AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_mjan_reg_300.orf -o00640_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: MJ0266 27 pyruvate ferredoxin oxidoreductase, subunit beta (porB) MJ0267 21 pyruvate ferredoxin oxidoreductase, subunit alpha (porA) MJ0538 24 M. jannaschii predicted coding region MJ0538 Input sequences: #1 MJ0210 86 succinyl-CoA synthetase, beta subunit #2 MJ0269 283 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #3 MJ0270 300 M. jannaschii predicted coding region MJ0270 #4 MJ0276 119 2-ketoglutarate ferredoxin oxidoreductase, subunit alpha (korA) #5 MJ0277 183 acetolactate synthase large subunit (ilvB) #6 MJ0278 82 peptidyl-prolyl cis-trans isomerase, FKBP-type rotamase (slyD) #7 MJ0487 282 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #8 MJ0490 47 L-lactate dehydrogenase EGAD|7256|705 #9 MJ0537 276 2-ketoglutarate ferredoxin oxidoreductase, subunit beta (korB) #10 MJ0539 267 tRNA synthetase, putative #11 MJ0541 89 conserved hypothetical protein #12 MJ0542 127 phosphoenolpyruvate synthase #13 MJ0543 132 ubiquinol-cytochrome C reductase complex, subunitVI requiring protein #14 MJ0544 103 dolichyl-phosphate mannose synthase #15 MJ0547 165 cell division inhibitor minD #16 MJ0548 111 conserved hypothetical protein #17 MJ1230 22 M. jannaschii predicted coding region MJ1230 #18 MJ1231 255 oxaloacetate decarboxylase alpha chain (oadA) #19 MJ1232 113 conserved hypothetical protein #20 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) Motif number 1 ATTTATCACCAAATTTTTTATATGATAATT 1 22 1 AAATTTTTTA 0.859838 -65 TTTTAATGCAAAATTTTAAAATTATCATAT 1 41 0 AAATTTTAAA 0.893352 -46 TTACTGTCATAAATCTTAATCTCCCAGCTT 2 15 0 AAATCTTAAT 0.624661 -269 CCATGTAAATTAATTTTATTTTTTCTTATG 2 168 1 TAATTTTATT 0.561366 -116 TTATTAAAAGTAATATATAAAGTTTTGGAG 2 227 0 TAATATATAA 0.776566 -57 TTTTTATGAAAAATTTTATATACAAAAATG 3 139 0 AAATTTTATA 0.791837 -162 TTTTTCATAAAAATATTTAAATACTTAGAA 3 156 1 AAATATTTAA 0.940634 -145 TCGCATGAGGAAATATTTTATTATATAATA 3 216 1 AAATATTTTA 0.873734 -85 TTAACGACTATAATATAATAGAGAAGAAAA 4 48 0 TAATATAATA 0.502219 -72 AACCTTGTGTTAATATTTAACGACTATAAT 4 64 0 TAATATTTAA 0.929165 -56 ATTTAATTACTAATCTTAAAGACTAAAAAT 5 35 0 TAATCTTAAA 0.772448 -149 TGTTGGTATTTAATATTTAATTACTAATCT 5 49 0 TAATATTTAA 0.929165 -135 TCATATATAAAAATTTTTATACTAAGGATT 5 118 0 AAATTTTTAT 0.845868 -66 TTTTAGTAGTTAATATTTAAT 7 2 0 TAATATTTAA 0.929165 -281 CTACTAAAATAAATTTTTATTAATTGAGAT 7 23 1 AAATTTTTAT 0.845868 -260 TTGATATTAGAAATTTTAATGGCAATCTTT 7 98 0 AAATTTTAAT 0.772834 -185 AGAAGGACGAAAATTTTTAAAATAAGAATA 7 146 1 AAATTTTTAA 0.931094 -137 CAGAACTGCTAAATTTTATTCTTTTTATAG 7 251 0 AAATTTTATT 0.60706 -32 CTTTTTAATTTAATTTTAAAATCTCTTTTG 8 16 1 TAATTTTAAA 0.874043 -32 CCACCTCAAATAATTTTTAATTTATAATGG 9 253 0 TAATTTTTAA 0.917991 -24 TTTTGGTAGTTAATATTTTAACAAATTATT 10 157 1 TAATATTTTA 0.846219 -111 ATATTATTTAAAATATAAAAATCAAAAAAT 10 208 0 AAATATAAAA 0.733093 -60 GGAATTGTTAAAATATATAATGATAAAATA 11 44 0 AAATATATAA 0.811877 -46 AAACTTTTTTTAATTTTTTATAACATTTTC 12 16 1 TAATTTTTTA 0.835539 -112 ATTTGAATGATAATATTATAAATAAAATAG 12 62 0 TAATATTATA 0.787042 -66 ATTATCATTCAAATATTTAAATTTATTTTA 12 78 1 AAATATTTAA 0.940634 -50 ATTTTTAACTTAATATTTAAAGCTTACTGT 13 18 0 TAATATTTAA 0.929165 -115 ATTGTGATGCTAATATTTTTAACTTAATAT 13 32 0 TAATATTTTT 0.69772 -101 GCATCACAATAAATTTTATATATTGGGAAT 13 52 1 AAATTTTATA 0.791837 -81 TATTACCATAAAATTTTAAAATTTTGTTAA 14 48 1 AAATTTTAAA 0.893352 -56 GGATGCTAGTAAATTTTTAACAAAATTTTA 14 64 0 AAATTTTTAA 0.931094 -40 AAGCGTGTCCTAATATTAAACCGAAGAGTA 15 89 1 TAATATTAAA 0.890613 -77 TCTAAAATCTTTATATTACCTATT 15 152 0 AAATCTTTAT 0.728604 -14 ATTTAATAACTAATATATAAGATTAACGAT 16 49 1 TAATATATAA 0.776566 -63 TAATACTAACTAATATTATTAGTCTAAGGG 16 84 1 TAATATTATT 0.600193 -28 TTTATCTCCTAAATCTTAAATTTTCTTAAT 18 108 1 AAATCTTAAA 0.803836 -148 TATCCCTCACAAATATTTATTTTGATTTAA 18 233 0 AAATATTTAT 0.865537 -23 TTATTGCCATAAATATTTATCATGGATGTC 19 43 1 AAATATTTAT 0.865537 -71 TGGATGTCAATAATCTATTATAATTTATAA 19 65 1 TAATCTATTA 0.405228 -49 TAATCTATTATAATTTATAATCATTAGTAT 19 75 1 TAATTTATAA 0.757721 -39 AGTGCCTTATAAATATATAAATTGTGAAAG 20 223 1 AAATATATAA 0.811877 -78 TTAAACCGTAAAATTTATATATCCCCTTTT 20 278 0 AAATTTATAT 0.605318 -23 ********** Masking position 6 Map Score: 48.3194 Number of sites scoring better than the average of aligned sites = 2281 Number in coding regions = 1492 Number in noncoding regions = 789 Number of orfs with sites within 600 bp upstream = 506 Fraction of orfs with sites within 600 bp upstream = 0.0812721 Motif number 2 ACCAAATTTTTTATATGATAATTTTAAAATTTTGCA 1 29 1 TTATAAATTA 0.636418 -58 GCCGATTTGATTTTTAAACAGCTTTATTGTTGAATT 2 43 0 TTTTTAATTA 0.943967 -241 TAGCAGTTCCTTTTTTAACTCCTTCAATATAATAGC 2 77 0 TTTTTATTTA 0.969062 -207 TATATATTACTTTTAATAATTGTTAATGATTGATAA 2 238 1 TTTTAATTTA 0.943967 -46 CTTCTCGGATTTTTAACAGAGTTTTTAATAATAGAT 3 39 0 TTTTAAATTT 0.737879 -262 ATTTAAATATTTTTATGAAAAATTTTATATACAAAA 3 142 0 TTTTAAATTT 0.737879 -159 AGTCCTATTTTATTTCCAATTATTTATAATTCTAAG 3 179 0 TATTTATTTA 0.748514 -122 ATGCTTCTATTTTTTTAAATTGTTATTTTCTTCTCT 4 23 1 TTTTTATTTT 0.906816 -97 TTCTATTTTTTATTTTTAGTCTTTAAGATTAGTAAT 5 24 1 TATTTATTTA 0.748513 -160 TATATCAAACTTTTTAAAGTTCTTCAAATGCTAAAT 5 85 1 TTTTTATTTA 0.969062 -99 ATGATTTCAATTTTATCATTACTTTACCCTTAACAT 5 144 1 TTTTAATTTA 0.943967 -40 TAATAAAAATTTATTTTAGTAGTTAATATTTAAT 7 9 0 TTATTATTTA 0.858179 -274 TTCGTCCTTCTTTTTCTATTTGTAAAACTTTGATAT 7 121 0 TTTTTATTAA 0.858172 -162 GTCCATATTCTTATTTTAAAAATTTTCGTCCTTCTT 7 145 0 TTATTAATTT 0.502768 -138 AATTTTATTCTTTTTATAGTATTATTTTCTTTAATA 7 234 0 TTTTTATTAT 0.652777 -49 TCGAACAACCTTTTAGAAAAGGTTGATCAAAACTTA 9 103 0 TTTTAAATTA 0.900604 -174 TCATCAAAAGTTTTTATAGTTATATAATAAACTTAT 10 74 0 TTTTTATTAA 0.858178 -194 GAAATTTGGATTTTTTGATTTTTATATTTTAAATAA 10 199 1 TTTTTATTAA 0.858178 -69 TAAGTTTTGTTTTTATGACTATTTTATCATTATATA 11 25 1 TTTTAATTTA 0.943967 -65 TTATGAAACTTTTTTTAATTTTTTATAACATTTTC 12 10 1 TTTTTATTTA 0.969062 -118 ATAGCTTTTATTTTAAAATAAATTTAAATATTTGAA 12 85 0 TTTTAAATTA 0.90059 -43 CCAATTCCTATTTTTCTACTTTTTCTTATTACCATA 14 22 1 TTTTTATTTT 0.906816 -82 GCTAGTAAATTTTTAACAAAATTTTAAAATTTTATG 14 54 0 TTTTAAATTA 0.900604 -50 TTAGATAACCTTATTCAATTAATTAATGATGTAATG 15 42 1 TTATTATTTA 0.857459 -124 AGGATAGAGATTTTTGTATTAATTAATTTAAACTCA 18 70 1 TTTTTATTTA 0.968977 -186 CCCCCACCATTTTTTAAATAACTTAAATCTTTCTGA 20 19 0 TTTTTAATTA 0.943964 -282 ***** * * ** * Masking position 4 Map Score: 36.396 Number of sites scoring better than the average of aligned sites = 948 Number in coding regions = 701 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 3 CTATAAATTTATCACCAAATTTTTTATATG 1 16 1 ATCACCAAAT 0.905242 -71 TTTTAAAATTATCATATAAAAAATTTGGTG 1 28 0 ATCATATAAA 0.566332 -59 CCTATCACCTTAAATGATAAATT 1 74 0 ATCACCTTAA 0.906787 -13 AATTGCTTAAATCTCCAAAACTTTATATAT 2 215 1 ATCTCCAAAA 0.936376 -69 ACACTCACCTTAAACTGTCATTA 2 271 0 CTCACCTTAA 0.708377 -13 CCAATCACCAAAAAATGTTAAGG 5 171 0 ATCACCAAAA 0.983383 -13 TCAATCATCAAAAATAGATAACA 10 4 1 ATCATCAAAA 0.945092 -264 ATTATAGTCAATCATCAAAAGTTTTTATAG 10 91 0 ATCATCAAAA 0.945092 -177 TGTATCACCAAAAATAGTGAAGA 11 77 0 ATCACCAAAA 0.983383 -13 AAATATTAGCATCACAATAAATTTTATATA 13 44 1 ATCACAATAA 0.857573 -89 ACTTTTTCTTATTACCATAAAATTTTAAAA 14 39 1 ATTACCATAA 0.59492 -65 AGGTAATCACAATATAAATTGGATG 14 89 0 ATCACAATAT 0.49289 -15 GGACACGCTTATCTTCAAAAACATTACATC 15 69 0 ATCTTCAAAA 0.810621 -97 AATATCACAAAAAAAGAGAAGT 17 10 0 ATCACAAAAA 0.927665 -13 ACTCAATTTTATCTCCTAAATCTTAAATTT 18 101 1 ATCTCCTAAA 0.837474 -155 ATAGTTACCCCTCATCAAAAATTGATTAAG 18 132 0 CTCATCAAAA 0.811243 -124 ********** Masking position 2 Map Score: 17.2961 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 408 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 4 AATAAATACAACATCATTTTTAGAGAAAGACTATG 2 129 1 ACATTTTTGG 0.504043 -155 TTCTTATGCCTAAACTATTTTCGTTAATTGCTTAA 2 190 1 TCTATTTTGT 0.964179 -94 TTAAGTATGTTTAACATTTTTGTATATAAAATTTT 3 125 1 TCATTTTTTT 0.818618 -176 CTCATGCGAAAGTCCTATTTTATTTCCAATTATTT 3 190 0 ACTATTTTTT 0.889982 -111 TTCTTTCTTTAATTCTATTTTTTATTTTTAGTCTT 5 12 1 ACTATTTTTT 0.889982 -172 ATTAAATACCAACACTTTTTTATATCAAACTTTTT 5 65 1 ACTTTTTTTT 0.818618 -119 TACTTTACCCTTAACATTTTTTGGTGATTGG 5 163 1 TCATTTTTGT 0.866271 -21 TTAGAAAATGTTATCTATTTTTGATGATTGA 10 7 0 TCTATTTTGT 0.964179 -261 TGACTATAATTCAGCTTTTTTGTCTAAAACTAAGT 10 111 1 TCTTTTTTTT 0.912762 -157 AATTTTTGTTTCTTCTATTTTATTGTCTATATTAT 10 231 0 TCTATTTTTG 0.872138 -37 ATTCCAAATCTTCACTATTTTTGGTGATACA 11 69 1 TCTATTTTGT 0.964179 -21 TTGTAATAACTCTACTATTTTATTTATAATATTAT 12 48 1 TCTATTTTTT 0.949376 -80 ATCATCACCTATTTTGGCTGTTTCGTTTT 13 114 0 TCTATTTTGT 0.964179 -19 CAATTCCTATTTTTCTACTTTTTCTTATTACCATA 14 23 1 TCTACTTTTT 0.690638 -81 ACTTCTCTTTTTTTGTGATATT 17 3 1 TCTTTTTTGG 0.845249 -20 AATTAATTTAAACTCAATTTTATCTCCTAAATCTT 18 90 1 ACAATTTTTT 0.777241 -166 TAAATTTTCTTAATCAATTTTTGATGAGGGGTAAC 18 124 1 TCAATTTTGT 0.920703 -132 * ******* * * Masking position 9 Map Score: 17.9267 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 245 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 AAATTTTAAAATTATCATATAAAAAATTTGGT 1 29 0 ATTATATTAA 0.748491 -58 TAAAAAGAAATTTATCATTTAAGGTGATAGG 1 66 1 TTTATATTAA 0.936159 -21 GAGGAAATATTTTATTATATAATAACACTCTT 3 222 1 TTTATATTAA 0.936139 -79 AACACAAGGTTATATTATATAAAAGTAGCTTA 4 83 1 TATATATTAA 0.835687 -37 AGTGTTGGTATTTAATATTTAATTACTAATCT 5 49 0 TTTAAATTAA 0.496727 -135 ATACCAACACTTTTTTATATCAAACTTTTTAA 5 70 1 TTTTTATTCA 0.838332 -114 AAAATTTTTATATATGATTTCAATTTTATCAT 5 131 1 TATATATTCA 0.828967 -53 ATAATGAACTTTAATAATCTCAATTAATAAAA 7 37 0 TTAATATTCA 0.78691 -246 GCCATTAAAATTTCTAATATCAAAGTTTTACA 7 105 1 TTTCTATTCA 0.654704 -178 TTCCTCTTTTTAATTTAATTTTAAAATC 8 7 1 TTTTTATTAA 0.844755 -41 CTTCTATAAGTTTATTATATAACTATAAAAAC 10 69 1 TTTATATTAA 0.936139 -199 TAAAACTAAGTTATTTATATCATTTTGGTAGT 10 135 1 TTATTATTCA 0.578096 -133 ATTTTAACAAATTATTATGTAACCTAAAGAAA 10 171 1 ATTATATTAA 0.748491 -97 TTTTATTGTCTATATTATTTAAAATATAAAAA 10 217 0 TATATATTAA 0.835684 -51 TACTATTTTATTTATAATATTATCATTCAAAT 12 60 1 TTTATATTTA 0.609456 -68 ATTCAATTAATTAATGATGTAATGTTTTTGAA 15 54 1 TTAATATTAA 0.794869 -112 GTAAAGCATATATATCATTTCAATCAATACTA 18 21 1 TATATATTCA 0.828967 -235 ATTTTTGTATTAATTAATTTAAACTCAATTTT 18 79 1 TAATTATTAA 0.332762 -177 TAGCCATAGTCTTATAATTTCAATCATAGTTA 18 155 0 CTTATATTCA 0.624563 -101 ACAAATATTTATTTTGATTTAAAAAAGGCACA 18 223 0 ATTTTATTAA 0.524783 -33 ***** ** *** Masking position 8 Map Score: 15.1816 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 434 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 6 TTTTGCATTAAAAAGAAATTTATCATTTAAGGT 1 58 1 AAAAATTTAT 0.892626 -29 GGCATAAGAAAAAATAAAATTAATTTACATGGA 2 167 0 AAAAAATTAA 0.635061 -117 AACAATTATTAAAAGTAATATATAAAGTTTTGG 2 229 0 AAAAATATAT 0.848755 -55 AGATGAATTAAAAGCAGAGATATTTAAAAAAT 3 10 0 AAAGAGATAT 0.820202 -291 CTAAAAATAAAAAATAGAATTAAAGAAAGAAA 5 10 0 AAAAAATTAA 0.635061 -174 AATAATAACAAAAAACTATTTATATACCCTTCA 6 34 1 AAAAATTTAT 0.892044 -49 AAGAGATTTTAAAATTAAATTAAAAAGAGGAA 8 10 0 AAAAAATTAA 0.634901 -38 AAGGTTGATCAAAACTTAGTTAAATAGGTATCC 9 88 0 AAAAAGTTAA 0.773315 -189 TTTAGACAAAAAAGCTGAATTATAGTCAATCAT 10 106 0 AAAGAATTAT 0.774107 -162 TTTTTTGTCTAAAACTAAGTTATTTATATCATT 10 126 1 AAAAAGTTAT 0.83509 -142 TATAAATAAAATAGTAGAGTTATTACAAGTGAA 12 43 0 ATAGAGTTAT 0.700639 -85 CTTTTATTTTAAAATAAATTTAAATATTTGAAT 12 84 0 AAAAATTTAA 0.820351 -44 ATTTTAAAATAAAAGCTATATATAATCCCCTAT 12 102 1 AAAAATATAT 0.84878 -26 CACTAAAGTTATAGTTAAGTTAAATATATACTC 15 114 0 ATAGAGTTAA 0.56255 -52 AGTGTTGTAAATAGGTAATATAAAGATTTTAGA 15 143 1 ATAGATATAA 0.537165 -23 TTACTATTTAATAACTAATATATAAGATTAACG 16 44 1 ATAAATATAT 0.62904 -68 GAACCTAAGTAAAGCATATATATCATTTCAATC 18 13 1 AAAGATATAT 0.859013 -243 TTATGGCAATAAAATAAATATATACTTATCGAT 19 22 0 AAAAATATAT 0.848775 -92 CGTCATTCCAATAGTAGATTTATTCCTGTGAAG 20 172 0 ATAGATTTAT 0.757573 -129 ATAAAAAGTAAAAGGGGATATATAAATTTTACG 20 269 1 AAAGATATAT 0.859014 -32 **** ****** Masking position 11 Map Score: 14.1361 Number of sites scoring better than the average of aligned sites = 920 Number in coding regions = 693 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 7 ACTATTTTCGTTAATTGCTTAAATCTCCAAA 2 203 1 TTAATGCTTA 0.709277 -81 ATAAAAATATTTAAATACTTAGAATTATAAA 3 162 1 TTAATACTTA 0.875735 -139 AATTTGGAATTTAAATACTCAAAGAGTGTTA 3 244 0 TTAATACTCA 0.855562 -57 ATTATAGTCGTTAAATATTAACACAAGGTTA 4 64 1 TTAATATTAA 0.786208 -56 ATTACTAATCTTAAAGACTAAAAATAAAAAA 5 29 0 TTAAGACTAA 0.842425 -155 TATTTAATATTTAATTACTAATCTTAAAGAC 5 42 0 TTAATACTAA 0.954099 -142 TAATTAAATATTAAATACCAACACTTTTTTA 5 56 1 TTAATACCAA 0.907778 -128 TTAAAGTTCTTCAAATGCTAAATCCTTAGTA 5 98 1 TCAATGCTAA 0.628243 -86 ATTAAATATTAACTACTAAAATAAATTTT 7 9 1 TTAATACTAA 0.961802 -274 TGTTAAAATATTAACTACCAAAATGATATAA 10 149 0 TTAATACCAA 0.907687 -119 ACAGTAAGCTTTAAATATTAAGTTAAAAATA 13 18 1 TTAATATTAA 0.786208 -115 ATATTACTATTTAATAACTAATATATAAGAT 16 41 1 TTAAAACTAA 0.71958 -71 **** ****** Masking position 4 Map Score: 8.51638 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 53 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 8 TTGTATTTATTTTTGAGAATGACACTATAGCAGT 2 106 0 TTTTGGATGA 0.769973 -178 TGCTTCTATTTTTTTAAATTGTTATTTTCTTCTC 4 24 1 TTTTTAATGA 0.443399 -96 TTTTGTTATTATTTTTTATGGACAAAAGCGTCAT 6 13 0 ATTTTTAGGA 0.789919 -70 TCCAAATACTTTTTGTGAAGGGTATATAAATAGT 6 48 0 TTTTGGAGGA 0.943862 -35 CACAAAAAGTATTTGGAAAGGTTAGGAG 6 65 1 ATTTGAAGGA 0.950236 -18 TGATATTAGAAATTTTAATGGCAATCTTTGAATA 7 93 0 AATTTAAGGA 0.63838 -190 TTAAAATCTCTTTTGTGAGGGGAAATT 8 31 1 TTTTGGAGGA 0.943862 -17 ATAATTTTTAATTTATAATGGATACCCCAAATAG 9 240 0 ATTTAAAGGA 0.680749 -37 ATTAAAAATTATTTGAGGTGGTAAA 9 262 1 ATTTGGGGGA 0.851373 -15 AATAGATAACATTTTCTAAGGTTATTGGTATAGA 10 23 1 ATTTTTAGGA 0.789919 -245 AAGAAACAAAAATTTTGAGGGAAATT 10 252 1 AATTTGAGGA 0.770517 -16 AATAGTGAAGATTTGGAATTGTTAAAATATATAA 11 54 0 ATTTGAATGA 0.791736 -36 CAAAATAAATATTTGTGAGGGATAGCT 18 239 1 ATTTGGAGGA 0.973203 -17 ***** ** ** * Masking position 14 Map Score: 5.44555 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 208 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 ATTTTTAGAGAAAGACTATGTAATCCATGT 2 144 1 AAAGACTATG 0.956081 -140 ATTTTTAAAATAAGAATATGGACGAAACTG 7 158 1 TAAGAATATG 0.856678 -125 AGATAAAGAGAAGGACTATGTGTGTTTTCA 13 82 0 AAGGACTATG 0.959183 -51 TATTGAACTTTAGGACTATG 15 1 0 TAGGACTATG 0.971159 -165 ATTGAAATTATAAGACTATGGCTAACCAAA 18 163 1 TAAGACTATG 0.968937 -93 ********** Masking position 5 Map Score: 2.39393 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 15 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 AGAACTTTAAAAAGTTTGATATAAAAAAGTG 5 77 0 AAAGTTTATA 0.912374 -107 CAAACTTTTTAAAGTTCTTCAAATGCTAAAT 5 90 1 AAAGTTCTCA 0.893764 -94 TCATATATAAAAATTTTTATACTAAGGATTT 5 117 0 AAATTTTATA 0.749557 -67 TGAGATTATTAAAGTTCATTATTGGATATAT 7 47 1 AAAGTTCTTA 0.943391 -236 TTCTAATATCAAAGTTTTACAAATAGAAAAA 7 116 1 AAAGTTTACA 0.840162 -167 TGAGCTTCTATAAGTTTATTATATAACTATA 10 65 1 TAAGTTTTTA 0.562097 -203 CAAAAAATCCAAATTTCTTTAGGTTACATAA 10 185 0 AAATTTCTTA 0.827298 -83 AAAATTAAAAAAAGTTTCATAA 12 2 0 AAAGTTTATA 0.912374 -126 TAAAATTTTAAAATTTTGTTAAAAATTTACT 14 56 1 AAATTTTTTA 0.776148 -48 CATAGTCCTAAAGTTCAATAAGCAAATGTT 15 10 1 AAAGTTCATA 0.935004 -156 CCTAAATCTTAAATTTTCTTAATCAATTTTT 18 115 1 AAATTTTTTA 0.776147 -141 TTTAGGCATCAAAGTGCCTTATAAATATATA 20 211 1 AAAGTGCTTA 0.724404 -90 ATAAATTGTGAAAGTTCTACAACGACACATA 20 239 1 AAAGTTCACA 0.878966 -62 ******* *** Masking position 3 Map Score: 10.7415 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 135 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 TATTGTTGAATTACTGTCATAAATCTTAATCTCC 2 21 0 TTATTCTAAT 0.943395 -263 GATGTTGTATTTATTTTTGAGAATGACACTATAG 2 110 0 TTATTTAAAT 0.700046 -174 ACTATTTTCGTTAATTGCTTAAATCTCCAAAACT 2 203 1 TTATGCTAAT 0.664877 -81 ACTTTATATATTACTTTTAATAATTGTTAATGAT 2 234 1 TTATTTAAAT 0.700046 -50 ATTTAAATACTTAGAATTATAAATAATTGGAAAT 3 170 1 TTAATTTAAT 0.5558 -131 GCCCATGCTTCTATTTTTTTAAATTGTTATTTTC 4 19 1 CTATTTTAAT 0.662347 -101 TTTCTTTCTTTAATTCTATTTTTT 5 1 1 TTTTTCTAAT 0.78276 -183 TAGTTTTTTGTTATTATTTTTTATGGACAAAAGC 6 18 0 TTATTTTTAT 0.5558 -65 ATAATGAACTTTAATAATCTCAATTAATAAAAAT 7 35 0 TTATATTAAT 0.584142 -248 TTTTATAGTATTATTTTCTTTAATAAATAGATAA 7 225 0 TTATTCTAAT 0.943395 -58 TTCCTCTTTTTAATTTAATTTTAA 8 1 1 TTCTTTTAAT 0.689236 -47 TTTTTTGATTTTTATATTTTAAATAATATAGACA 10 209 1 TTTTTTTAAT 0.79084 -59 TATTTGAATGATAATATTATAAATAAAATAGTAG 12 59 0 ATATTTTAAT 0.569619 -69 AACTATAACTTTAGTGTTGTAAATAGGTAATATA 15 131 1 TTATTTTAAT 0.945913 -35 GTTAGTATTATTATTATCGTTAATCTTATATATT 16 60 0 TTATTCTAAT 0.943395 -52 TAAACTCAATTTTATCTCCTAAATCTTAAATTTT 18 98 1 TTTTTCTAAT 0.78276 -158 TCCTAAATCTTAAATTTTCTTAATCAATTTTTGA 18 114 1 TAATTTTAAT 0.5558 -142 TATATTTATTTTATTGCCATAAATATTTATCATG 19 33 1 TTATCCTAAT 0.664877 -81 TTTATAATCATTAGTATTTTTAATAAGGGGGTTT 19 88 1 TTATTTTAAT 0.945913 -26 *** * ** * *** Masking position 14 Map Score: 14.1794 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 134 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 12 GGAGTTAAAAAAGGAACTGCTATAGTGTCA 2 91 1 AAGGAACTGC 0.971207 -193 AAGAATATGGACGAAACTGATGAATTGTAG 7 169 1 ACGAAACTGA 0.839181 -114 ATCCCACCATACAGAACTGCTAAATTTTAT 7 262 0 ACAGAACTGC 0.939109 -21 TATCTATAAAACGAAACAGCCAAAATAGGT 13 107 1 ACGAAACAGC 0.947584 -26 TAACCAAATAACGGAACTGCATTGCCGTTT 18 185 1 ACGGAACTGC 0.990076 -71 TGATTTAAAAAAGGCACAGCCAAATAAAAC 18 211 0 AAGGCACAGC 0.868599 -45 ********** Masking position 6 Map Score: 1.46751 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 38 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 CATCTATTATTAAAAACTCTGTTAAAAATC 3 38 1 TAAAAACTCT 0.72081 -263 TCTATCATGTTAATAATACTTTACATTATG 3 95 1 TAATAATACT 0.914588 -206 ACAAAAATGTTAAACATACTTAACATAATG 3 118 0 TAAACATACT 0.66177 -183 AAATTTTTCATAAAAATATTTAAATACTTA 3 153 1 TAAAAATATT 0.71179 -148 TTTTATTATATAATAACACTCTTTGAGTAT 3 231 1 TAATAACACT 0.916047 -70 GAAAATCCTATAAAACCACT 3 291 1 TAAAACCACT 0.66597 -10 TTATTAAAGAAAATAATACTATAAAAAGAA 7 233 1 AAATAATACT 0.532606 -50 TTTTCACTTGTAATAACTCTACTATTTTAT 12 41 1 TAATAACTCT 0.690269 -87 AATATTAAGTTAAAAATATTAGCATCACAA 13 31 1 TAAAAATATT 0.71179 -102 AACTAAAAACACCAATTCCTATT 14 4 1 TAAAAACACC 0.66597 -100 TTAACGATAATAATAATACTAACTAATATT 16 71 1 TAATAATACT 0.914588 -41 CCCCTTAGACTAATAATATTAGTTAGTATT 16 85 0 TAATAATATT 0.680699 -27 ACCCCCTTATTAAAAATACTAATGATTATA 19 90 0 TAAAAATACT 0.925401 -24 ********** Masking position 3 Map Score: 7.52272 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 167 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 ATGATAATTTTAAAATTTTGCATTAAAAAG 1 43 1 TAAAATTTTG 0.527959 -44 TTTTATATACAAAAATGTTAAACATACTTA 3 126 0 AAAAATGTTA 0.780215 -175 TCTATTTTTTTAAATTGTTATTTTCTTCTC 4 28 1 TAAATTGTTA 0.50853 -92 CCAATCACCAAAAAATGTTAAGGGTAAAGT 5 164 0 AAAAATGTTA 0.780215 -20 AAAAGTATTTGGAAAGGTTAGGAG 6 69 1 GGAAAGGTTA 0.695819 -14 CAACCTTTTAGAAAAGGTTGATCAAAACTT 9 104 0 GAAAAGGTTG 0.931404 -173 CAACCTTTTCTAAAAGGTTGTTCGAGTAAC 9 114 1 TAAAAGGTTG 0.910024 -163 AACCTTTTAGTAAAAGGTTACTCGAACAAC 9 130 0 TAAAAGGTTA 0.907848 -147 AACCTTTTACTAAAAGGTTGGGAGCAATGT 9 141 1 TAAAAGGTTG 0.910024 -136 AATAACCTTAGAAAATGTTATCTATTTTTG 10 19 0 GAAAATGTTA 0.927968 -249 TATTACAAGTGAAAATGTTATAAAAAATTA 12 26 0 GAAAATGTTA 0.927968 -102 CTTATTACCATAAAATTTTAAAATTTTGTT 14 46 1 TAAAATTTTA 0.399715 -58 AGTTCAATAAGCAAATGTTGTTAGATAACC 15 22 1 GCAAATGTTG 0.695818 -144 ********** Masking position 4 Map Score: 9.15055 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 288 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 15 ATTTATATACCCTTCACAAAAAGTATTTGG 6 51 1 CCTTCACAAA 0.962984 -32 AATTTCCCCTCACAAAAGAGATTTTA 8 32 0 CCCTCACAAA 0.983226 -16 AATTTCCCTCAAAATTTTTGTTTCT 10 253 0 CCCTCAAAAT 0.886862 -15 AGCTATCCCTCACAAATATTTATTTT 18 240 0 CCCTCACAAA 0.983226 -16 CGTTGTAGAACTTTCACAATTTATATATTT 20 233 0 CTTTCACAAT 0.776738 -68 ********** Masking position 6 Map Score: 1.48031 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 11 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493