AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_mjan_reg_300.orf -o00020_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 MJ0087 23 hemin permease (hemU) MJ1425 25 malate dehydrogenase Input sequences: #1 MJ0030 300 coenzyme F420-reducing hydrogenase, delta subunit (frcD) #2 MJ0033 254 succinate dehydrogenase, flavoprotein subunit (sdhA) #3 MJ0081 300 methyl coenzyme M reductase II, subunit beta (mrtB) #4 MJ0084 261 CODH nickel-insertion accessory protein (cooC) #5 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #6 MJ0090 80 collagenase (prtC) #7 MJ0091 95 Na+/Ca+ exchanger protein, putative #8 MJ0210 86 succinyl-CoA synthetase, beta subunit #9 MJ0617 108 tartrate dehydratse, subunit beta (ttdB) #10 MJ0634 300 conserved hypothetical protein #11 MJ0635 219 M. jannaschii predicted coding region MJ0635 #12 MJ0636 239 dihydrolipoamide dehydrogenase #13 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #14 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) #15 MJ1296 38 biotin synthetase (bioB) #16 MJ1424 202 tRNA intron endonuclease (endA) #17 MJ1596 226 3-isopropylmalate dehydrogenase 2 (leuB2) Motif number 1 ACCAGTGCCTTATTAAAAATATTACTATTT 2 111 1 TATTAAAAAT 0.792159 -144 GGCATAGTATAAATAAAAAAAGAACAAGAA 2 140 0 AAATAAAAAA 0.932087 -115 TAAAACTTATAAATCAAAATAGCTTTGATG 2 197 0 AAATCAAAAT 0.868704 -58 CTCTGTGAGGAATTCAAAATTTTTTTAAAG 3 131 1 AATTCAAAAT 0.832797 -170 AAAATGATAAAATTAAAAAAATCTTTAAAA 3 162 0 AATTAAAAAA 0.911344 -139 TAAAATAATAATATTAAAATGATAAAATTA 3 177 0 ATATTAAAAT 0.644649 -124 AAAATTTTAAAATTAAAAATAAAGTCCAAA 4 40 0 AATTAAAAAT 0.930428 -222 CATAAAAATTATATAAAAAATAGAAAAAAG 5 11 0 ATATAAAAAA 0.931624 -124 ACATCAATATTCATAAAAATTATATAAAAA 5 22 0 TCATAAAAAT 0.797226 -113 TTTCGGTAGTTTATCAAAAATAATCGTTAA 5 56 0 TTATCAAAAA 0.582075 -79 ATATATTAGATATTAAAAATTTTTGTTCAT 5 89 1 TATTAAAAAT 0.792159 -46 TGACCTCATTATATAAAAAAGA 6 3 0 ATATAAAAAA 0.931624 -78 ATAATTTAAAATTTAAAAAAATTTCTAA 6 63 1 ATTTAAAAAA 0.857328 -18 TTGCAGAATATATTCAAAAACAAACTTTAA 7 56 1 TATTCAAAAA 0.511964 -40 TAAAATTATCATATAAAAAATTTGGTGATA 8 25 0 ATATAAAAAA 0.931624 -62 TTATATGATAATTTTAAAATTTTGCATTAA 8 39 1 ATTTTAAAAT 0.413634 -48 AAAATCTCTTACATAAAAATTTAGACCTTT 9 22 0 ACATAAAAAT 0.93362 -87 TTTTAAAACTAATTATAAATAAATTATGGT 9 48 1 AATTATAAAT 0.692784 -61 ATCTAATACAACATAAAAATAAGAAATGGT 10 45 1 ACATAAAAAT 0.93362 -256 CAATCTCAAATAATAAAAAAATTTTTATAT 10 83 1 TAATAAAAAA 0.793223 -218 GTTGATAATCATATAAAAATTTTTTTATTA 10 93 0 ATATAAAAAT 0.946288 -208 AACTTAGAGCTTTTAAAAATTAGCATTTTC 10 136 0 TTTTAAAAAT 0.690131 -165 TCAAATCTTTAAATAAAAATAGGAAAAATT 10 178 0 AAATAAAAAT 0.947967 -123 ACAATAATATAAATAAAAAAGAGTGCGCAA 11 58 0 AAATAAAAAA 0.932087 -162 AATAGATATTATTTAAAAAATTTTAA 12 7 0 ATTTAAAAAA 0.857328 -233 TTTTTTAATCAAATAAAAAATAAGAACAAC 12 157 0 AAATAAAAAA 0.932087 -83 AATTAAAAATTGGTTTAATG 12 230 0 AATTAAAAAT 0.930428 -10 ATGATTTTAAAATTAAAAATAAAACTTTTA 13 23 1 AATTAAAAAT 0.930428 -172 AAACAACACAAAATATAAATACTTATAATG 13 65 0 AAATATAAAT 0.759912 -130 GACTTAAACCATATCAAAAATGATTAAAAT 13 105 0 ATATCAAAAA 0.83285 -90 AAATACTTTCACATAAAAATGTTTTGTTGG 13 136 0 ACATAAAAAT 0.93362 -59 ATAGCAATATTAATAAAAATACTTTCACAT 13 152 0 TAATAAAAAT 0.835876 -43 GATTTAAGTTATTTAAAAAATGGTGGGGGT 14 26 1 ATTTAAAAAA 0.857328 -275 TGCCTTATAAATATATAAATTGTGAAAGTT 14 225 1 ATATATAAAT 0.747244 -76 CTACAACGACACATATAAAAAGTAAAAGGG 14 255 1 ACATATAAAA 0.648024 -46 GTAAAAGGGGATATATAAATTTTACGGTTT 14 276 1 ATATATAAAT 0.747244 -25 CGCAGTTTTTATATTAAAAAGGTATTTAGA 16 80 0 ATATTAAAAA 0.58272 -123 AGTTATTATTTATAAAATCTTAAAATT 16 186 0 ATTTATAAAA 0.484052 -17 CCGTATTAATACTTAAAAATATCTTTAAAC 17 59 1 ACTTAAAAAT 0.91213 -168 AACTATACTGTCTTCAAAATTAATTAAAGT 17 86 1 TCTTCAAAAT 0.518088 -141 GCTACTGGTTACTTCAAAATGTTTTTGAAA 17 175 1 ACTTCAAAAT 0.793616 -52 GAAAGACACTATATAAAAAAGTTTTTGGTG 17 201 1 ATATAAAAAA 0.931624 -26 ********** Masking position 4 Map Score: 52.935 Number of sites scoring better than the average of aligned sites = 1919 Number in coding regions = 1331 Number in noncoding regions = 588 Number of orfs with sites within 600 bp upstream = 411 Fraction of orfs with sites within 600 bp upstream = 0.0660135 Motif number 2 CCCTCGAGGCTTATAACATTTTTCTAACTTCTA 1 119 0 TTTACTTTTT 0.597908 -182 CTTATTAAAAATATTACTATTTTCTTGTTCTTT 2 119 1 ATTTCATTTT 0.802334 -136 TACTATTTTCTTGTTCTTTTTTTATTTATACTA 2 133 1 TTTTTTTTTT 0.789541 -122 TTCAAAATTTTTTTAAAGATTTTAAAGATTTTT 3 143 1 TTTAAATTTT 0.866393 -158 ATTTTAAAGATTTTTTTAATTTTATCATTTTAA 3 161 1 TTTTTATTTT 0.949018 -140 TATCATTTTAATATTATTATTTTAACATTTTTT 3 183 1 ATTTTATTTT 0.875426 -118 TTTTAACATTTTTTAGTAATTTTTAGGATAAAA 3 202 1 TTTATATTTT 0.927401 -99 TATATACCTATTACTATCATTTTCTATAGCTGT 3 245 1 TTCTTATTTT 0.740492 -56 TCTTTATTATCTTATTTTAAGTTTTATT 4 6 1 ATATTATTTT 0.787738 -256 TTTATTTTTAATTTTAAAATTTTAATTGGAGGG 4 47 1 ATTTAATTTT 0.781055 -215 GTCTCTTCCATTAATATTATTTTATCTAAAACT 4 110 0 TTATTATTTT 0.907667 -152 CTTTTTTCTATTTTTTATATAATT 5 2 1 TTTTCATTTT 0.914908 -133 TTTCTATTTTTTATATAATTTTTATGAATATTG 5 15 1 TTTAATTTTT 0.566511 -120 TTTATGAATATTGATGTATTTTTAACGATTATT 5 35 1 TTATTTTTTT 0.664561 -100 GTCATATTGGTTATTGCTATTTTATACTTCAAA 6 29 1 TTTTCATTTT 0.914908 -52 TTAGAAATTTTTTTAAATTTTAAATTATATT 6 60 0 TTTTAATTTT 0.904302 -21 TTATATGATAATTTTAAAATTTTGCATTAAAAA 8 39 1 ATTTAATTTT 0.781055 -48 GTTGATAATCATATAAAAATTTTTTTATTATTT 10 90 0 ATTAAATTTT 0.709981 -211 GCTAAAGGAATTTTTCCTATTTTTATTTAAAGA 10 170 1 TTTTCATTTT 0.914908 -131 ATTTAAAGATTTGATGTAATTTTCGATGAAATT 10 194 1 TTATTATTTT 0.907668 -107 AAACATCTTCATAAACTTTTTTTGTTAGAATTT 10 222 0 ATAATTTTTT 0.339167 -79 ACTTTCTACTTTTTTTATTCTAATTT 11 4 1 TTTATTTTTT 0.720236 -216 TCTAATTTATTTTATCTAATTTTTATCAATTGC 11 29 1 TTATTATTTT 0.907668 -191 CTCTTTTTTATTTATATTATTGTATTTATATAG 11 65 1 TTATTATTGT 0.498694 -155 ATAGATATTATTTAAAAAATTTTAA 12 3 0 TTAAAATTTT 0.773987 -237 AATATCTATTTTCTTTTTATTTTCTTTTTAAGA 12 27 1 TTTTTATTTT 0.949018 -213 TAAGAGAAAGTTATTCTCATTTTTGCAGAAAAA 12 55 1 TTTTTATTTT 0.949018 -185 TTGCATGGTTTTATTTCAATTGTTATTGTTGTT 12 127 1 TTTTCATTGT 0.52108 -113 GTTATTGTTGTTGTTCTTATTTTTTATTTGATT 12 148 1 TTTTTATTTT 0.949018 -92 TTCAATAACATTAAACCAATTTTTAATT 12 222 1 TTAACATTTT 0.795774 -18 ATTTTTAATTTTAAAATCATTTTGGTGATTAA 13 10 0 TTAATATTTT 0.870902 -185 TTGTTGAGTATTTTAATCATTTTTGATATGGTT 13 96 1 TTTATATTTT 0.927401 -99 GTAAAAGGGGATATATAAATTTTACGGTTTAAT 14 276 1 ATTAAATTTT 0.709981 -25 ATATTAATTCATTCATTAATTTTGTTAAATAAC 16 117 1 ATCATATTTT 0.425035 -86 TCCACAATAAATTTTAAGATTTTATAAATAATA 16 177 1 ATTTAATTTT 0.781055 -26 ACAGTATAGTTTAAAGATATTTTTAAGTATTAA 17 64 0 TTAAAATTTT 0.773987 -163 ATTAATAAACTTTAATTAATTTTGAAGACAGTA 17 91 0 TTAATATTTT 0.870902 -136 ** ** * ***** Masking position 10 Map Score: 46.8076 Number of sites scoring better than the average of aligned sites = 2060 Number in coding regions = 1455 Number in noncoding regions = 605 Number of orfs with sites within 600 bp upstream = 435 Fraction of orfs with sites within 600 bp upstream = 0.0698683 Motif number 3 TATTTATTCCTGCGAAAGTCCTGTTATGCCTC 1 171 0 TGGAAAGTCT 0.996139 -130 CATCCAAAGATGTCAAAGTTCCAAAGTGCATA 1 219 1 TGCAAAGTCC 0.934915 -82 ATATATAAACTGCGAAAGTCCTGTTTCTTTGG 1 248 1 TGGAAAGTCT 0.996139 -53 GTATAGCCTCTGCGTAAGTTCCATTGTGGGAG 3 21 0 TGGTAAGTCC 0.96859 -280 TTCAAAAAAATGCGTAAGTTCTATTGAATAGG 3 93 1 TGGTAAGTCT 0.986248 -208 ATTATTGATATGAGAAAATGCTAATTTTTAAA 10 123 1 TGGAAAATCT 0.97807 -178 AACATTTTTATGTGAAAGTATTTTTATTAATA 13 143 1 TGGAAAGTTT 0.957519 -52 GATTTATTCCTGTGAAGATTCTACATTGATGC 14 157 0 TGGAAGATCT 0.902922 -144 ATATATAAATTGTGAAAGTTCTACAACGACAC 14 235 1 TGGAAAGTCT 0.996139 -66 CATTTATTCCTGCGAAAGTTCTATAATATTGA 16 20 0 TGGAAAGTCT 0.996139 -183 ** ****** ** Masking position 6 Map Score: 16.9763 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 18 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 TCGAGGCTTATAACATTTTTCTAACTTCTA 1 119 0 TAACATTTTT 0.651625 -182 TTTAAGTTTTTTAAGGGTTTAA 1 289 0 TAAGTTTTTT 0.865865 -12 TTTTGATTTATAAGTTTTAAATATCTGATG 2 208 1 TAAGTTTTAA 0.793049 -47 TGAGGAATTCAAAATTTTTTTAAAGATTTT 3 136 1 AAAATTTTTT 0.807556 -165 TAAAGATTTTAAAGATTTTTTTAATTTTAT 3 156 1 AAAGATTTTT 0.814249 -145 ATTATTATTTTAACATTTTTTAGTAATTTT 3 195 1 TAACATTTTT 0.651625 -106 GATAAAATAGAAAATTTTATATACCTATTA 3 228 1 AAAATTTTAT 0.75183 -73 TATCTTATTTTAAGTTTTATTTTTTGGACT 4 18 1 TAAGTTTTAT 0.809547 -244 CCCTCCAATTAAAATTTTAAAATTAAAAAT 4 50 0 AAAATTTTAA 0.732021 -212 TAATAGATTCAAACATTTTATCAAAAGTTT 4 85 1 AAACATTTTA 0.700357 -177 CATTTTATCAAAAGTTTTAGATAAAATAAT 4 98 1 AAAGTTTTAG 0.710125 -164 CTTGTTAGAAAAAGATTTATACTAAATAAG 4 199 1 AAAGATTTAT 0.760529 -63 CAGTCTGATTTAAATTTAATTAAAACCTAA 4 232 0 TAAATTTAAT 0.462976 -30 CAATATTCATAAAAATTATATAAAAAATAG 5 18 0 AAAAATTATA 0.463144 -117 ATTAGATATTAAAAATTTTTGTTCATATCA 5 93 1 AAAAATTTTT 0.458984 -42 GAAATTTTTTTAAATTTTAAATTATATTTG 6 58 0 TAAATTTTAA 0.664016 -23 AAATTTTGCTTAAGTTTAAATATTATTGCA 7 31 1 TAAGTTTAAA 0.601059 -65 ATTCAAAAACAAACTTTAATTAATTTAGTA 7 67 1 AAACTTTAAT 0.564104 -29 AATTTGGTGATAAATTTATAGGTTTA 8 7 0 TAAATTTATA 0.541517 -80 TTTTTAATGCAAAATTTTAAAATTATCATA 8 42 0 AAAATTTTAA 0.732021 -45 CAAAAAGGTCTAAATTTTTATGTAAGAGAT 9 19 1 TAAATTTTTA 0.741794 -90 TGTATTAGATAAAGATTTTATGAGAAATAT 10 25 0 AAAGATTTTA 0.803029 -276 CAAATAATAAAAAAATTTTTATATGATTAT 10 89 1 AAAAATTTTT 0.458984 -212 TTAAAAGCTCTAAGTTTTTAGCTAAAGGAA 10 150 1 TAAGTTTTTA 0.853398 -151 ACATCTTCATAAACTTTTTTTGTTAGAATT 10 223 0 AAACTTTTTT 0.833308 -78 TTTTCGTCTATAAATTTATTTAACTATATA 11 91 0 TAAATTTATT 0.567101 -129 TTATAGACGAAAAGTTTATATATTAGAATC 11 108 1 AAAGTTTATA 0.75993 -112 TTAAAATTTTTTAAATAATATC 12 3 1 AAAATTTTTT 0.807556 -237 AATGGTATCGAAAGTTTTAGATAAGTTTTT 12 99 1 AAAGTTTTAG 0.710125 -141 AAGTTTTAGATAAGTTTTTGCATGGTTTTA 12 110 1 TAAGTTTTTG 0.729266 -130 CAATTACAATTAAATTTTTTAATCAAATAA 12 171 0 TAAATTTTTT 0.757279 -69 TATTAACCATTAACTTTATATTCAATAACA 12 202 1 TAACTTTATA 0.56195 -38 TTATATTCAATAACATTAAACCAATTTTTA 12 217 1 TAACATTAAA 0.313395 -23 ACTTCCCTTAAAAGTTTTATTTTTAATTTT 13 31 0 AAAGTTTTAT 0.854559 -164 GTCACCAACAAAACATTTTTATGTGAAAGT 13 132 1 AAACATTTTT 0.717644 -63 TTATCACCAAAAAGATTAATTATAGCAATA 13 173 0 AAAGATTAAT 0.555418 -22 AATAAATCAGAAAGATTTAAGTTATTTAAA 14 13 1 AAAGATTTAA 0.741177 -288 ATTAAACCGTAAAATTTATATATCCCCTTT 14 279 0 AAAATTTATA 0.62014 -22 AAATAAACATTAACTTTTAAAATTTA 15 7 0 TAACTTTTAA 0.682208 -32 CAATAAATTTTAAGATTTTATAAATAATAA 16 181 1 TAAGATTTTA 0.750433 -22 AAAATTAATTAAAGTTTATTAATAAATATT 17 101 1 AAAGTTTATT 0.77833 -126 TGTCTTTCAAAAACATTTTGAAGTAACCAG 17 179 0 AAACATTTTG 0.529969 -48 ACTATATAAAAAAGTTTTTGGTGCTGTCT 17 208 1 AAAGTTTTTG 0.78829 -19 ********** Masking position 6 Map Score: 37.255 Number of sites scoring better than the average of aligned sites = 2662 Number in coding regions = 1889 Number in noncoding regions = 773 Number of orfs with sites within 600 bp upstream = 520 Fraction of orfs with sites within 600 bp upstream = 0.0835207 Motif number 5 TTAGTAAAAGGTTCATCAAAACGGATGCAC 2 37 0 GTTCATCAAA 0.842691 -218 GGATTATTTTTTTCATCAAAGCTATTTTGA 2 184 1 TTTCATCAAA 0.960993 -71 TTTTTATCACCAAAAATAGGATAC 2 241 0 TATCACCAAA 0.964889 -14 AGCCTAAAAGTATCATCAATAGCAAATAGA 3 53 0 TATCATCAAT 0.741607 -248 GATTCAAACATTTTATCAAAAGTTTTAGAT 4 90 1 TTTTATCAAA 0.705303 -172 CCTATAAATTTATCACCAAATTTTTTATAT 8 15 1 TATCACCAAA 0.964889 -72 CTTTTCACCAAAAAGGTCTAAA 9 3 1 TTTCACCAAA 0.96936 -106 TAGCTTACTCTATAATCAAAACCATAATTT 9 68 0 TATAATCAAA 0.789211 -41 TCATCGAAAATTACATCAAATCTTTAAATA 10 193 0 TTACATCAAA 0.768635 -108 TTTGTTAGAATTTCATCGAAAATTACATCA 10 205 0 TTTCATCGAA 0.831144 -96 AATTAAATTTTTTAATCAAATAAAAAATAA 12 164 0 TTTAATCAAA 0.806089 -76 TTAATCACCAAAATGATTTTAA 13 3 1 AATCACCAAA 0.760964 -192 ACTTATCACCAAAAAGATTAATT 13 182 0 TATCACCAAA 0.964889 -13 ********** Masking position 5 Map Score: 13.2101 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 179 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 TCTTATTTTAAGTTTTATTTTTTGGACTTTA 4 20 1 ATTTTATTTT 0.674133 -242 TTATGAATATTGATGTATTTTTAACGATTAT 5 36 1 TATGTATTTT 0.671445 -99 TTAATATCTAATATATATTTTTCGGTAGTTT 5 74 0 AATATATTTT 0.554588 -61 CTTAAATGATAAATTTCTTTTTAATGCAAAA 8 58 0 AATTTCTTTT 0.621722 -29 ATCAAAACCATAATTTATTTATAATTAGTTT 9 53 0 TATTTATTTA 0.77689 -56 TTTTTTATTCTAATTTATTTTATCTAATTTT 11 21 1 TATTTATTTT 0.944854 -199 GCACTCTTTTTTATTTATATTATTGTATTTA 11 62 1 TATTTATATT 0.551216 -158 TTTCGTCTATAAATTTATTTAACTATATAAA 11 89 0 AATTTATTTA 0.758359 -131 TTTTTAAATAATATCTATTTTCTTTTTATTT 12 18 1 AATCTATTTT 0.648557 -222 TTCCCTTAAAAGTTTTATTTTTAATTTTAAA 13 28 0 ATTTTATTTT 0.674133 -167 TAAATCTTTCTGATTTATTTT 14 1 0 TATTTATTTT 0.944954 -300 AAGTTAATGTTTATTTATTGTATATAGG 15 21 1 TATTTATTGT 0.910381 -18 CAGGAATAAATGATTTATTGAATAATGATGC 16 40 1 TATTTATTGA 0.673375 -163 ATTAATTCATTCATTAATTTTGTTAAATAAC 16 119 1 TATTAATTTT 0.695803 -84 AAACCATATGTTATTTATTTTATTATCCACA 16 152 1 TATTTATTTT 0.944954 -51 TAAAATCTTAAAATTTATTGTGGATAATAAA 16 170 0 AATTTATTGT 0.901224 -33 TTAATACGGTATATTTATTGTTTCTATTTCT 17 37 0 AATTTATTGT 0.901694 -190 TAATAAACTTTAATTAATTTTGAAGACAGTA 17 91 0 TATTAATTTT 0.695573 -136 AGGCATTTAAATATTTATTGTCAAATATTTA 17 123 0 AATTTATTGT 0.901694 -104 * ********* Masking position 4 Map Score: 14.1586 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 270 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 7 GGACTTTCGCAGGAATAAATATTCAATGGA 1 182 1 AGGAATAAAT 0.911701 -119 AATAGAGCATAGGAAAGAATTAGGATTACC 2 84 1 AGGAAAGAAT 0.873409 -171 ATAATCCTAAATGAAAAAATTGGCATAGTA 2 161 0 ATGAAAAAAT 0.925584 -94 AATAGCTTTGATGAAAAAAATAATCCTAAA 2 180 0 ATGAAAAAAA 0.590274 -75 TAATATTAAAATGATAAAATTAAAAAAATC 3 169 0 ATGATAAAAT 0.832052 -132 AGTAATTTTTAGGATAAAATAGAAAATTTT 3 216 1 AGGATAAAAT 0.888012 -85 ATCACCTTAAATGATAAATTTCTTTTTAAT 8 64 0 ATGATAAATT 0.526072 -23 CATTATTGATATGAGAAAATGCTAATTTTT 10 122 1 ATGAGAAAAT 0.743988 -179 AAATAAAAATAGGAAAAATTCCTTTAGCTA 10 168 0 AGGAAAAATT 0.816864 -133 GAATCTTCACAGGAATAAATCTACTATTGG 14 168 1 AGGAATAAAT 0.911701 -133 GAACTTTCGCAGGAATAAATGATTTATTGA 16 31 1 AGGAATAAAT 0.911701 -172 AACAAAATTAATGAATGAATTAATATAGAA 16 113 0 ATGAATGAAT 0.690951 -90 ********** Masking position 4 Map Score: 8.16256 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 271 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 AAATGTTATAAGCCTCGAGGGGAACCCGAAA 1 131 1 AGCCTGAGGG 0.942462 -170 GCCTCTCGGGTCCCTTTCGGGTTCCCCTCGA 1 145 0 TCCCTTCGGG 0.965534 -156 AGTCCTGTTATGCCTCTCGGGTCCCTTTCGG 1 156 0 TGCCTTCGGG 0.991882 -145 GGACTCCAGTTGCCTATAGGGCGCTGGACCA 14 95 0 TGCCTTAGGG 0.993261 -206 GGCACTTTGATGCCTAAAGGGTATCGTCATT 14 198 0 TGCCTAAGGG 0.978163 -103 TGAATAATGATGCCTTTAGGCATCTAAATAC 16 58 1 TGCCTTAGGC 0.971259 -145 ***** ***** Masking position 5 Map Score: 4.10263 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 9 ACACACGTTATAGTTAAAGATGAAGAGACA 1 79 1 TAGTTAAAGA 0.734293 -222 TTATAGAAGTTAGAAAAATGTTATAAGCCT 1 116 1 TAGAAAAATG 0.717882 -185 ATGAACCTTTTAGTAAAAGGTTCATCAAAA 2 46 0 TAGTAAAAGG 0.944972 -209 TAGAAAATGATAGTAATAGGTATATAAAAT 3 241 0 TAGTAATAGG 0.793712 -60 ACTACAGCTATAGAAAATGATAGTAATAGG 3 251 0 TAGAAAATGA 0.604275 -50 CTCCACTTGTTAGAAAAAGATTTATACTAA 4 194 1 TAGAAAAAGA 0.929496 -68 ATATAAAAAATAGAAAAAAG 5 1 0 TAGAAAAAAG 0.817754 -134 TATGTTGTATTAGATAAAGATTTTATGAGA 10 30 0 TAGATAAAGA 0.824165 -271 TCTAAGTTTTTAGCTAAAGGAATTTTTCCT 10 158 1 TAGCTAAAGG 0.73336 -143 TATGAAGAGATAGAAAAAAGCAGTGGGTTA 11 173 1 TAGAAAAAAG 0.817754 -47 CACATATAAAAAGTAAAAGGGGATATATAA 14 264 1 AAGTAAAAGG 0.665445 -37 TAACGTTTAATAGAAATAGAAACAATAAAT 17 26 1 TAGAAATAGA 0.747081 -201 ********** Masking position 6 Map Score: 5.16969 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 297 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 GCAGTATGCTGAAGTCATAATGAGAGCTTAT 1 27 1 GAAGTCATAT 0.860828 -274 AATATCTGATGAGGGTATCCTATTTTTGGTG 2 227 1 GAGGGTATCT 0.843723 -28 AACTTACGCAGAGGCTATACTCTATTTGCTA 3 33 1 GAGGCTATAT 0.905071 -268 ATTTTAATTGGAGGGCATAATAATAGATTCA 4 65 1 GAGGGCATAT 0.975329 -197 TTTATATAATGAGGTCATATTGGTTATTGCT 6 16 1 GAGGTCATAT 0.97946 -65 AAATGGTGTAGAGGTGATATT 10 290 1 GAGGTGATAT 0.970359 -11 TTCACAAATGGAGGTGATAATATGAAGAGAT 11 153 1 GAGGTGATAT 0.970359 -67 ********* * Masking position 7 Map Score: 2.38834 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 37 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 GATGTCTATATTCCATTGAATATTTATTCC 1 193 0 TTCCATTGAA 0.872804 -108 AATGCGTAAGTTCTATTGAATAGGGCTCAC 3 101 1 TTCTATTGAA 0.864266 -200 TCAAAGTCTCTTCCATTAATATTATTTTAT 4 118 0 TTCCATTAAT 0.731813 -144 TTTTAAAATTTTGCATTAAAAAGAAATTTA 8 50 1 TTGCATTAAA 0.715504 -37 AATCGTATATTTCTCATAAAATCTTTATCT 10 19 1 TTCTCATAAA 0.61549 -282 TAATTTGATATTCTATTAACGACCTCCAAA 10 252 0 TTCTATTAAC 0.788715 -49 GAGAATAACTTTCTCTTAAAAAGAAAATAA 12 43 0 TTCTCTTAAA 0.919192 -197 AATGCATTACTTCCCTTAAAAGTTTTATTT 13 39 0 TTCCCTTAAA 0.924946 -156 TTCGCAGTTTTTATATTAAAAAGGTATTTA 16 82 0 TTATATTAAA 0.61033 -121 TTGTTTCTATTTCTATTAAACGTTAATAAG 17 21 0 TTCTATTAAA 0.940877 -206 ********** Masking position 7 Map Score: 1.89828 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 149 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 ********** No masking Map Score: 3.44146e-12 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 Motif number 13 ********** No masking Map Score: 3.44146e-12 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 Motif number 14 ********** No masking Map Score: 3.44146e-12 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