AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_rpxx_reg_300.orf -o00310_rpxx_300.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RP009 300 UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE (lpxD) #2 RP179 24 DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT (sucB) #3 RP180 300 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (sucA) #4 RP215 297 unknown #5 RP216 172 CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT I (cydA) #6 RP217 93 CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT II (cydB) #7 RP218 259 unknown #8 RP219 138 MITOCHONDRIAL PROTEASE (mpp) #9 RP366 75 APOLIPOPROTEIN N-ACYLTRANSFERASE (lnt) #10 RP525 138 PROTEASE IV (sppA) #11 RP526 300 TRANSCRIPTION TERMINATION FACTOR RHO (rho) #12 RP719 300 unknown #13 RP738 300 POLY-BETA-HYDROXYBUTYRATE POLYMERASE (phbC1) #14 RP743 79 SERINE HYDROXYMETHYLTRANSFERASE (glyA) #15 RP744 102 unknown #16 RP745 52 GLUTAREDOXIN-LIKE PROTEIN GRLA (grxC2) #17 RP876 300 PROBABLE LIPOATE-PROTEIN LIGASE B (lipB) Motif number 1 TAATGTGAGAAATTTAAATTAATAATATTGATTTA 1 91 0 AATATAATAA 0.924194 -210 TTACATGTTCTACTTCAATTAATAACTTGAATCTC 1 123 1 TATATAATAA 0.932093 -178 ATTTAAATCATTATCTAAATAATAATTTGAGAAAT 3 59 1 TTTATAATAA 0.914637 -242 GAGCTATTACATTTGCACAAAAAAATAAACAATAC 3 266 1 ATTAAAAAAA 0.678871 -35 TGCTGGAATAATACCAAATAAAATACAAATT 4 7 1 AAAAAAATAA 0.852868 -291 ATAAAATACAAATTACAGTTAATAAAGTAATCTTA 4 28 1 AATATAATAA 0.924454 -270 AATTTTATCAAATTTTAAAAAATAAATACCTAAGC 4 62 1 AATAAAATAA 0.905334 -236 ATTAACACAAATTAATATTTAAGAATTGAGGTACC 4 139 0 ATAATAAGAA 0.639797 -159 TTTGAGGTATATTTTTACAAAAAAAATTTTAATAA 4 181 0 ATTAAAAAAA 0.678722 -117 TTTGTAGCATTATTTAATGTAAGAAGCAAGGCTTG 4 243 0 TATATAAGAA 0.808916 -55 TAATGCTACAAAATTCAGAAAATAACTTCAAAATC 4 266 1 AATAAAATAA 0.905336 -32 GTCAGGAAGCAAAAATATATAAAAAATTTGCTTTT 5 59 1 AAAATAAAAA 0.677185 -114 AAATAACTGTAATATGATTTAATAATTATATGTCC 5 106 0 AAAATAATAA 0.881192 -67 ATTTCTAAAAAATTTAAAAAAATAACTACTTGTCT 7 22 1 AATAAAATAA 0.905334 -238 AAGTTAAAAGTAATGTAGATAATAACCCACTCAGC 7 87 0 TATATAATAA 0.932587 -173 TAGTAAAAAATTCTGTAAATAAGAATTTTCCAA 8 9 0 TTTATAAGAA 0.76798 -130 TGTAAAATGATTATTTAGAAAATAAAAATAAATT 8 115 1 TTTAAAATAA 0.832314 -24 AAGTTTAAATATAATGAGTAAATAA 9 1 0 ATAAAAATAA 0.819164 -75 TATCGATTATTTGTTTACAAAATAATACATCATGC 9 48 0 TTTAAAATAA 0.893184 -28 AGTTAAATTTTTGACGAAGTAAAAATCAAAAATCT 10 35 1 TTAATAAAAA 0.649571 -104 AGGAATGTAGTAATTCAAAAAATAATCAGATTTTT 10 62 0 TATAAAATAA 0.915332 -77 GAGTGCACTATTAAAAATATAATAAATC 10 121 1 TTAATAATAA 0.867609 -18 TAAAACAAACTTCTCAATCTAATAATATAGAATCA 11 20 0 TTTATAATAA 0.915069 -281 TTTAAACCGCAACAAGAATAAATAAAATTTTCTAA 11 180 1 AAAAAAATAA 0.852868 -121 AGGTATTGATTACAAGCTAAAAAAGCAGTGTAG 12 9 1 ATAATAAAAA 0.621137 -292 AAATATTAGTTAATGCAGGAAATAAAATTAAGTGA 12 147 1 TATAAAATAA 0.915348 -154 ATTTTACGATTATATTAGATAATAAAGCAATAAAT 12 237 1 TAAATAATAA 0.893454 -64 GTTTATGATTTACAGCAATTAAAAATAAAGTCAAA 12 275 0 TAAATAAAAA 0.703421 -26 GTTCAGCACCTTCAGAATGTAATAACAGTATATAT 13 82 0 TTAATAATAA 0.867615 -219 GAGTATATCCTAATTAAATAAAGAATAGCATAATG 13 273 0 TATAAAAGAA 0.703832 -28 CTCAACTTTAATATTAAAGTAATAAACATATGAAA 15 67 1 ATTATAATAA 0.904437 -36 ATAGAAAGTGTATTTTAGAAAATAATATTTATATC 16 19 1 TATAAAATAA 0.915147 -34 ** * * ****** Masking position 7 Map Score: 38.1995 Number of sites scoring better than the average of aligned sites = 1246 Number in coding regions = 809 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 2 AAATTAATAATATTGATTTATTTGAGATTCATCT 1 77 0 TATTTATTTG 0.501044 -224 GTTGTTTGTATTGTTTATTTTTTTGTGCAAATGT 3 274 0 TTGTTTTTTT 0.557422 -27 TAACTGTAATTTGTATTTTATTTGGTATTATTCC 4 15 0 TTGTTATTTG 0.747793 -283 GTAATCTTAATTTTATCAAATTTTAAAAAATAAA 4 54 1 TTTAAATTTT 0.817661 -244 ACATTTAGCTTAGGTATTTATTTTTTAAAATTTG 4 70 0 TAGTTATTTT 0.768671 -228 TAATTGTTAGTTTATTAAAATTTTTTTTGTAAAA 4 170 1 TTTAAATTTT 0.817661 -128 ATTTAATATTTTGAGGTATATTTTTACAAAAAAA 4 191 0 TTGATATTTT 0.909461 -107 GAAGCAAGGCTTGTTTATTATTTTTCAATAGATT 4 222 0 TTGTTATTTT 0.927057 -76 TTCTTATGATTTTGAAGTTATTTTCTGAATTTTG 4 274 0 TTTTTATTTT 0.942739 -24 CTTGATGTTATTGTATGTAATTTTTCTGTGGCGT 5 27 1 TTGTAATTTT 0.814124 -146 AAAAGCAAATTTTTTATATATTTTTGCTTCCTGA 5 60 0 TTTATATTTT 0.928634 -113 AAAAATTTGCTTTTTATATATTTTCCGGACATAT 5 80 1 TTTATATTTT 0.928634 -93 ATTAAATCATATTACAGTTATTTTTATGGATATT 5 118 1 ATTTTATTTT 0.709525 -55 ACAATATATTTTGAGTAATATTTTATACTGCAAG 6 32 0 TTGATATTTT 0.909461 -62 CAAGTAGTTATTTTTTTAAATTTTTTAGAAATTT 7 20 0 TTTAAATTTT 0.817661 -240 AAAATTCTTATTTACAGAATTTTTTACTAAGTTG 8 15 1 TTTAATTTTT 0.307666 -124 AATTTATTTTTATTTTCTAAATAATC 8 123 0 TTTTTATTTT 0.942739 -16 AAAAATCAAAAATCTGATTATTTTTTGAATTACT 10 55 1 AATTTATTTT 0.38973 -84 GATTTATTATATTTTTAATAGTGCA 10 124 0 ATTATATTTT 0.658767 -15 TACTAGTACGTATTATTATATTTGTATTTACTGT 11 55 0 TATATATTTG 0.442482 -246 TCAAATTAGATTTTAGAAAATTTTATTTATTCTT 11 193 0 TTTAAATTTT 0.817661 -108 ACATTTGCATTTTACGATTATATTAGATAATAAA 12 229 1 TTTTTATATT 0.470111 -72 AATAAATATGTTTGACTTTATTTTTAATTGCTGT 12 265 1 TTTTTATTTT 0.942739 -36 TCACGGTATCTAGTCGTTTATTTTTCTTTGTACT 14 11 1 TAGTTATTTT 0.768671 -69 TGAAAATCCATTTTCTTTCATTTTAGAGTTTAAA 17 191 0 TTTTCATTTT 0.635809 -110 *** ******* Masking position 11 Map Score: 20.2597 Number of sites scoring better than the average of aligned sites = 953 Number in coding regions = 632 Number in noncoding regions = 321 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 3 TTATTAATTTAAATTTCTCACATTACATGTTC 1 101 1 AAATTCTACA 0.88847 -200 ATAATGATTTAAATTACTAAAATCACCCCTTA 3 41 0 AAATTCTAAA 0.959072 -260 TAACGAACCGAAATTTCTCAAATTATTATTTA 3 74 0 AAATTCTAAA 0.959072 -227 TAATTTTATCAAATTTTAAAAAATAAATACCT 4 61 1 AAATTTAAAA 0.578934 -237 CGCCACAGAAAAATTACATACAATAACATCAA 5 28 0 AAATTCAACA 0.515288 -145 TATAAAAAGCAAATTTTTTATATATTTTTGCT 5 66 0 AAATTTTATA 0.468531 -107 GCAGTATAAAATATTACTCAAAATATATTGTA 6 35 1 ATATTCTAAA 0.626382 -59 GTTCTGTGAAAATTTCTAAAAAATTTAAAAA 7 10 1 AAATTCTAAA 0.959072 -250 TCACAAATTTTACTTCTTTAAAATATCATTCT 7 142 0 TACTTTTAAA 0.721449 -118 GCGACGAAGCAACTTAGTAAAAAATTCTGTAA 8 26 0 AACTTGTAAA 0.818087 -113 ATTATATTTAAACTTGCTGAAATGATAGCATG 9 21 1 AACTTCTAAA 0.95439 -55 TTTTGATTTTTACTTCGTCAAAAATTTAACTT 10 34 0 TACTTGTAAA 0.558695 -105 GAATAAATAAAATTTTCTAAAATCTAATTTGA 11 195 1 AATTTCTAAA 0.827171 -106 GTAAGTAATATACTTATTTAAATTAGGAATCA 11 224 0 TACTTTTAAA 0.721449 -77 CCAGTTAGTGAAATTCTTGAAAAGATGTAAGA 12 53 1 AAATTTTAAA 0.911528 -248 TGAGTACACTAAATTCTTGACAAAAAGCTGAA 13 130 0 AAATTTTACA 0.777905 -171 ACAAATAAACAACTTTTTAAAATCCTATCTGA 13 159 0 AACTTTTAAA 0.901963 -142 ATATAAATATTATTTTCTAAAATACACTTTCT 16 21 0 TATTTCTAAA 0.573987 -32 TTCAACATCTAAATCACTAAAAACATTACTAA 17 228 0 AAATCCTAAA 0.713041 -73 ***** ** *** Masking position 4 Map Score: 12.02 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 317 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 CTAATATAGTAATTTTAAACTAAATTTGAGA 1 154 0 AATTTAAACT 0.922186 -147 TAGTAATTTAAATCATTATCTAAATAATAAT 3 54 1 AATATTATCT 0.736831 -247 TCATTATCTAAATAATAATTTGAGAAATTTC 3 66 1 AATATAATTT 0.835896 -235 TTAATAAAGTAATCTTAATTTTATCAAATTT 4 46 1 AATTTAATTT 0.877791 -252 TCAATTCTTAAATATTAATTTGTGTTAATTG 4 145 1 AATTTAATTT 0.877791 -153 TATACCTCAAAATATTAAATCTATTGAAAAA 4 205 1 AATTTAAATC 0.723456 -93 TCAGCCATAGAATAATAAACCATTGCCACAC 7 61 0 AATATAAACC 0.815091 -199 TTTTCTGTAAAATGATTATTTAGAAAATAAA 8 110 1 AATATTATTT 0.540914 -29 CTCAATTTTCAATTATAATCTATTAATAATA 11 275 1 AATATAATCT 0.923684 -26 CAATTCCCATAATTATTAACTCTTACATCTT 12 74 0 AATATTAACT 0.66483 -227 TTTCGTAACAAATTTTAATCCCAATACAATT 12 100 0 AATTTAATCC 0.897631 -201 AATTGCTGTAAATCATAAACT 12 290 1 AATATAAACT 0.895635 -11 ACTCAACTTTAATATTAAAGTAATAAACATA 15 66 1 AATTTAAAGT 0.742546 -37 CTATTACTACAATATTAATTTATTACTTTAA 17 21 0 AATTTAATTT 0.877791 -280 AAACTACAGGAATTTTAAACTCTAAAATGAA 17 178 1 AATTTAAACT 0.922186 -123 TAACATTTCCAATATTAATGCATCTAAAATT 17 268 0 AATTTAATGC 0.676331 -33 TAATATTGGAAATGTTAATCTGAATTAAT 17 282 1 AATTTAATCT 0.944666 -19 *** ******* Masking position 6 Map Score: 15.302 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 143 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 TTAGTTTAAAATTACTATATTAGTATTTTTAT 1 162 1 ATTACTTATA 0.797904 -139 TTACAATTTTATTGCATAATAAAAGCATAACT 1 240 1 ATTGCAAATA 0.908877 -61 TAAAATTAAGATTACTTTATTAACTGTAATTT 4 37 0 ATTACTTATA 0.797904 -261 CTGCAAGCAAATTGCTGTATAATACAAA 6 7 0 ATTGCTTATA 0.968949 -87 CAGCAATTTGCTTGCAGTATAAAATATTACTC 6 22 1 CTTGCATATA 0.885088 -72 TTGGATGCAAATTGCATTATGACAATGTAGGC 6 67 1 ATTGCATATA 0.979934 -27 TTTCCTTGCAATTGCAATATAAAATAT 7 243 1 ATTGCATATA 0.979934 -17 TAACTGTGTGAGTGCACTATTAAAAATATAAT 10 112 1 AGTGCATATA 0.885088 -27 AAACATATTTATTGCTTTATTATCTAATATAA 12 246 0 ATTGCTTATA 0.968949 -55 TAAATAAAGAATAGCATAATGAAGATAAACGT 13 262 0 ATAGCAAATA 0.670745 -39 TATTAAATGAATAGCAATAGCAAACAAAACAA 15 33 0 ATAGCATAGA 0.759101 -70 ATATTGCTATAGAAAGTGTATTTT 16 3 1 ATTGCTTAGA 0.907906 -50 TATAATCAATATTGCAGTATTTAGCAAAATGT 17 122 1 ATTGCATATT 0.838627 -179 ****** *** * Masking position 9 Map Score: 11.7363 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 96 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 GGTATATTTTTACAAAAAAAATTTTAATAA 4 181 0 TACAAAAAAA 0.747252 -117 TATTTTATACTGCAAGCAAATTGCTGTATA 6 18 0 TGCAAGCAAA 0.890413 -76 ATATTGCAATTGCAAGGAAATTAAAAACTC 7 233 0 TGCAAGGAAA 0.958274 -27 TGAGAACAACTACAAGGAATGTAGTAATTC 10 81 0 TACAAGGAAT 0.882565 -58 TACTTTTACATACATAGAAAGCGCCTATAA 11 130 1 TACATAGAAA 0.762314 -171 AGGTATTGATTACAAGCTAAAAAAGCAGTG 12 11 1 TACAAGCTAA 0.726695 -290 TTTATCAGTATACAAGGAAAAACAGGTAAT 12 188 1 TACAAGGAAA 0.981621 -113 AGTACTTGAGTACAAATAAACAACTTTTTA 13 172 0 TACAAATAAA 0.747252 -129 GTTACTACAGTACAAAGAAAAATAAACGAC 14 23 0 TACAAAGAAA 0.957971 -57 ATGTAAAATTTACAAGGAAACATTGGTGTA 17 77 0 TACAAGGAAA 0.981621 -224 ********** Masking position 4 Map Score: 7.45043 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 26 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 AATAAATCAATATTATTAATTTAAATTTCTCACATTACATGT 1 89 1 TTTATTATTA 0.960963 -212 AAACTAAATTTGAGATTCAAGTTATTAATTGAAGTAGAACAT 1 127 0 TTTAATAATA 0.643389 -174 AATCTCAAATTTAGTTTAAAATTACTATATTAGTATTTTTAT 1 152 1 TTTAATAATA 0.643377 -149 ATAAACTTTAACTGACTTAATCACTAGCGATAT 1 278 0 TTTAATATTA 0.931129 -23 TAAAATTTGATAAAATTAAGATTACTTTATTAACTGTAATTT 4 37 0 TTTAGTATTA 0.78218 -261 TTTATTATTTTTCAATAGATTTAATATTTTGAGGTATATTTT 4 201 0 TTAATTATTA 0.625472 -97 TTCTTATGATTTTGAAGTTATTTTCTGAATTTTGTAGC 4 270 0 TTTAATATTA 0.931129 -28 TCCATAAAAATAACTGTAATATGATTTAATAATTATATGTCC 5 106 0 TGTATTATTA 0.712245 -67 TTACAGTTATTTTTATGGATATTACCTCTTCAGGATCAGGAA 5 129 1 TTGATTATTA 0.712245 -44 ATTATCTACATTACTTTTAACTTATATAGTTAAATTAGTGTT 7 99 1 TTTAATATTA 0.931129 -161 TCTACGCATTTCATTTTTCTGTAAAATGATTATTTAGAAAAT 8 96 1 TTTCTTATTA 0.701778 -43 GTTTGTTATTGATTCTATATTATTAGATTGAGAAG 11 4 1 TTTATCATTA 0.874962 -297 TATTTGTATTTACTGTTAAAACAAACTTCTCAATCTAATAAT 11 29 0 TTTAACATTA 0.793522 -272 GTATATTACTTACCTTTAAACTTAATTGCTAACTCAATTTTC 11 243 1 TTTAATATTA 0.931129 -58 CATTTGCATTTTACGATTATATTAGATAATAAAGCAATAAAT 12 230 1 TATATTATTA 0.625345 -71 CTGAAGGTGCTGAACTTAATACAATATATTCAGCTTTTTGTC 13 102 1 TTTATCATTA 0.874918 -199 GTATATGCTCTGTTCTTCATATTAAGCTCTTAGCTCTTTTTA 13 220 1 TTTATTACTA 0.734125 -81 TGTTTGCTATTGCTATTCATTTAATATACTCAACTTTAATAT 15 39 1 TTTATTATTA 0.960963 -64 GGTTTACTTTATTTCATATGTTTATTACTTTAAT 15 79 0 TTTATTATTA 0.960963 -24 TTTTAGAAAATAATATTTATATCAGGTTTTGA 16 31 1 TTTATTATTA 0.960963 -22 GAAAATCCATTTTCTTTCATTTTAGAGTTTAAAATTCCTGTA 17 182 0 TTTATTAGTA 0.734125 -119 * ** ** * * * * * Masking position 20 Map Score: 22.1239 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 97 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 TGAATACTAAGTAATCTCTAAATAAAAGAACT 1 22 1 GTAACTTAAA 0.915436 -279 ATAAACTTTAACTGACTTAATC 1 289 0 ATAACTTAAC 0.825876 -12 ATCTCAGAATATAACCTATAAATATTTCTCTT 3 182 0 ATAACTTAAA 0.961809 -119 TTGTAAACAAATAATCGATAAAA 9 63 1 ATAACGTAAA 0.958905 -13 ATTTTCAATTATAATCTATTAATAATAAAATA 11 279 1 ATAACTTTAA 0.761749 -22 ATTATCTAATATAATCGTAAAATGCAAATGTT 12 228 0 ATAACGAAAA 0.749527 -73 ATAACAGTATATATGCTCTAAAGTTTTAGGGG 13 64 0 ATATCTTAAA 0.779942 -237 CATAATGAAGATAAACGTTAAAAAGAGCTAAG 13 248 0 ATAACGTAAA 0.958905 -53 GTTTTGGTTTATACTCGTTAAATCTATTACTA 17 43 0 ATACCGTAAA 0.830861 -258 ATATAGAGCTGTAAGCTTTAAACTACAGGAAT 17 159 1 GTAACTTAAA 0.915436 -142 TACAGGAATTTTAAACTCTAAAATGAAAGAAA 17 182 1 TTAACTTAAA 0.798649 -119 **** ** **** Masking position 3 Map Score: 6.26654 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 43 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 TTTATTTTACTCCTAAAAACGG 2 3 0 TCCTAAAAAC 0.900225 -22 TGATTTAAATTACTAAAATCACCCCTTAAT 3 39 0 TACTAAAATC 0.904241 -262 TCAGCCGATTTACTAAAAAGTGCTAGTGAT 3 112 1 TACTAAAAAG 0.848994 -189 AAATAAACAATACAAACAACAAT 3 288 1 TACAAACAAC 0.802382 -13 GGTATATTTTTACAAAAAAAATTTTAATAA 4 181 0 TACAAAAAAA 0.650279 -117 CTGTGAAAATTTCTAAAAAATTTAAAAAAA 7 14 1 TTCTAAAAAA 0.678847 -246 TGTAAAAGTATACTAACAACGTAATAGCAC 11 110 0 TACTAACAAC 0.935924 -191 AAATAAAATTTTCTAAAATCTAATTTGATT 11 199 1 TTCTAAAATC 0.748996 -102 TACAGATAAATACTAAAAACATATGAGGAT 14 58 1 TACTAAAAAC 0.971404 -22 ACATCTAAATCACTAAAAACATTACTAATT 17 226 0 CACTAAAAAC 0.876304 -75 ********** Masking position 5 Map Score: 3.27222 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 86 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 GATTACTTAGTATTCATAGATACGATA 1 7 0 TATTCAAGAT 0.949727 -294 GTAGTTCTTTTATTTAGAGATTACTTAGTAT 1 25 0 TATTTAAGAT 0.939917 -276 AAACCTTAGCTATTCAAAGATGAATCTCAAA 1 60 1 TATTCAAGAT 0.949727 -241 AGAAGAGAAATATTTATAGGTTATATTCTGA 3 180 1 TATTTAAGGT 0.857225 -121 TTATAGGTTATATTCTGAGATCTTTTATGTC 3 193 1 TATTCTAGAT 0.882693 -108 ATAGATTTAATATTTTGAGGTATATTTTTAC 4 198 0 TATTTTAGGT 0.705144 -100 GGAAAATTCTTATTTACAGAATTTTTTACTA 8 13 1 TATTTAAGAA 0.665294 -126 ATTGATTCTATATTATTAGATTGAGAAGTTT 11 18 1 TATTATAGAT 0.861709 -283 TATTTTATTATTAATAGATTATAATTGAA 11 282 0 TATTAAAGAT 0.939917 -19 TTCAAGATTTTATGAAAAGATATTTCCCCTA 13 39 1 TATGAAAGAT 0.74658 -262 ATTAATATTGTAGTAATAGATTTAACGAGTA 17 33 1 TAGTAAAGAT 0.74658 -268 ****** **** Masking position 8 Map Score: 5.77494 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 49 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 AATCTCAAATAAATCAATATTATTAATTTA 1 82 1 AAATCAATAT 0.621057 -219 TTTGTATTATACAGCAATTTGCTTGCAGTA 6 11 1 ACAGCAATTT 0.886431 -83 ATTTGCATCCAATACAATATATTTTGAGTA 6 49 0 AATACAATAT 0.669823 -45 ACATTGTCATAATGCAATTTGCATCCAATA 6 65 0 AATGCAATTT 0.83957 -29 TTTCCTTGCAATTGCAATATAAAATAT 7 243 1 ATTGCAATAT 0.869238 -17 ATTAGATAATAAAGCAATAAATATGTTTGA 12 250 1 AAAGCAATAA 0.659612 -51 TTTATGATTTACAGCAATTAAAAATAAAGT 12 279 0 ACAGCAATTA 0.614521 -22 TGCTGAACTTAATACAATATATTCAGCTTT 13 109 1 AATACAATAT 0.669823 -192 TACACTTTCTATAGCAATAT 16 1 0 ATAGCAATAT 0.885062 -52 TAAATCTATTACTACAATATTAATTTATTA 17 27 0 ACTACAATAT 0.72313 -274 AATATTGATTATATCAATTTCCATTATCAT 17 105 0 ATATCAATTT 0.459403 -196 TTTGCTAAATACTGCAATATTGATTATATC 17 120 0 ACTGCAATAT 0.913375 -181 TGTTGAAACCATAGCAATTTTAGATGCATT 17 253 1 ATAGCAATTT 0.831095 -48 ********** Masking position 6 Map Score: 6.6351 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 198 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 12 TCTTTGAATAGCTAAGGTTTTTGTGTAGTT 1 50 0 GCTAAGGTTT 0.880234 -251 TATTATATAAGTTATGCTTTTATTATGCAA 1 251 0 GTTATGCTTT 0.907348 -50 ACACATTAGGGTTAATGTTTTCCTCATCAC 3 137 0 GTTAATGTTT 0.80319 -164 CTGTCTTGATGTTATTGTATGTAATTTTTC 5 23 1 GTTATTGTAT 0.676363 -150 TAGACAAGTAGTTATTTTTTTAAATTTTTT 7 28 0 GTTATTTTTT 0.647481 -232 TAAAAGTGTGGCAATGGTTTATTATTCTAT 7 56 1 GCAATGGTTT 0.790079 -204 GTTTGTTATTGATTCTATATTATT 11 5 1 GTTATTGATT 0.80319 -296 TCTTCATTATGCTATTCTTTATTTAATTAG 13 269 1 GCTATTCTTT 0.907348 -32 GTTTGCTATTGCTATTCATTTAATATACTC 15 40 1 GCTATTCATT 0.708442 -63 TTGGTGTAGGGTTTTGGTTTATACTCGTTA 17 55 0 GTTTTGGTTT 0.737159 -246 ATCTAAAATTGCTATGGTTTCAACATCTAA 17 248 0 GCTATGGTTT 0.967343 -53 ********** Masking position 10 Map Score: 1.79593 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 84 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 ********** No masking Map Score: -1.3441e-11 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: -1.3441e-11 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 15 ********** No masking Map Score: -1.3441e-11 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