AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_mjan_reg_300.orf -o00720_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) MJ0266 27 pyruvate ferredoxin oxidoreductase, subunit beta (porB) MJ1425 25 malate dehydrogenase MJ0267 21 pyruvate ferredoxin oxidoreductase, subunit alpha (porA) 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 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 MJ0269 283 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #10 MJ0270 300 M. jannaschii predicted coding region MJ0270 #11 MJ0276 119 2-ketoglutarate ferredoxin oxidoreductase, subunit alpha (korA) #12 MJ0277 183 acetolactate synthase large subunit (ilvB) #13 MJ0278 82 peptidyl-prolyl cis-trans isomerase, FKBP-type rotamase (slyD) #14 MJ0537 276 2-ketoglutarate ferredoxin oxidoreductase, subunit beta (korB) #15 MJ0539 267 tRNA synthetase, putative #16 MJ0541 89 conserved hypothetical protein #17 MJ0542 127 phosphoenolpyruvate synthase #18 MJ0543 132 ubiquinol-cytochrome C reductase complex, subunitVI requiring protein #19 MJ0544 103 dolichyl-phosphate mannose synthase #20 MJ0547 165 cell division inhibitor minD #21 MJ0548 111 conserved hypothetical protein #22 MJ0617 108 tartrate dehydratse, subunit beta (ttdB) #23 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #24 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) #25 MJ1296 38 biotin synthetase (bioB) #26 MJ1424 202 tRNA intron endonuclease (endA) #27 MJ1596 226 3-isopropylmalate dehydrogenase 2 (leuB2) Motif number 1 TTCTTGTTCTTTTTTTATTTATACTATGCC 2 140 1 TTTTTTATTT 0.885152 -115 GATTTATAAGTTTTAAATATCTGATGAGGG 2 212 1 TTTTAAATAT 0.68851 -43 TTTTAAAGATTTTTTTAATTTTATCATTTT 3 162 1 TTTTTTAATT 0.87607 -139 TAATTTTATCATTTTAATATTATTATTTTA 3 177 1 ATTTTAATAT 0.582273 -124 TTTATTTTTAATTTTAAAATTTTAATTGGA 4 47 1 ATTTTAAAAT 0.490292 -215 CCTCAGTCTGATTTAAATTTAATTAAAACC 4 235 0 ATTTAAATTT 0.466549 -27 CTTTTTTCTATTTTTTATATAATTTTTATG 5 11 1 TTTTTTATAT 0.946006 -124 TGAACAAAAATTTTTAATATCTAATATATA 5 88 0 TTTTTAATAT 0.873348 -47 TCTTTTTTATATAATGAGGTCA 6 3 1 TTTTTTATAT 0.946006 -78 TTAGAAATTTTTTTAAATTTTAAATTAT 6 63 0 TTTTTTAAAT 0.931788 -18 TATCACCAAATTTTTTATATGATAATTTTA 8 25 1 TTTTTTATAT 0.946006 -62 TTATATGATAATTTTAAAATTTTGCATTAA 8 39 1 ATTTTAAAAT 0.490292 -48 ATTTTTTAAATATCTCTGCTT 10 2 1 TTTTTTAAAT 0.931788 -299 TTTCATAAAAATATTTAAATACTTAGAATT 10 158 1 ATATTTAAAT 0.478045 -143 ATTTCCAATTATTTATAATTCTAAGTATTT 10 174 0 ATTTATAATT 0.654589 -127 ATGCTTCTATTTTTTTAAATTGTTATTTTC 11 23 1 TTTTTTAAAT 0.931788 -97 TTTAATTCTATTTTTTATTTTTAGTCTTTA 12 19 1 TTTTTTATTT 0.885152 -165 TTGGTATTTAATATTTAATTACTAATCTTA 12 47 0 ATATTTAATT 0.539367 -137 ATACCAACACTTTTTTATATCAAACTTTTT 12 70 1 TTTTTTATAT 0.946006 -114 TATATCAAACTTTTTAAAGTTCTTCAAATG 12 85 1 TTTTTAAAGT 0.660194 -99 TAGTATAAAAATTTTTATATATGATTTCAA 12 124 1 ATTTTTATAT 0.746374 -60 ACCTCAAATAATTTTTAATTTATAATGGAT 14 251 0 ATTTTTAATT 0.855369 -26 TAAAACTAAGTTATTTATATCATTTTGGTA 15 135 1 TTATTTATAT 0.771332 -133 GGATTTTTTGATTTTTATATTTTAAATAAT 15 206 1 ATTTTTATAT 0.746374 -62 TTATGAAACTTTTTTTAATTTTTTATAACA 17 11 1 TTTTTTAATT 0.87607 -117 TATCATTCAAATATTTAAATTTATTTTAAA 17 80 1 ATATTTAAAT 0.478045 -48 ATTTAAATTTATTTTAAAATAAAAGCTATA 17 92 1 ATTTTAAAAT 0.490292 -36 TCACAATAAATTTTATATATTGGGAATTGA 18 55 1 TTTTATATAT 0.849426 -78 TTACCATAAAATTTTAAAATTTTGTTAAAA 19 50 1 ATTTTAAAAT 0.490292 -54 AAAGGTCTAAATTTTTATGTAAGAGATTTT 22 22 1 ATTTTTATGT 0.8275 -87 ACCATAATTTATTTATAATTAGTTTTAAAA 22 48 0 ATTTATAATT 0.654589 -61 CACCAAAATGATTTTAAAATTAAAAATAAA 23 16 1 ATTTTAAAAT 0.490292 -179 CATTATAAGTATTTATATTTTGTGTTGTTT 23 65 1 ATTTATATTT 0.689592 -130 CCAACAAAACATTTTTATGTGAAAGTATTT 23 136 1 ATTTTTATGT 0.8275 -59 GAAAGTATTTTTATTAATATTGCTATAATT 23 156 1 TTATTAATAT 0.572218 -39 ACCCCCACCATTTTTTAAATAACTTAAATC 24 26 0 TTTTTTAAAT 0.931788 -275 AACTTTCACAATTTATATATTTATAAGGCA 24 225 0 ATTTATATAT 0.585754 -76 CCCTTTTACTTTTTATATGTGTCGTTGTAG 24 255 0 TTTTATATGT 0.629385 -46 AAACCGTAAAATTTATATATCCCCTTTTAC 24 276 0 ATTTATATAT 0.585754 -25 AAACATTAACTTTTAAAATTTA 25 3 0 TTTTAAAATT 0.474848 -36 TCTAAATACCTTTTTAATATAAAAACTGCG 26 80 1 TTTTTAATAT 0.873348 -123 AAACCATATGTTATTTATTTTATTATCCAC 26 152 1 TTATTTATTT 0.589045 -51 AATTTTAAGATTTTATAAATAATAACT 26 186 1 TTTTATAAAT 0.817557 -17 GTTTAAAGATATTTTTAAGTATTAATACGG 27 59 0 ATTTTTAAGT 0.806535 -168 TTGACAATAAATATTTAAATGCCTTCCTTT 27 130 1 ATATTTAAAT 0.478045 -97 CACCAAAAACTTTTTTATATAGTGTCTTTC 27 201 0 TTTTTTATAT 0.946006 -26 ********** Masking position 4 Map Score: 50.5964 Number of sites scoring better than the average of aligned sites = 2575 Number in coding regions = 1758 Number in noncoding regions = 817 Number of orfs with sites within 600 bp upstream = 516 Fraction of orfs with sites within 600 bp upstream = 0.0828783 Motif number 2 CACATGAACCTTTTAGTAAAAGGTTCATCAA 2 48 0 TTTTAGTAAA 0.790101 -207 CTTGTTCTTTTTTTATTTATACTATGCCAAT 2 142 1 TTTTATTATA 0.859788 -113 GGTATCCTATTTTTGGTGATAAAAA 2 240 1 TTTTGGTATA 0.92473 -15 TTCAAAATTTTTTTAAAGATTTTAAAGATTT 3 143 1 TTTTAAAATT 0.676374 -158 TTTTAACATTTTTTAGTAATTTTTAGGATAA 3 202 1 TTTTAGTATT 0.848169 -99 ACACCAACCTTTTTGTTAATATATTACTACA 3 275 0 TTTTGTTATA 0.890649 -26 TATCTAAAACTTTTGATAAAATGTTTGAATC 4 90 0 TTTTGATAAA 0.787365 -172 TTATCAAAAGTTTTAGATAAAATAATATTAA 4 102 1 TTTTAGAAAA 0.771643 -160 AGATATTAGGTTTTAATTAAATTTAAATCAG 4 227 1 TTTTAATAAA 0.754743 -35 TTTTTCTATTTTTTATATAATTTTTATGAAT 5 13 1 TTTTATAAAT 0.576128 -122 TATTAAAAATTTTTGTTCATATCATATAGCC 5 99 1 TTTTGTTATA 0.890937 -36 TCTTTTTTATATAATGAGGTCATAT 6 5 1 TTTTATAAAT 0.576128 -76 TAAAGTTTGTTTTTGAATATATTCTGCAATA 7 54 0 TTTTGAAATA 0.821308 -42 ACAACATCATTTTTAGAGAAAGACTATGTAA 9 136 1 TTTTAGAAAA 0.771643 -148 ATATATAAAGTTTTGGAGATTTAAGCAATTA 9 214 0 TTTTGGAATT 0.818026 -70 TATATATTACTTTTAATAATTGTTAATGATT 9 238 1 TTTTAATATT 0.775367 -46 TTAACAGAGTTTTTAATAATAGATGAATTAA 10 32 0 TTTTAATATA 0.828121 -269 TGTTTAACATTTTTGTATATAAAATTTTTCA 10 132 1 TTTTGTAATA 0.831693 -169 TCTAAGCTACTTTTATATAATATAACCTTGT 11 86 0 TTTTATAAAT 0.576128 -34 CCTTAACATTTTTTGGTGATTGG 12 171 1 TTTTGGTATT 0.881397 -13 GCTCCCAACCTTTTAGTAAAAGGTTACTCGA 14 135 0 TTTTAGTAAA 0.790101 -142 TTAAGCCCTATTTTAATCAAACGAACTCATC 14 201 0 TTTTAATAAA 0.754743 -76 TGTTATCTATTTTTGATGATTGA 15 3 0 TTTTGATATT 0.821308 -265 CTATAAAAACTTTTGATGATTGACTATAATT 15 91 1 TTTTGATATT 0.821308 -177 AATAACTTAGTTTTAGACAAAAAAGCTGAAT 15 119 0 TTTTAGAAAA 0.771643 -149 GATTTTTATATTTTAAATAATATAGACAATA 15 215 1 TTTTAAAAAT 0.558347 -53 TCTTCACTATTTTTGGTGATACA 16 77 1 TTTTGGTATA 0.92473 -13 AACTCTACTATTTTATTTATAATATTATCAT 17 55 1 TTTTATTATA 0.859788 -73 TCACAATAAATTTTATATATTGGGAATTGAA 18 55 1 TTTTATAATT 0.692024 -78 GGCTGTTTCGTTTTATAGATAAAGAGAAGGA 18 97 0 TTTTATAATA 0.787894 -36 AATTTTAAAATTTTGTTAAAAATTTACTAGC 19 59 1 TTTTGTTAAA 0.799498 -45 GATGTAATGTTTTTGAAGATAAGCGTGTCCT 20 69 1 TTTTGAAATA 0.821308 -97 ATTTAGACCTTTTTGGTGAAAAG 22 3 0 TTTTGGTAAA 0.88139 -106 TAAATTATGGTTTTGATTATAGAGTAAGCTA 22 67 1 TTTTGATATA 0.883696 -42 TTTAAAATCATTTTGGTGATTAA 23 3 0 TTTTGGTATT 0.881397 -192 TTGTTGAGTATTTTAATCATTTTTGATATGG 23 96 1 TTTTAATATT 0.775536 -99 GTGAAAGTATTTTTATTAATATTGCTATAAT 23 154 1 TTTTATTATA 0.838355 -41 TAATTAATCTTTTTGGTGATAAGT 23 181 1 TTTTGGTATA 0.92473 -14 CATTCATTAATTTTGTTAAATAACATAAACC 26 126 1 TTTTGTTAAT 0.749075 -77 AATTTTAAGATTTTATAAATAATAACT 26 186 1 TTTTATAATA 0.787606 -17 ******* *** Masking position 4 Map Score: 51.0043 Number of sites scoring better than the average of aligned sites = 1090 Number in coding regions = 789 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 270 Fraction of orfs with sites within 600 bp upstream = 0.0433665 Motif number 3 AAAGAACAAGAAAATAGTAATATTTTTAATAA 2 120 0 AAAATAGATA 0.971125 -135 TTTGATGAAAAAAATAATCCTAAATGAAAAAA 2 172 0 AAAATAACTA 0.864525 -83 AAAAAATGTTAAAATAATAATATTAAAATGAT 3 184 0 AAAATAAATA 0.961392 -117 TTTTTAGGATAAAATAGAAAATTTTATATACC 3 221 1 AAAATAGAAT 0.828295 -80 AATAAAACTTAAAATAAGATAATAAAGA 4 7 0 AAAATAAAAA 0.868081 -255 TAAAGTCCAAAAAATAAAACTTAAAATAAGAT 4 19 0 AAAATAAATT 0.931111 -243 AGTTTTAGATAAAATAATATTAATGGAAGAGA 4 110 1 AAAATAAATA 0.961392 -152 AATTATATAAAAAATAGAAAAAAG 5 3 0 AAAATAGAAA 0.898861 -132 TAGTTTATCAAAAATAATCGTTAAAAATACAT 5 48 0 AAAATAACTT 0.775972 -87 TTTGAAGTATAAAATAGCAATAACCAATATGA 6 30 0 AAAATAGATA 0.971125 -51 GGCATAAGAAAAAATAAAATTAATTTACATGG 9 168 0 AAAATAAATA 0.961392 -116 AATTGGAAATAAAATAGGACTTTCGCATGAGG 10 194 1 AAAATAGATT 0.948065 -107 ACAATTTAAAAAAATAGAAGCATGGGCTAATT 11 14 0 AAAATAGACA 0.914766 -106 AATAGAGAAGAAAATAACAATTTAAAAAAATA 11 30 0 AAAATAAATT 0.931111 -90 CTAAAAATAAAAAATAGAATTAAAGAAAGAAA 12 11 0 AAAATAGATA 0.971125 -173 TTGTCCATAAAAAATAATAACAAAAAACTATT 13 22 1 AAAATAAACA 0.888224 -61 TATAGACAATAAAATAGAAGAAACAAAAATTT 15 235 1 AAAATAGAAA 0.898861 -33 ATATAATGATAAAATAGTCATAAAAACAAAAC 16 28 0 AAAATAGCTA 0.896036 -62 AATTTATTTTAAAATAAAAGCTATATATAATC 17 97 1 AAAATAAACT 0.811789 -31 CAAAATAACAGTAAGCTTTAAAT 18 2 1 AAAATAAATA 0.961392 -131 AAAAAGTAGAAAAATAGGAATTGGTGTTTTTA 19 14 0 AAAATAGATT 0.948065 -90 TTTAAAATTAAAAATAAAACTTTTAAGGGAAG 23 28 1 AAAATAAATT 0.931111 -167 AAAACAACACAAAATATAAATACTTATAATGC 23 64 0 AAAATATATA 0.726025 -131 ******* * ** Masking position 5 Map Score: 34.662 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 146 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 4 TATTTATTCCTGCGAAAGTCCTGTTATGCCT 1 172 0 TGCGAAAGTC 0.995707 -129 CATCCAAAGATGTCAAAGTTCCAAAGTGCAT 1 219 1 TGTCAAAGTC 0.916975 -82 ATATATAAACTGCGAAAGTCCTGTTTCTTTG 1 248 1 TGCGAAAGTC 0.995707 -53 GTATAGCCTCTGCGTAAGTTCCATTGTGGGA 3 22 0 TGCGTAAGTC 0.986539 -279 TTCAAAAAAATGCGTAAGTTCTATTGAATAG 3 93 1 TGCGTAAGTC 0.986539 -208 TATTTCCTCATGCGAAAGTCCTATTTTATTT 10 200 0 TGCGAAAGTC 0.995707 -101 AACATTTTTATGTGAAAGTATTTTTATTAAT 23 143 1 TGTGAAAGTT 0.881683 -52 ATATATAAATTGTGAAAGTTCTACAACGACA 24 235 1 TGTGAAAGTC 0.987015 -66 CATTTATTCCTGCGAAAGTTCTATAATATTG 26 21 0 TGCGAAAGTC 0.995707 -182 ********* * Masking position 6 Map Score: 19.271 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 8 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 5 CTCGAGGCTTATAACATTTTTCTAACTTCT 1 120 0 ATAACATTTT 0.895548 -181 TTTTTTAATTTTATCATTTTAATATTATTA 3 172 1 TTATCATTTT 0.842999 -129 TATTATTATTTTAACATTTTTTAGTAATTT 3 194 1 TTAACATTTT 0.929189 -107 TAATAGGTATATAAAATTTTCTATTTTATC 3 228 0 ATAAAATTTT 0.854976 -73 TGCCCTCCAATTAAAATTTTAAAATTAAAA 4 52 0 TTAAAATTTT 0.900229 -210 TCTTCCATTAATATTATTTTATCTAAAACT 4 110 0 ATATTATTTT 0.685361 -152 TCTATTTTTTATATAATTTTTATGAATATT 5 17 1 ATATAATTTT 0.70694 -118 CAAATATAATTTAAAATTTAAAAAAATTTC 6 58 1 TTAAAATTTA 0.854976 -23 ATATTCTGCAATAATATTTAAACTTAAGCA 7 37 0 ATAATATTTA 0.775954 -59 TATGATAATTTTAAAATTTTGCATTAAAAA 8 42 1 TTAAAATTTT 0.900229 -45 AAAAAGAAATTTATCATTTAAGGTGATAGG 8 67 1 TTATCATTTA 0.778185 -20 TTAAGTATGTTTAACATTTTTGTATATAAA 10 125 1 TTAACATTTT 0.929189 -176 ATTTTTGTATATAAAATTTTTCATAAAAAT 10 140 1 ATAAAATTTT 0.854976 -161 TAACCTTGTGTTAATATTTAACGACTATAA 11 65 0 TTAATATTTA 0.841332 -55 GTGTTGGTATTTAATATTTAATTACTAATC 12 50 0 TTAATATTTA 0.841332 -134 TACTTTACCCTTAACATTTTTTGGTGATTG 12 163 1 TTAACATTTT 0.929189 -21 TAGTTTTTTGTTATTATTTTTTATGGACAA 13 22 0 TTATTATTTT 0.769257 -61 TCAAAAATAGATAACATTTTCTAAGGTTAT 15 18 1 ATAACATTTT 0.895548 -250 TAAGTTATTTATATCATTTTGGTAGTTAAT 15 141 1 ATATCATTTT 0.778185 -127 ATTTTGGTAGTTAATATTTTAACAAATTAT 15 156 1 TTAATATTTT 0.890317 -112 TTTATTGTCTATATTATTTAAAATATAAAA 15 218 0 ATATTATTTA 0.587326 -50 TTAATTTTTTATAACATTTTCACTTGTAAT 17 25 1 ATAACATTTT 0.895548 -103 TATTTTTAACTTAATATTTAAAGCTTACTG 18 19 0 TTAATATTTA 0.841332 -114 TTCCCAATATATAAAATTTATTGTGATGCT 18 51 0 ATAAAATTTA 0.793896 -82 TAACAAAATTTTAAAATTTTATGGTAATAA 19 47 0 TTAAAATTTT 0.900229 -57 ACATTAACTTTTAAAATTTA 25 1 0 TTAAAATTTA 0.854976 -38 TTATAAAATCTTAAAATTTATTGTGGATAA 26 174 0 TTAAAATTTA 0.854976 -29 AGTTATTATTTATAAAATCTTA 26 191 0 TTATTATTTA 0.685361 -12 ********** Masking position 6 Map Score: 40.6296 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 367 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 6 GATGTCAAAGTTCCAAAGTGCATATATAAACTGCGAAAG 1 227 1 TTATATATAA 0.931484 -74 TTTAAGTTTTTTAAGGGTTTAATTTAAGCTTCCAAAG 1 274 0 TTAAATTTAA 0.608726 -27 ATTTTTTTAATTTTATCATTTTAATATTATTATTTTAAC 3 170 1 TTAAATATTA 0.616148 -131 GTTATTGCTATTTTATACTTCAAATATAATTTAAAATTT 6 38 1 TTAAATATAA 0.595694 -43 TAATGCAAAATTTTAAAATTATCATATAAAAAATTTGGT 8 29 0 TTACATATAA 0.667911 -58 CAGTTCCTTTTTTAACTCCTTCAATATAATAGCCGATTT 9 71 0 TTAAATATAA 0.93503 -213 TACAAAAATGTTAAACATACTTAACATAATGTAAAGTAT 10 110 0 TTAAACATAA 0.72325 -191 AGTATTTAAATTCCAAATTCAATATATAAACTGTGGAAA 10 256 1 TTATATATAA 0.931484 -45 TGTGTTAATATTTAACGACTATAATATAATAGAGAAGAA 11 50 0 TTAAATATAA 0.936914 -70 ATTACTAATCTTAAAGACTAAAAATAAAAAATAGAATTA 12 21 0 TTAAATAAAA 0.606367 -163 TTTGAAGAACTTTAAAAAGTTTGATATAAAAAAGTGTTG 12 74 0 TTAGATATAA 0.712999 -110 TCCAAATACTTTTTGTGAAGGGTATATAAATAGTTTTTT 13 43 0 TTGTATATAA 0.519246 -40 TTTTGAGCTTCTATAAGTTTATTATATAACTATAAAAAC 15 62 1 CTATATATAA 0.541477 -206 ATTTAAATATTTGAATGATAATATTATAAATAAAATAGT 17 61 0 TTAATTATAA 0.465614 -67 TATGTGTGTTTTCAATTCCCAATATATAAAATTTATTGT 18 57 0 TTATATATAA 0.910701 -76 AACTTTAGTGTTGTAAATAGGTAATATAAAGATTTTAGA 20 137 1 TTAAATATAA 0.926651 -29 CCCGTTTATTTTCAAACTAACAAATATTACTATTTAATA 21 18 1 TTAAATATTA 0.618412 -94 AATATTACTATTTAATAACTAATATATAAGATTAACGAT 21 40 1 TTATATATAA 0.819635 -72 TATAATTAGTTTTAAAATCTCTTACATAAAAATTTAGAC 22 26 0 TTATACATAA 0.705108 -83 CCAAAATGATTTTAAAATTAAAAATAAAACTTTTAAGGG 23 18 1 TTAAATAAAA 0.612739 -177 CACAATAAATTTTAAGATTTTATAAATAATAACT 26 179 1 TTATAAATAA 0.467803 -24 TTAATAAATATTTGACAATAAATATTTAAATGCCTTCCT 27 119 1 TTATATTTAA 0.596165 -108 TCAAAATGTTTTTGAAAGACACTATATAAAAAAGTTTTT 27 188 1 TTATATATAA 0.930469 -39 ** * ******* Masking position 2 Map Score: 19.2914 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 168 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 ATCCGTTTTGATGAACCTTTTACTAAAAGG 2 41 1 ATGAACCTTT 0.923221 -214 TTTCCTTCACATGAACCTTTTAGTAAAAGG 2 56 0 ATGAACCTTT 0.923221 -199 TACCAACACCAACCTTTTTGTTAATAT 3 284 0 ACCAACCTTT 0.958106 -17 TATATTCAAAAACAAACTTTAATTAATTTA 7 64 1 AACAAACTTT 0.824289 -32 ACTTTTTTATATCAAACTTTTTAAAGTTCT 12 78 1 ATCAAACTTT 0.882708 -106 CTCCTAACCTTTCCAAATACTT 13 71 0 CCTAACCTTT 0.722045 -12 CTAAGTTTTGATCAACCTTTTCTAAAAGGT 14 102 1 ATCAACCTTT 0.958903 -175 AGGTTACTCGAACAACCTTTTAGAAAAGGT 14 116 0 AACAACCTTT 0.935668 -161 AGGTTGTTCGAGTAACCTTTTACTAAAAGG 14 128 1 AGTAACCTTT 0.736572 -149 AAACATTGCTCCCAACCTTTTAGTAAAAGG 14 143 0 CCCAACCTTT 0.887969 -134 TTATGAAACTTTTTTTAATTTT 17 3 1 ATGAAACTTT 0.795013 -125 AATATTTATTAATAAACTTTAATTAATTTT 27 101 0 AATAAACTTT 0.605909 -126 ********** Masking position 5 Map Score: 7.91992 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 156 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 CAACACCAACCTTTTTGTTAATATATTACTAC 3 276 0 CTTTTGTTAT 0.795983 -25 CGAAAAATATATATTAGATATTAAAAATTTTT 5 81 1 ATATTGATAT 0.658926 -54 GATATTAAAAATTTTTGTTCATATCATATAGC 5 97 1 ATTTTGTTCT 0.795982 -38 TAATGAGGTCATATTGGTTATTGCTATTTTAT 6 22 1 ATATTGTTAT 0.957588 -59 TGCCTAAACTATTTTCGTTAATTGCTTAAATC 9 196 1 ATTTTGTTAT 0.965729 -88 ATTACTTTTAATAATTGTTAATGATTGATAAT 9 243 1 ATAATGTTAT 0.784459 -41 ATATAAATAGTTTTTTGTTATTATTTTTTATG 13 27 0 TTTTTGTTAT 0.724702 -56 TTCCCTCAAAATTTTTGTTTCTTCTATTTTAT 15 243 0 ATTTTGTTTT 0.724701 -25 TTAAATAGTAATATTTGTTAGTTTGAAAATAA 21 23 0 ATATTGTTAT 0.957588 -89 TTAATCTTATATATTAGTTATTAAATAGTAAT 21 43 0 ATATTGTTAT 0.957588 -69 TAGTATTATTATTATCGTTAATCTTATATATT 21 60 0 ATTATGTTAT 0.796752 -52 TAGACTAATAATATTAGTTAGTATTATTATTA 21 78 0 ATATTGTTAT 0.957588 -34 TTTTAAAATCATTTTGGTGATTAA 23 3 0 ATTTTGTGAT 0.784795 -192 ATGTGAAAGTATTTTTATTAATATTGCTATAA 23 152 1 ATTTTATTAT 0.741491 -43 AATCAGAAAGATTTAAGTTATTTAAAAAATGG 24 17 1 ATTTAGTTAT 0.711022 -284 TTATTGTCAAATATTTATTAATAAACTTTAAT 27 108 0 ATATTATTAT 0.692564 -119 ***** **** * Masking position 2 Map Score: 10.0024 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 78 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TAACTTCTATAATCTCTTTTGTCTCTTCATC 1 97 0 AATCTTTTTG 0.914918 -204 CGAGGCAGTGCATCCGTTTTGATGAACCTTT 2 30 1 CATCCTTTTG 0.969428 -225 TTTTTCATCAAAGCTATTTTGATTTATAAGT 2 192 1 AAGCTTTTTG 0.932634 -63 TACCAACACCAACCTTTTTGTTAATATATT 3 281 0 CAACCTTTTG 0.886639 -20 ATTTTCAGTTCATCCATATTGTAT 7 4 0 CATCCTATTG 0.887233 -92 GATTTTTAAACAGCTTTATTGTTGAATTACT 9 40 0 CAGCTTATTG 0.903377 -244 CGAGGTAATGCATCTGTTTTGATCAACGCAC 14 39 1 CATCTTTTTG 0.966962 -238 ATTGGTATAGAAGCCCTTTTGAGCTTCTATA 15 46 1 AAGCCTTTTG 0.937496 -222 GACTATAATTCAGCTTTTTTGTCTAAAACTA 15 112 1 CAGCTTTTTG 0.974147 -156 ATCATCACCTATTTTGGCTGTTTCGT 18 117 0 CACCTTTTTG 0.914544 -16 TGAGTATTTTAATCATTTTTGATATGGTTTA 23 100 1 AATCATTTTG 0.690639 -95 ***** ***** Masking position 2 Map Score: 8.3658 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 68 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 TTGTTCTTTTTTTATTTATACTATGCCAAT 2 143 1 TTTATTTATA 0.684439 -112 TTTTTGTTAATATATTACTACAGCTATAGA 3 267 0 TATATTACTA 0.575401 -34 TTATCCCTACTAAATTAATTAAAGTTTGTT 7 74 0 TAAATTAATT 0.723005 -22 AATTTGGTGATAAATTTATAGGTTTA 8 7 0 TAAATTTATA 0.684438 -80 CCTTAAATGATAAATTTCTTTTTAATGCAA 8 60 0 TAAATTTCTT 0.552641 -27 GTAATCCATGTAAATTAATTTTATTTTTTC 9 163 1 TAAATTAATT 0.723005 -121 CAAAACTTTATATATTACTTTTAATAATTG 9 230 1 TATATTACTT 0.597845 -54 AAAAGATGGGTAAATTACTTCTCGGATTTT 10 62 0 TAAATTACTT 0.575401 -239 TATTTAATATTTAATTACTAATCTTAAAGA 12 43 0 TTAATTACTA 0.529659 -141 CAAATAATTTTTAATTTATAATGGATACCC 14 247 0 TTAATTTATA 0.664118 -30 ACTCTACTATTTTATTTATAATATTATCAT 17 56 1 TTTATTTATA 0.684439 -72 TTCAAATATTTAAATTTATTTTAAAATAAA 17 85 1 TAAATTTATT 0.704089 -43 CATTACATCATTAATTAATTGAATAAGGTT 20 48 0 TTAATTAATT 0.704089 -118 AAAACCATAATTTATTTATAATTAGTTTTA 22 51 0 TTTATTTATA 0.684439 -58 TGAAAGTATTTTTATTAATATTGCTATAAT 23 155 1 TTTATTAATA 0.704089 -40 TCACAATTTATATATTTATAAGGCACTTTG 24 220 0 TATATTTATA 0.703735 -81 AAAGTTAATGTTTATTTATTGTATATAGG 25 20 1 TTTATTTATT 0.704089 -19 TGCGAAGTTCTATATTAATTCATTCATTAA 26 106 1 TATATTAATT 0.741157 -97 ATTAATACGGTATATTTATTGTTTCTATTT 27 39 0 TATATTTATT 0.723 -188 TTAATAAACTTTAATTAATTTTGAAGACAG 27 93 0 TTAATTAATT 0.704089 -134 TTGTCAAATATTTATTAATAAACTTTAATT 27 107 0 TTTATTAATA 0.704089 -120 ********** Masking position 5 Map Score: 15.3837 Number of sites scoring better than the average of aligned sites = 1154 Number in coding regions = 738 Number in noncoding regions = 416 Number of orfs with sites within 600 bp upstream = 319 Fraction of orfs with sites within 600 bp upstream = 0.0512367 Motif number 11 AGGCACTGGTAATCCTAATTCTTTCCTATGCTCT 2 87 0 AATCAATTTT 0.947105 -168 TTATTTATACTATGCCAATTTTTTCATTTAGGAT 2 154 1 TATCAATTTT 0.729848 -101 CTCTGTGAGGAATTCAAAATTTTTTTAAAGATTT 3 131 1 AATCAATTTT 0.947105 -170 CTTTATTTTTAATTTTAAAATTTTAATTGGAGGG 4 46 1 AATTAAATTT 0.750623 -216 CATAATAATAGATTCAAACATTTTATCAAAAGTT 4 80 1 GATCAAATTT 0.790514 -182 GGTCTGAAACTATGCCAACAGCTTGATTCTCTAT 4 149 0 TATCAAACTT 0.437729 -113 ATTTCTTTTTAATGCAAAATTTTAAAATTATCAT 8 43 0 AATCAATTTA 0.575384 -44 AATTATTTATAATTCTAAGTATTTAAATATTTTT 10 164 0 AATCAATTTT 0.947105 -137 GTCCTATTTTATTTCCAATTATTTATAATTCTAA 10 180 0 ATTCAATTTT 0.575384 -121 TTAAATATTAAATACCAACACTTTTTTATATCAA 12 59 1 AATCAAATTT 0.941755 -125 AAGTTCTTCAAATGCTAAATCCTTAGTATAAAAA 12 101 1 AATCAATCTT 0.851055 -83 AAAATCAAAAAATCCAAATTTCTTTAGGTTACAT 15 187 0 AATCAATCTT 0.851055 -81 ATATTTTAACAATTCCAAATCTTCACTATTTTTG 16 58 1 AATCAATTTC 0.667595 -32 AATTTATTGTGATGCTAATATTTTTAACTTAATA 18 33 0 GATCAAATTT 0.790514 -100 ATTACCATAAAATTTTAAAATTTTGTTAAAAATT 19 49 1 AATTAAATTT 0.750623 -55 GTAAATAGGTAATATAAAGATTTTAGA 20 149 1 AATTAAATTT 0.750623 -17 TAGCAATATTAATAAAAATACTTTCACATAAAAA 23 147 0 AATAAAATTT 0.477771 -48 ATCCACAATAAATTTTAAGATTTTATAAATAATA 26 176 1 AATTAAATTT 0.750623 -27 GCTACTGGTTACTTCAAAATGTTTTTGAAAGACA 27 175 1 ACTCAATTTT 0.667595 -52 *** * ** * *** Masking position 3 Map Score: 10.733 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 291 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 12 ATAATAATATTAAAATGATAAAATTAAAAA 3 173 0 TAAAATGATA 0.402268 -128 ATAGCTGTAGTAATATATTAACAAAAAGGT 3 270 1 TAATATATTA 0.299229 -31 TTCATAAAAATTATATAAAAAATAGAAAAA 5 13 0 TTATATAAAA 0.58166 -122 CCATTTTAGGCTATATGATATGAACAAAAA 5 108 0 CTATATGATA 0.622826 -27 TATGACCTCATTATATAAAAAAGA 6 5 0 TTATATAAAA 0.58166 -76 TTTTTAAATTTTAAATTATATTTGAAGTAT 6 52 0 TTAAATTATA 0.506197 -29 ACCAAATTTTTTATATGATAATTTTAAAAT 8 29 1 TTATATGATA 0.852839 -58 CCTATCACCTTAAATGATAAATTTCTTTT 8 68 0 TTAAATGATA 0.620447 -19 TTAACTCCTTCAATATAATAGCCGATTTGA 9 69 0 CAATATAATA 0.476112 -215 CTCCAAAACTTTATATATTACTTTTAATAA 9 227 1 TTATATATTA 0.536259 -57 AAAGTATTATTAACATGATAGAGGAAAAAG 10 87 0 TAACATGATA 0.357955 -214 AAGAGTGTTATTATATAATAAAATATTTCC 10 224 0 TTATATAATA 0.88449 -77 TTCTTCTCTATTATATTATAGTCGTTAAAT 11 50 1 TTATATTATA 0.784279 -70 TAAGCTACTTTTATATAATATAACCTTGTG 11 85 0 TTATATAATA 0.88449 -35 GTTTTTATAGTTATATAATAAACTTATAGA 15 71 0 TTATATAATA 0.88449 -197 TTTCTTTAGGTTACATAATAATTTGTTAAA 15 173 0 TTACATAATA 0.643506 -95 TTTTTATATTTTAAATAATATAGACAATAA 15 217 1 TTAAATAATA 0.685469 -51 ATTTGAATGATAATATTATAAATAAAATAG 17 62 0 TAATATTATA 0.598811 -66 ATCGTTAATCTTATATATTAGTTATTAAAT 21 49 0 TTATATATTA 0.536259 -63 AGATTCACCTCAATATTATAGAACTTTCGC 26 11 1 CAATATTATA 0.299111 -192 TTCGCAGTTTTTATATTAAAAAGGTATTTA 26 82 0 TTATATTAAA 0.396648 -121 ********** Masking position 6 Map Score: 9.42277 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 253 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 13 AAATGTTATAAGCCTCGAGGGGAACCCGAAA 1 131 1 AGCCTGAGGG 0.891744 -170 GCCTCTCGGGTCCCTTTCGGGTTCCCCTCGA 1 145 0 TCCCTTCGGG 0.96856 -156 AGTCCTGTTATGCCTCTCGGGTCCCTTTCGG 1 156 0 TGCCTTCGGG 0.98649 -145 TAAATAGGTATCCCAATAGGGCGAAGCTATG 14 70 0 TCCCATAGGG 0.904798 -207 GGACTCCAGTTGCCTATAGGGCGCTGGACCA 24 95 0 TGCCTTAGGG 0.990869 -206 GGCACTTTGATGCCTAAAGGGTATCGTCATT 24 198 0 TGCCTAAGGG 0.96399 -103 TGAATAATGATGCCTTTAGGCATCTAAATAC 26 58 1 TGCCTTAGGC 0.954257 -145 ***** ***** Masking position 4 Map Score: 3.45048 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 12 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 GGATGCACTGCCTCGCTACGCTCGGCAGTGCCT 2 12 0 CTGCTAGCTC 0.994839 -243 AATCCTAATTCTTTCCTATGCTCTATTTCCTTC 2 78 0 CTCCTAGCTC 0.982062 -177 AGATGCATTACCTCGCTACGCTCGGTAATGCCT 14 21 0 CTGCTAGCTC 0.994839 -256 ATCAACGCACCATAGCTTCGCCCTATTGGGATA 14 60 1 CTGCTTGCCC 0.963495 -217 ATAACTACCGCATGGCTAAGCTCAAACATTGCT 14 163 0 CTGCTAGCTC 0.994839 -114 * * **** **** Masking position 7 Map Score: 2.22079 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 15 AGGACTTTCGCAGTTTATATATGCACTTTGG 1 239 0 CAGTTTTATA 0.84162 -62 TAAAATAGAAAATTTTATATACCTATTACTA 3 230 1 AATTTTTATA 0.915429 -71 CTATTACTATCATTTTCTATAGCTGTAGTAA 3 252 1 CATTTTTATA 0.873978 -49 CTTTTTTCTATTTTTTATATAATTTTTAT 5 9 1 TATTTTTATA 0.43644 -126 TATGAACAAAAATTTTTAATATCTAATATAT 5 89 0 AATTTTAATA 0.517535 -46 AATTTTGCTTAAGTTTAAATATTATTGCAGA 7 32 1 AAGTTTAATA 0.451133 -64 TTTATCACCAAATTTTTTATATGATAATTTT 8 23 1 AATTTTTATA 0.915429 -64 AAATCTCCAAAACTTTATATATTACTTTTAA 9 223 1 AACTTTTATA 0.578545 -61 TTTTATGAAAAATTTTATATACAAAAATGTT 10 137 0 AATTTTTATA 0.915429 -164 TTTTATTTCCAATTATTTATAATTCTAAGTA 10 177 0 AATTATTATA 0.507041 -124 GGATTTTCCACAGTTTATATATTGAATTTGG 10 268 0 CAGTTTTATA 0.84162 -33 CTTCTAAGCTACTTTTATATAATATAACCTT 11 88 0 ACTTTTTATA 0.707339 -32 AAATACCAACACTTTTTTATATCAAACTTTT 12 68 1 ACTTTTTATA 0.707339 -116 TCATATATAAAAATTTTTATACTAAGGATTT 12 117 0 AAATTTTATA 0.700619 -67 CAATCATCAAAAGTTTTTATAGTTATATAAT 15 82 0 AAGTTTTATA 0.892404 -186 AACTTTTTTTAATTTTTTATAACATTTTCAC 17 17 1 AATTTTTATA 0.915429 -111 CATCACAATAAATTTTATATATTGGGAATTG 18 53 1 AATTTTTATA 0.915429 -80 TATTATCGTTAATCTTATATATTAGTTATTA 21 52 0 AATCTTTATA 0.463669 -60 AATGCATTATAAGTATTTATATTTTGTGTTG 23 61 1 AAGTATTATA 0.440754 -134 GTATTTTAATCATTTTTGATATGGTTTAAGT 23 103 1 CATTTTGATA 0.366147 -92 GCACCCCCACCATTTTTTAAATAACTTAAAT 24 27 0 CATTTTTAAA 0.264137 -274 AGAACTTTCACAATTTATATATTTATAAGGC 24 226 0 CAATTTTATA 0.599898 -75 TTAAACCGTAAAATTTATATATCCCCTTTTA 24 277 0 AAATTTTATA 0.700619 -24 TAGAACTTCGCAGTTTTTATATTAAAAAGGT 26 87 0 CAGTTTTATA 0.84162 -116 AATAAATTTTAAGATTTTATAAATAATAACT 26 182 1 AAGATTTATA 0.308888 -21 AGCACCAAAAACTTTTTTATATAGTGTCTTT 27 202 0 ACTTTTTATA 0.707339 -25 ****** **** Masking position 6 Map Score: 27.7624 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 208 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 201 Fraction of orfs with sites within 600 bp upstream = 0.032284