTA 5 98 1 AATTTAATAA 0.845407 -164 CTTGTTAGAAAAAGATTTATACTAAATAAGATAT 5 199 1 AATTTAACTA 0.623109 -63 TATTCATAAAAATTATATAAAAAATAGAAAAAAG 6 11 0 AATATAAAAA 0.58687 -124 TAAACTACCGAAAAATATATATTAGATATTAAAA 6 73 1 AATATAATTA 0.86335 -62 AATTTTGCTTAAGTTTAAATATTATTGCAGAATA 9 32 1 AATAAAATTA 0.839175 -64 TTTTATAGTAAGATTTAAAAATAATAAAATAGAT 10 273 0 AGTAAAATAA 0.812132 -28 TGTCATTCTCAAAAATAAATACAACATCATTTTT 12 116 1 AATAAAACAA 0.871684 -168 AAATCTCCAAAACTTTATATATTACTTTTAATAA 12 223 1 AATATAATTA 0.863347 -61 TCATGTTAATAATACTTTACATTATGTTAAGTAT 13 99 1 AATTTAATTA 0.725018 -202 TTTTATGAAAAATTTTATATACAAAAATGTTAAA 13 134 0 AATATAACAA 0.891509 -167 TTAAATACTTAGAATTATAAATAATTGGAAATAA 13 172 1 AGTATAATAA 0.839465 -129 TATAGTCGTTAAATATTAACACAAGGTTATATTA 14 66 1 AATTAAACAA 0.739231 -54 ACTAATCTTAAAGACTAAAAATAAAAAATAGAAT 15 23 0 AATAAAATAA 0.915494 -161 TTAGTAATTAAATATTAAATACCAACACTTTTTT 15 52 1 AATAAAACCA 0.646771 -132 TCATATATAAAAATTTTTATACTAAGGATTTAGC 15 114 0 AATTTAACTA 0.622793 -70 TAACTACCAAAATGATATAAATAACTTAGTTTTA 18 135 0 AATATAATAA 0.929102 -133 ATATTATTTAAAATATAAAAATCAAAAAATCCAA 18 204 0 AATAAAATCA 0.744823 -64 TTATATTTTAAATAATATAGACAATAAAATAGAA 18 220 1 AATATAACAA 0.89151 -48 ATGATAAAATAGTCATAAAAACAAAACTTAAAAG 19 21 0 AGTAAAACAA 0.730511 -69 TACAAGTGAAAATGTTATAAAAAATTAAAAAAAG 20 19 0 AATATAAAAA 0.58687 -109 TTTGAATGATAATATTATAAATAAAATAGTAGAG 20 57 0 AATATAATAA 0.929102 -71 TTTTAAAATAAAAGCTATATATAATCCCCTATAT 20 103 1 AATATAATAA 0.929102 -25 AATAACAGTAAGCTTTAAATATTAAGTTAAAAAT 21 14 1 AGTAAAATTA 0.675768 -119 TCTAAAATCTTTATATTACCTATTTACA 23 148 0 AATTTAATTA 0.724647 -18 TATTATCGTTAATCTTATATATTAGTTATTAAAT 24 49 0 AATATAATTA 0.863354 -63 CTCTATAAAAAGAATTTAAAATAATACTAAAATT 26 78 1 AGTTAAATAA 0.643361 -101 ** **** **** Masking position 6 Map Score: 35.5025 Number of sites scoring better than the average of aligned sites = 732 Number in coding regions = 462 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 269 Fraction of orfs with sites within 600 bp upstream = 0.0432059 Motif number 4 AAAAAAGAACAAGAAAATAGTAATATTTTT 2 125 0 AAGAAAATAG 0.835537 -130 ATATTAAAATGATAAAATTAAAAAAATCTT 4 167 0 GATAAAATTA 0.415765 -134 ACTAAAAAATGTTAAAATAATAATATTAAA 4 189 0 GTTAAAATAA 0.415765 -112 TAATTTTTAGGATAAAATAGAAAATTTTAT 4 218 1 GATAAAATAG 0.948383 -83 AAAAGTTTTAGATAAAATAATATTAATGGA 5 107 1 GATAAAATAA 0.797431 -155 ATATTTGAAGTATAAAATAGCAATAACCAA 8 35 0 TATAAAATAG 0.704424 -46 ATTTAAAAATAATAAAATAGATATTTAGTA 10 265 0 AATAAAATAG 0.963009 -36 TAACTCCTTCAATATAATAGCCGATTTGAT 12 68 0 AATATAATAG 0.756946 -216 CATAAGAAAAAATAAAATTAATTTACATGG 12 168 0 AATAAAATTA 0.502073 -116 AATAATTGGAAATAAAATAGGACTTTCGCA 13 191 1 AATAAAATAG 0.963009 -110 GTTATTATATAATAAAATATTTCCTCATGC 13 218 0 AATAAAATAT 0.579136 -83 ATAACAATTTAAAAAAATAGAAGCATGGGC 14 19 0 AAAAAAATAG 0.650665 -101 TATAATAGAGAAGAAAATAACAATTTAAAA 14 35 0 AAGAAAATAA 0.521186 -85 TAACGACTATAATATAATAGAGAAGAAAAT 14 47 0 AATATAATAG 0.756946 -73 GTAAAGTAATGATAAAATTGAAATCATATA 15 141 0 GATAAAATTG 0.768598 -43 AGTTCGTTTGATTAAAATAGGGCTTAACTC 17 205 1 ATTAAAATAG 0.824753 -72 TTATATTTTAAATAATATAGACAATAAAAT 18 220 1 AATAATATAG 0.62675 -48 TAATATAGACAATAAAATAGAAGAAACAAA 18 232 1 AATAAAATAG 0.963009 -36 AATATATAATGATAAAATAGTCATAAAAAC 19 33 0 GATAAAATAG 0.948383 -57 TAATATTATAAATAAAATAGTAGAGTTATT 20 52 0 AATAAAATAG 0.963009 -76 TAATACTAAAATTAAAATAGAATTTAATAA 26 99 1 ATTAAAATAG 0.824753 -80 ********** Masking position 8 Map Score: 24.4774 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 179 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 CACAGCAGTATGCTGAAGTCATAATGAGAGC 1 23 1 TGCTAAGTCA 0.92034 -278 TATTTATTCCTGCGAAAGTCCTGTTATGCCT 1 172 0 TGCGAAGTCC 0.993553 -129 ATATATAAACTGCGAAAGTCCTGTTTCTTTG 1 248 1 TGCGAAGTCC 0.993553 -53 GTATAGCCTCTGCGTAAGTTCCATTGTGGGA 4 22 0 TGCGAAGTTC 0.991716 -279 TTCAAAAAAATGCGTAAGTTCTATTGAATAG 4 93 1 TGCGAAGTTC 0.991716 -208 CTGAAAATTTTGCTTAAGTTTAAATATTATT 9 27 1 TGCTAAGTTT 0.835772 -69 TATTTCCTCATGCGAAAGTCCTATTTTATTT 13 200 0 TGCGAAGTCC 0.993553 -101 AGCTTAGCCATGCGGTAGTTATGAGGAGATG 17 174 1 TGCGTAGTTA 0.811903 -103 CATAGTCCTAAAGTTCAATAAGCAAA 23 6 1 TCCTAAGTTC 0.850762 -160 **** ****** Masking position 7 Map Score: 11.1313 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 8 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 CCTTCACATGAACCTTTTAGTAAAAGGTTCATCAAA 2 47 0 AATTAAAAAG 0.971809 -208 AAAATCTTTAAAATCTTTAAAAAAATTTTGAATTCC 4 139 0 AATTAAAAAT 0.841324 -162 TAGCTGTAGTAATATATTAACAAAAAGGTTGGTGTT 4 271 1 AATTAAAAAA 0.677255 -30 AATAGATTCAAACATTTTATCAAAAGTTTTAGATAA 5 86 1 AATTAAAAAG 0.971809 -176 TATGTTCCTCCACTTGTTAGAAAAAGATTTATACTA 5 187 1 CATTAAAAAG 0.813839 -75 TTTAGATGCCAATTAATTAACAAAAGAAAAATTAAG 10 159 1 AATTAAAAAG 0.971804 -142 TATTATATTGAAGGAGTTAAAAAAGGAACTGCTATA 12 79 1 AATTAAAAGG 0.959536 -205 TATCAATCATTAACAATTATTAAAAGTAATATATAA 12 237 0 TATTAAAAAG 0.746815 -47 AGAAGAAAATAACAATTTAAAAAAATAGAAGCATGG 14 21 0 AATTAAAAAT 0.841324 -99 CCCTTCACAAAAAGTATTTGGAAAGGTTAGGAG 16 60 1 AATTTAAAGG 0.669863 -23 TTACTCGAACAACCTTTTAGAAAAGGTTGATCAAAA 17 107 0 AATTAAAAGG 0.959536 -170 CATTGCTCCCAACCTTTTAGTAAAAGGTTACTCGAA 17 134 0 AATTAAAAAG 0.971809 -143 AAAATGTTATAAAAAATTAAAAAAAGTTTCATAA 20 9 0 AATTAAAAAG 0.971809 -119 GGATGCTAGTAAATTTTTAACAAAATTTTAAAATTT 22 58 0 AATTAAAAAT 0.841288 -46 TGAATTTTGAACGCTTTCATAAAGGGGGTGTTTAT 26 10 1 AATTCAAAGG 0.750455 -169 AATGTTTTAAAAGACTCTATAAAAAGAATTTAAAAT 26 64 1 AACTAAAAAG 0.804065 -115 AAATTATTCAAAGGCTTTACTAAAGGTTAAGTGAGA 26 151 1 AATTAAAAGG 0.959536 -28 ** *** ***** Masking position 8 Map Score: 23.4824 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 134 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 7 ATCCGTTTTGATGAACCTTTTACTAAAAGG 2 41 1 ATGAACCTTT 0.948878 -214 TTTCCTTCACATGAACCTTTTAGTAAAAGG 2 56 0 ATGAACCTTT 0.948878 -199 TACCAACACCAACCTTTTTGTTAATAT 4 284 0 ACCAACCTTT 0.967435 -17 TATATTCAAAAACAAACTTTAATTAATTTA 9 64 1 AACAAACTTT 0.744287 -32 ACTTTTTTATATCAAACTTTTTAAAGTTCT 15 78 1 ATCAAACTTT 0.888277 -106 CTCCTAACCTTTCCAAATACTT 16 71 0 CCTAACCTTT 0.844796 -12 CTAAGTTTTGATCAACCTTTTCTAAAAGGT 17 102 1 ATCAACCTTT 0.972985 -175 AGGTTACTCGAACAACCTTTTAGAAAAGGT 17 116 0 AACAACCTTT 0.929504 -161 AGGTTGTTCGAGTAACCTTTTACTAAAAGG 17 128 1 AGTAACCTTT 0.784115 -149 AAACATTGCTCCCAACCTTTTAGTAAAAGG 17 143 0 CCCAACCTTT 0.943208 -134 TTATGAAACTTTTTTTAATTTT 20 3 1 ATGAAACTTT 0.803821 -125 GTTCTCACTTAACCTTTAGTAAAGCCT 26 162 0 CTTAACCTTT 0.868404 -17 ********** Masking position 5 Map Score: 10.5446 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 157 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GCATAGTATAAATAAAAAAAGAACAAGAAA 2 139 0 AATAAAAAAA 0.601633 -116 AATAATCCTAAATGAAAAAATTGGCATAGT 2 162 0 AATGAAAAAA 0.922699 -93 AAATAGCTTTGATGAAAAAAATAATCCTAA 2 181 0 GATGAAAAAA 0.57244 -74 AAAACTTATAAATCAAAATAGCTTTGATGA 2 196 0 AATCAAAATA 0.544928 -59 ATAATATTAAAATGATAAAATTAAAAAAAT 4 170 0 AATGATAAAA 0.936746 -131 ATTACTAAAAAATGTTAAAATAATAATATT 4 192 0 AATGTTAAAA 0.528468 -109 AGCTATAGAAAATGATAGTAATAGGTATAT 4 246 0 AATGATAGTA 0.474695 -55 AAGATTTAAAAATAATAAAATAGATATTTA 10 268 0 AATAATAAAA 0.65202 -33 TTAAGCAATTAACGAAAATAGTTTAGGCAT 12 195 0 AACGAAAATA 0.675328 -89 AGGGTAAAGTAATGATAAAATTGAAATCAT 15 144 0 AATGATAAAA 0.936746 -40 TTTATTATATAACTATAAAAACTTTTGATG 18 79 1 AACTATAAAA 0.477189 -189 TAACTACCAAAATGATATAAATAACTTAGT 18 139 0 AATGATATAA 0.543266 -129 AAAATATAAAAATCAAAAAATCCAAATTTC 18 199 0 AATCAAAAAA 0.700248 -69 TAAAATATATAATGATAAAATAGTCATAAA 19 36 0 AATGATAAAA 0.936746 -54 TGTTATAAAAAATTAAAAAAAGTTTCATAA 20 11 0 AATTAAAAAA 0.683948 -117 TAAATATTTGAATGATAATATTATAAATAA 20 67 0 AATGATAATA 0.883594 -61 ATATAAGATTAACGATAATAATAATACTAA 24 63 1 AACGATAATA 0.72072 -49 ATAATACTAAAATTAAAATAGAATTTAATA 26 98 1 AATTAAAATA 0.525885 -81 ********** Masking position 7 Map Score: 7.61634 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 244 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 9 TAACTTCTATAATCTCTTTTGTCTCTTCATC 1 97 0 AATCTTTTTG 0.872024 -204 CGAGGCAGTGCATCCGTTTTGATGAACCTTT 2 30 1 CATCCTTTTG 0.960741 -225 TTTTTCATCAAAGCTATTTTGATTTATAAGT 2 192 1 AAGCTTTTTG 0.897673 -63 TACCAACACCAACCTTTTTGTTAATATATT 4 281 0 CAACCTTTTG 0.857881 -20 ACTATCACATTTTTTGAATTATT 7 8 0 CACATTTTTG 0.66387 -16 ATTTTCAGTTCATCCATATTGTAT 9 4 0 CATCCTATTG 0.845752 -92 GATTTTTAAACAGCTTTATTGTTGAATTACT 12 40 0 CAGCTTATTG 0.859033 -244 AACCTTTCCAAATACTTTTTGTGAAGGGTAT 16 57 0 AATACTTTTG 0.523059 -26 CGAGGTAATGCATCTGTTTTGATCAACGCAC 17 39 1 CATCTTTTTG 0.954803 -238 ATTGGTATAGAAGCCCTTTTGAGCTTCTATA 18 46 1 AAGCCTTTTG 0.910411 -222 GACTATAATTCAGCTTTTTTGTCTAAAACTA 18 112 1 CAGCTTTTTG 0.964536 -156 ATCATCACCTATTTTGGCTGTTTCGT 21 117 0 CACCTTTTTG 0.934278 -16 ***** ***** Masking position 2 Map Score: 9.6791 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 74 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 TAATGAGAGCTTATGATATATGAGCTTCATG 1 44 1 TTATATATAT 0.683274 -257 CAATATGACCTCATTATATAAAAAAGA 8 7 0 TCATATATAA 0.902706 -74 TTAGTAGAACTCACCATATAATAATTATGAT 10 240 0 TCACATATAA 0.936742 -61 TTTTTAAATCTTACTATAAAAAGGA 10 286 1 TTACATAAAA 0.832273 -15 AGGAAATATTTTATTATATAATAACACTCTT 13 223 1 TTATATATAA 0.86734 -78 AATTCCAAATTCAATATATAAACTGTGGAAA 13 264 1 TCAAATATAA 0.852693 -37 TTCTATAAGTTTATTATATAACTATAAAAAC 18 70 1 TTATATATAA 0.86734 -198 TCTATATTATTTAAAATATAAAAATCAAAAA 18 210 0 TTAAATATAA 0.804394 -58 GACTATTTTATCATTATATATTTTAACAATT 19 41 1 TCATATATAT 0.748826 -49 TAAATTTATTTTAAAATAAAAGCTATATATA 20 95 1 TTAAATAAAA 0.659766 -33 AATATTAGCATCACAATAAATTTTATATATT 21 45 1 TCACATAAAT 0.687597 -88 CTTTTTCTTATTACCATAAAATTTTAAAATT 22 40 1 TTACATAAAA 0.832273 -64 AGGTAATCACAATATAAATTGGATGCT 22 87 0 TCACATATAA 0.936665 -17 **** ****** Masking position 6 Map Score: 6.80699 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 109 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 11 AAGAAAATAGTAATATTTTTAATAAGGCACTGGT 2 111 0 TATTTTTAAA 0.598327 -144 GATACCCTCATCAGATATTTAAAACTTATAAATC 2 212 0 TAGTATTAAA 0.896428 -43 CTCACCTCTGTGAGGAATTCAAAATTTTTTTAAA 4 126 1 TAGAATTAAA 0.934345 -175 AAATTTTTTTAAAGATTTTAAAGATTTTTTTAAT 4 147 1 AAGTTTTAAA 0.49202 -154 TTTTTTAATTTTATCATTTTAATATTATTATTTT 4 172 1 TATATTTAAA 0.710083 -129 CATTTTAATATTATTATTTTAACATTTTTTAGTA 4 186 1 TATATTTAAA 0.710083 -115 AAACTTAAAATAAGATAATAAAGA 5 1 0 TAGTAATAAA 0.327238 -261 AAAATATATATTAGATATTAAAAATTTTTGTTCA 6 84 1 TAGTATTAAA 0.896428 -51 AATTTAGTTATGAAAAATTGAACACCCTCTATCG 10 74 1 TAAAATTAAA 0.554496 -227 AAGATTTATGACAGTAATTCAACAATAAAGCTGT 12 28 1 AAGAATTAAA 0.688548 -256 TTTGGAGATTTAAGCAATTAACGAAAATAGTTTA 12 200 0 TAGAATTACA 0.542368 -84 AATTAAAAGCAGAGATATTTAAAAAAT 13 4 0 AAGTATTAAA 0.573445 -297 AAATTACTTCTCGGATTTTTAACAGAGTTTTTAA 13 47 0 TGGTTTTAAA 0.60365 -254 TTTATAATTCTAAGTATTTAAATATTTTTATGAA 13 159 0 TAGATTTAAA 0.911147 -142 TATATTGAATTTGGAATTTAAATACTCAAAGAGT 13 248 0 TGGATTTAAA 0.714656 -53 GTCTTTAAGATTAGTAATTAAATATTAAATACCA 15 42 1 TAGAATTAAA 0.934345 -142 TACTAAGGATTTAGCATTTGAAGAACTTTAAAAA 15 95 0 TAGATTTAAA 0.911147 -89 GGGGTATCCATTATAAATTAAAAATTATTTGAGG 17 246 1 TATAATTAAA 0.772217 -31 TTTTTGATTTTTATATTTTAAATAATATAGACAA 18 210 1 TATTTTTAAA 0.598327 -58 GAAAATGTTATAAAAAATTAAAAAAAGTTTCATA 20 12 0 TAAAATTAAA 0.554496 -116 ATTTTATATATTGGGAATTGAAAACACACATAGT 21 64 1 TGGAATTAAA 0.776559 -69 ATTACATCATTAATTAATTGAATAAGGTTATCTA 23 43 0 TATAATTAAA 0.772217 -123 ATCTTATATATTAGTTATTAAATAGTAATATTTG 24 38 0 TAGTATTAAA 0.896428 -74 TTATTGGTCCTTAGTATTTCAAAATGTTTTAAAA 26 42 1 TAGATTTAAA 0.911147 -137 * ** **** ** * Masking position 9 Map Score: 25.9788 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 342 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 12 GGATGCACTGCCTCGCTACGCTCGGCAGTGCCT 2 12 0 CTGCTAGCTC 0.994052 -243 AATCCTAATTCTTTCCTATGCTCTATTTCCTTC 2 78 0 CTCCTAGCTC 0.979365 -177 AGATGCATTACCTCGCTACGCTCGGTAATGCCT 17 21 0 CTGCTAGCTC 0.994052 -256 ATCAACGCACCATAGCTTCGCCCTATTGGGATA 17 60 1 CTGCTTGCCC 0.958127 -217 ATAACTACCGCATGGCTAAGCTCAAACATTGCT 17 163 0 CTGCTAGCTC 0.994052 -114 * * **** **** Masking position 7 Map Score: 2.79212 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 1 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 TTTTGTCTCTTCATCTTTAACTATAACGTGTGTT 1 78 0 TTCTTAACTT 0.964072 -223 ATTACTATCATTTTCTATAGCTGTAGTAATATAT 4 254 1 TTCTTAGCTT 0.862437 -47 TAATATTATTTTATCTAAAACTTTTGATAAAATG 5 98 0 TTCTAAACTT 0.932963 -164 GAACATACACTGGTCTGAAACTATGCCAACAGCT 5 160 0 TTCTAAACTT 0.932963 -102 ACATTTATTATGTCCTTTATCTTTAGAATATTTG 10 112 1 TCCTTATCTT 0.883855 -189 ACACTCACCTTAAACTGTCATTATCAAT 12 266 0 TCCTAAACTT 0.908332 -18 AAAATAGGGCTTAACTCTATCTCTATTTGGGGTA 17 218 1 TACTTATCTT 0.771558 -59 TCTATAAGTTTATTATATAACTATAAAAACTTTT 18 71 1 TTATTAACTT 0.658158 -197 TTCAGCTTTTTTGTCTAAAACTAAGTTATTTATA 18 120 1 TTCTAAACTA 0.617147 -148 TTACCTTTAACTTTTAAGTTTTGT 19 1 1 TCCTTAACTT 0.950262 -89 CACATAGTCCTTCTCTTTATCTATAAAACGAAAC 21 90 1 TTCTTATCTT 0.914443 -43 TATATTTAACTTAACTATAACTTTAGTGTTGTAA 23 119 1 TACTTAACTT 0.894508 -47 * *** ***** * Masking position 9 Map Score: 6.41196 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 240 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 GGTATCCTATTTTTGGTGATAAAAA 2 240 1 TTTGGTGATA 0.88747 -15 CTCTATTTGCTATTGATGATACTTTTAGGCT 4 52 1 TTTGATGATA 0.896596 -249 TTTTAGGCTTTCTTTATGATTCAAAAAAATG 4 74 1 TTTTATGATT 0.742391 -227 TTTTTAAAGATTTTAAAGATTTTTTTAATTT 4 152 1 TTTAAAGATT 0.621739 -149 AATGAGGTCATATTGGTTATTGCTATTTTAT 8 23 1 TTTGGTTATT 0.534533 -58 ATATATAAAGTTTTGGAGATTTAAGCAATTA 12 214 0 TTTGGAGATT 0.914966 -70 TTTTAATAATTGTTAATGATTGATAATGACA 12 248 1 TTTAATGATT 0.742391 -36 TTATTTTTAGTCTTTAAGATTAGTAATTAAA 15 33 1 TTTTAAGATT 0.621739 -151 CCTTAACATTTTTTGGTGATTGG 15 171 1 TTTGGTGATT 0.949661 -13 TGTTATCTATTTTTGATGATTGA 18 3 0 TTTGATGATT 0.954005 -265 CTATAAAAACTTTTGATGATTGACTATAATT 18 91 1 TTTGATGATT 0.954005 -177 TCACCAAAAATAGTGAAGATTTGGAATTGTT 19 65 0 TGTGAAGATT 0.633121 -25 TCTTCACTATTTTTGGTGATACA 19 77 1 TTTGGTGATA 0.88747 -13 GATGTAATGTTTTTGAAGATAAGCGTGTCCT 23 69 1 TTTGAAGATA 0.831804 -97 * ********* Masking position 9 Map Score: 12.2435 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 257 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 15 GAGGCACTGCCGAGCGTAGCGAGGC 2 4 1 GCATCCGAGC 0.987591 -251 CAAAACGGATGCACTGCCTCGCTACGCTCGGC 2 19 0 GCATCCTCGC 0.987591 -236 ATGCTAAGAGGCATTACCGAGCGTAGCGAGGT 17 13 1 GCATCCGAGC 0.99099 -264 CAAAACAGATGCATTACCTCGCTACGCTCGGT 17 28 0 GCATCCTCGC 0.99099 -249 *** * ****** Masking position 5 Map Score: 0.463494 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0