AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_rpxx_reg_300.orf -o00190_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 Purged sequences: RP022 33 ATP SYNTHASE C CHAIN (atpE) RP040 24 30S RIBOSOMAL PROTEIN S18 (rpsR) RP124 30 PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR (htrA) Input sequences: #1 RP024 51 unknown #2 RP025 90 unknown #3 RP039 300 30S RIBOSOMAL PROTEIN S6 (rpsF) #4 RP042 158 CELL CYCLE PROTEIN MESJ (mesJ) #5 RP043 50 CELL DIVISION PROTEIN FTSH (ftsH) #6 RP044 244 SUCCINATE DEHYDROGENASE IRON-SULFUR PROTEIN (sdhB) #7 RP114 71 PROTEIN-EXPORT MEMBRANE PROTEIN SECF (secF) #8 RP115 163 NADH DEHYDROGENASE I CHAIN F (nuoF) #9 RP122 98 HFLK PROTEIN (hflK) #10 RP123 143 HFLC PROTEIN (hflC) #11 RP125 104 unknown #12 RP126 137 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT (sdhC) #13 RP127 158 SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN (sdhD) #14 RP128 133 SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT (sdhA) #15 RP191 300 CYTOCHROME C OXIDASE POLYPEPTIDE III (coxC) #16 RP264 300 unknown #17 RP265 102 ISOCITRATE DEHYDROGENASE (icd) #18 RP266 90 unknown #19 RP267 83 unknown #20 RP269 76 unknown #21 RP282 300 NADH DEHYDROGENASE I CHAIN N (nuoL3) #22 RP283 51 NADH DEHYDROGENASE I CHAIN L (nuoL2) #23 RP284 300 NADH DEHYDROGENASE I CHAIN N (nuoN2) #24 RP346 112 CYTOCHROME C OXIDASE ASSEMBLY FACTOR (ctaB) #25 RP353 66 NADH DEHYDROGENASE I CHAIN E (nuoE) #26 RP354 209 NADH DEHYDROGENASE I CHAIN D (nuoD) #27 RP357 130 NADH DEHYDROGENASE I CHAIN A (nuoA) #28 RP359 300 unknown #29 RP405 78 CYTOCHROME C OXIDASE POLYPEPTIDE I (coxA) #30 RP406 300 CYTOCHROME C OXIDASE POLYPEPTIDE II (coxB) #31 RP537 300 NADH DEHYDROGENASE I CHAIN N (nuoN1) #32 RP585 300 unknown #33 RP587 147 SCO2 PROTEIN PRECURSOR (sco2) #34 RP588 101 CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCME (ccmE) #35 RP589 128 INORGANIC PYROPHOSPHATASE (ppa) #36 RP780 245 unknown #37 RP782 175 unknown #38 RP784 254 VIRB4 PROTEIN PRECURSOR (virB4) #39 RP785 112 unknown #40 RP787 55 unknown #41 RP789 87 unknown #42 RP790 72 NADH DEHYDROGENASE I CHAIN J (nuoJ) #43 RP793 149 NADH DEHYDROGENASE I CHAIN M (nuoM) #44 RP796 143 NADH DEHYDROGENASE I CHAIN H (nuoH) #45 RP798 173 unknown #46 RP799 152 ACONITATE HYDRATASE (acnA) #47 RP800 113 ATP SYNTHASE EPSILON CHAIN (atpC) #48 RP801 108 ATP SYNTHASE BETA CHAIN (atpD) #49 RP802 86 ATP SYNTHASE GAMMA CHAIN (atpG) #50 RP803 136 ATP SYNTHASE ALPHA CHAIN (atpA) #51 RP804 118 ATP SYNTHASE DELTA CHAIN (atpH) #52 RP805 249 DIHYDROLIPOAMIDE DEHYDROGENASE (pdhD) #53 RP806 300 unknown Motif number 1 TTATTTCAATAAAAATATATACTTTATAATAGAAGCA 2 15 0 AATATTATTT 0.482372 -76 GCCTTTGTCTTTGTTTATTTAATTTTTTATGTCATTT 3 95 1 TTTATTATTT 0.691526 -206 AACAAATTAATAAGATTTTTAATTTTTGAAGATAATA 3 201 1 TATTTTATTT 0.912738 -100 TATAAATACCTTTATTTTAAAGTTTGTTTATTGGAGA 3 262 1 TTTTTAATTT 0.79814 -39 ATAGTACCGATAAAATTTTTATTAGGTTTTATATCG 5 25 1 TATTTTATAT 0.806969 -26 ATTTTTATGTATAAATTTATAGATTTTTACGGGACAT 6 133 1 AATTTTAATT 0.56024 -112 TCTCTTAAAATTGATTTTATACATTTTGTCTATATCA 6 210 0 TTTTTTAATT 0.754009 -35 AAAACGTTTAACCTTTTTGAATTTACTATATAATACA 7 14 1 ATTTTAATTT 0.751588 -58 TGAATAAAAGTTATATTTGTATTATATAGTAAATTCA 7 31 0 TATTTTATAT 0.806969 -41 TTCAAAATACTAGTATTTTTAGTTATTTTTCCTTCGA 8 53 1 TATTTTATTT 0.912738 -111 TTGCTTTTTTATATTATTTTAAGATTA 9 82 0 TTTTTTAATT 0.754009 -17 AACTTTAATTTAATTTAAAATTGTTACTGCTTAGC 11 80 0 TATTTAATTT 0.676241 -25 CAGAAAATTATTATATTTGTATTTCTTGGTTATGAAG 12 32 0 TATTTTATTT 0.912738 -106 TGAAACTAAGAGTTTTTTATAGTTGATACTATGGTCA 12 67 1 ATTTTTATTT 0.93669 -71 ACTATAGTATTAAATTTTATTATTTTTATATTGAATA 12 108 1 TTTTTTTTTT 0.777825 -30 GTGAGATAAAACGAATTTTTAATTTTTTAAAAATAGT 13 32 1 AATTTTATTT 0.881766 -127 GACTTTATTAAATGATTTTTATTTCATTTCAGAACAA 13 85 0 AATTTTATTT 0.889146 -74 GTTTTATTTTATCATTTTCTAATTAATACTGCAAAAT 15 273 0 ATTTTTATTT 0.935439 -28 TCTTTTTAAAAAGCATTTTTAATTATTTTTTGGATTG 16 208 0 AATTTTATTT 0.889092 -93 TTTTCAAATCTTTCATTTAAAGTTAATAGATGATAAT 21 229 0 TATTTAATTT 0.681884 -72 GATGATATACAGAATTTTTAAATTTTTCTATATTACT 23 75 1 ATTTTAATTT 0.629903 -226 AAGAAATGTATATATTTTTTTGTAATTAAAAAGTTAA 24 22 0 TTTTTTTTAT 0.583204 -91 TTTAACCTAATATTTTTTATATTTAATTAAAAAATAT 24 81 1 TTTTTTATTT 0.950726 -32 TATTTTTGTTATTTATTTCTAGATTTTCTATACTTAT 26 181 0 AATTTTAATT 0.560267 -29 ATGTTTTTATTATTTATATGTTACTAC 27 114 0 ATTTTTTTTT 0.728559 -17 TCAGTTTATATTCGTTTTCTATTTTTTTTCAAATTTT 28 71 1 TTTTTTATTT 0.950726 -230 CTATAGTATATAATATTTAAAATATATTTTGATCT 28 276 1 TATTTAATAT 0.459871 -25 ACAATAGATCAACCTTATATAATAAATGTACTTTTAA 29 24 1 ATTATTATAT 0.407255 -55 AGCAATTGTAATTTTTATAAATTTTATATTAAAAG 29 54 0 TTTTTTAATT 0.754005 -25 ATTAACGAGCAAAAATTTTAAGTTTTTTCACATTTGT 30 48 1 AATTTAATTT 0.616604 -253 ACTAATGTGGTAACTTATATACTTGCT 30 284 1 TTTATTATTT 0.691526 -17 TCACTAAATGTTAATTTTATTATTGCTGATAACTTAC 31 43 0 TTTTTTTTTT 0.777825 -258 TTATGGCGAAATAATTTTATTTTTATTGTATGTAGTA 31 189 1 ATTTTTTTTT 0.728603 -112 GCTATTAGGTAGCTATTTTTATTTTATTAGACTTCTT 32 124 1 AATTTTATTT 0.88913 -177 TACTATGTGCTGGGTTTTTTACAAATTTACCATTATT 32 174 0 TTTTTTAAAT 0.550579 -127 AGTTGTCGATAATGATTTTTATTATATTATTGTGTAC 33 13 1 AATTTTATAT 0.76223 -135 TTGTTAATAGTAAATTTTTTAAATTATAAAATATTAA 34 57 1 TTTTTTAATT 0.753999 -45 TAAAGTTTTGTTTATTTTTTAATATTTTATAATTTAA 34 75 0 TTTTTTATAT 0.885206 -27 AACTGATACTTTAAATTTTTTATAGATACCGTAGTCA 35 36 0 TATTTTTTAT 0.431344 -93 CAGTTGTTGCAACATTTTTAACTAGATGCCGTGTTCA 35 68 1 ATTTTAATAT 0.54716 -61 GTTTTTGTTTTATTTTTTTTGTCATGCAGC 35 109 0 TTTTTTTTTT 0.777826 -20 AATTTTTTGTGATTTTTATATTAAATTTTTAAATTA 36 10 1 TTTTTTATAT 0.885212 -236 GAATATTATAAACCTTTTTTAATAATTG 37 2 0 ATTTTTATAT 0.855349 -174 CTATCTACTTTTCATTATTTACTTATT 37 159 1 TTTATTATTT 0.691526 -17 AACTTTACCTTATTATTTATATTTAATAAAGAA 38 7 0 TATTTTATTT 0.912738 -248 ATTTAAATTATAGATTTTTTACTATATTATTGCACCG 38 218 0 TTTTTTATAT 0.885212 -37 TTGATGCTCGTTGTTTTTATAATTCATAATAAACTAT 39 75 0 TTTTTTATTT 0.950724 -38 GGATATATAATGTTTTTTTTATTTTGTAAGCAACAAT 40 28 1 TTTTTTATTT 0.950726 -28 TGCGCATTTATAGTTTTTATTATTACTACACTTATTG 43 76 1 TTTTTTTTTT 0.777825 -74 AATGTTATTTGATTTTTAATTAATCATCATTGCA 44 120 0 TATTTTATTT 0.912738 -24 ATCTAGTAAAACAAATATTTACTTCCTATATCAAGAT 45 92 0 AATATTATTT 0.482372 -82 CACGGGGGCCAGTCTTTTTTATTTTTTATGAATCCCG 48 43 1 ATTTTTATTT 0.936692 -66 ATCGTTGTTTTATATTTTTTAGTTTTTAAGTACTAGT 52 25 1 TTTTTTATTT 0.950726 -225 AAAAGAGCTAAATGTTTTATATTTCTTAACTGCAATA 52 65 0 ATTTTTATTT 0.936692 -185 TTTATTTTTATTTTATTGGTTCTATTT 52 233 0 TTTTTATTTT 0.417742 -17 ACTTCTATTCTTTTTTAGTACTTAATTTCCGTC 53 7 1 ATTTTTATAT 0.855357 -294 TTTCCGTCATATTATTTTATATATGGTAATTCAAGAC 53 36 1 ATTTTTAATT 0.701527 -265 AAGACAATCAAATGTTTTGTATTAGATAATTTTCTTA 53 68 1 ATTTTTATAT 0.855357 -233 TTTGTATTTAAAAATTTTTAATTAAATAATTAATATA 53 188 1 ATTTTAATAT 0.54716 -113 ATTAAATTATATAATTTTCTATTATATATTAATTATT 53 212 0 ATTTTTATAT 0.855351 -89 * **** ** ** * Masking position 8 Map Score: 60.2309 Number of sites scoring better than the average of aligned sites = 964 Number in coding regions = 629 Number in noncoding regions = 335 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 2 ACAAATTAATAAGATTTTTAATTTTTGAAGATAA 3 202 1 AAGATTTATT 0.66982 -99 TATAGCAACTAAAACTATTAAATTCAAGTATTAT 3 232 0 AAAATTTATT 0.920227 -69 ATAATTATTAATTATTTTAACTTTCGTATAAAAA 6 50 0 ATTATTAATT 0.637012 -195 TAAAATTGCGAAAAATTGTAATTTGTAGTGAAAA 6 84 1 AAAATGTATT 0.820915 -161 TTACGGTATAATTAGTTGTAAATT 8 1 0 ATTATGTATT 0.679621 -163 AATAACTAAAAATACTAGTATTTTGAACTGAATC 8 46 0 AATATGTATT 0.775353 -118 GCTTTTTTATATTATTTTAAGATTAAGTGATTAT 9 73 0 ATTATTAATT 0.637034 -26 TTAGTTTCAGAAAATTATTATATTTGTATTTCTT 12 42 0 AAAATTTATT 0.899396 -96 TCAACTATAAAAAACTCTTAGTTTCAGAAAATTA 12 59 0 AAAATTTATT 0.920228 -79 ATTAAATTTTATTATTTTTATATTGAATAGTT 12 116 1 ATTATTTATT 0.842143 -22 ACTATTTTTAAAAAATTAAAAATTCGTTTTATCT 13 35 0 AAAATAAATT 0.668083 -124 TTAATTTTTTAAAAATAGTATGTTTATATTTGCG 13 50 1 AAAATGTATT 0.820912 -109 ATACCGTATCAAAAGTAAAAAATTAATTGA 14 114 1 AAAATAAATT 0.668021 -20 GTAGTTTGAGATAACTGTTACATTAATAACATTA 18 59 1 ATAATTTATT 0.876266 -32 TAAGATGACTATTATTAATAAATTTTTTTTTGAG 20 46 1 ATTATATATT 0.739126 -31 GTAGTTTTATAAAACTTTTAGCTTTTAGAATATG 21 90 1 AAAATTTATT 0.920228 -211 GTAATATAGAAAAATTTAAAAATTCTGTATATCA 23 77 0 AAAATAAATT 0.659984 -224 CTTAATTACGAAGATTGTTACATTGAACAATCTT 23 260 0 AAGATTTATT 0.669912 -41 ATTAAATATAAAAAATATTAGGTTAAAAATCAAT 24 74 0 AAAATTTATT 0.920229 -39 AAATATCAATAATATTGATATTTTTAACTAAATG 26 124 0 AATATATATT 0.821536 -86 ATGTTTTTATTATTTATATGTTACTACGTAGC 27 109 0 ATTATATATT 0.739126 -22 TGTAATTTTTATAAATTTTATATTAAAAGTACAT 29 49 0 ATAATTTATT 0.876265 -30 ATTAACGAGCAAAAATTTTAAGTTTTTTCACATT 30 48 1 AAAATTTATT 0.920229 -253 TTTATGGCGAAATAATTTTATTTTTATTGTATGT 31 188 1 AATATTTATT 0.896739 -113 ATGTTCCCATAATAATATTAGTTTAT 31 285 1 AATATTTATT 0.896862 -16 TTAGCATATAAATATTTAAATGTTTAATTAGATA 32 49 0 AATATAAATT 0.585695 -252 TAAGATAGCTAATAATGGTAAATTTGTAAAAAAC 32 164 1 AATATGTATT 0.775556 -137 AATATAACGTATAATTTAAAAATTTAATATAAAA 36 24 0 ATAATAAATT 0.552724 -222 TAATCCAGTAAAAATTTTTAATTTACAGCGTTTT 38 151 0 AAAATTTATT 0.920101 -104 GGATTACTTCAAAACTGATAATTTTTGATGACTA 38 179 1 AAAATATATT 0.8596 -76 TATTCACGTAAAAAATTTTAACTTCTACAAATTT 39 30 1 AAAATTTATT 0.920228 -83 ATTATTCAAAATTTTGTAAATTGC 43 136 0 ATTATAAATT 0.482285 -14 ATTCAAAAAAATAACTTTAATCTTGATATAGGAA 45 73 1 ATAATTAATT 0.699586 -101 AAAGTTAAGTATAAGTTTTAAGTTCTCATTAAGT 46 39 1 ATAATTTATT 0.876266 -114 ATTTAGTGGAATTACTTTTAGTTTCTTGAGCATG 46 115 0 ATTATTTATT 0.842232 -38 CACGGGATCTAATATTGTTACTTTTATTGGCTCC 50 75 0 AATATTTATT 0.89686 -62 CTTTTTTGGAATAATTTATACCTTAAAATAGAAC 52 208 1 ATAATATATT 0.789854 -42 **** * *** ** Masking position 6 Map Score: 37.8074 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 420 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 3 ATATATTTTTATTGAAATAAAATTGATACACT 2 32 1 ATGAATAAAA 0.958625 -59 TATTAAAAGAAATGACATAAAAAATTAAATAA 3 109 0 ATGAATAAAA 0.958625 -192 CTATGTGTTTAATGACATACTATGTTTGATCA 4 93 1 ATGAATACTA 0.742546 -66 TGTAATTTGTAGTGAAAAATAATTACAATTAT 6 100 1 ATGAAAATAA 0.622761 -145 GACATAAGAAAATCATAAACAAATACTGTTGA 6 165 1 ATCAAAACAA 0.710658 -80 TTAATCTTAAAATAATATAAAAAAGCAA 9 81 1 ATAAATAAAA 0.720986 -18 GCAAAGATCCAATGAGATAAAATCTTATCCTA 10 54 0 ATGAATAAAA 0.958625 -90 TTCAGTGTAAAGTGAGATAAAACGAATTTTTA 13 21 1 ATGAATAAAA 0.958625 -138 ATTGTTCTGAAATGAAATAAAAATCATTTAAT 13 84 1 ATGAATAAAA 0.958625 -75 GTTCTGGAATATTGAAAAACAATTAATAGCAT 14 29 1 ATGAAAACAA 0.87831 -105 TTAATTAGAAAATGATAAAATAAAACT 15 284 1 ATGAAAAATA 0.766601 -17 TTGACATGAGAATCATATAAAACATCTTAAGA 19 23 0 ATCAATAAAA 0.887444 -61 TTATTAATGTAGTGATATAAAATAAGATGACT 20 24 1 ATGAATAAAA 0.958625 -53 GAATGAACTAAAACAATTTCAAC 31 2 1 ATGACTAAAA 0.63097 -299 ATTAACATTTAGTGATAAAATAATATTGACAA 31 65 1 ATGAAAAATA 0.766601 -236 ATATCAATTTATTGATAAAAAATGCTTTATTC 31 243 1 ATGAAAAAAA 0.932432 -58 CAAGAAGTCTAATAAAATAAAAATAGCTACCT 32 130 0 ATAAATAAAA 0.720986 -171 CGAGTACTGAATTGACATACAAATGACCTTTA 32 232 1 ATGAATACAA 0.923769 -69 TTAATATAAAAATCACAAAAAATT 36 3 0 ATCAAAAAAA 0.82444 -243 CATTGCAAACAATCATATACTACGTTTTGCAA 38 104 1 ATCAATACTA 0.495327 -151 TTAATTAAATAATCAAATAAAAATGCGCATTT 43 53 1 ATCAATAAAA 0.887444 -97 CTTTTGCAGGAGTGACATAAAATGCTGTGTGA 45 134 1 ATGAATAAAA 0.958625 -40 CACTAAATCAAGTGAGAAACAA 46 141 1 ATGAAAACAA 0.87831 -12 AAACCACGGGATTCATAAAAAATAAAAAAGAC 48 54 0 ATCAAAAAAA 0.82444 -55 TTTAACCTTTACTGAAAAAATATATAGAATTT 52 116 0 ATGAAAAATA 0.766601 -134 AAATAGAACCAATAAAATAAAAATAAA 52 233 1 ATAAATAAAA 0.720986 -17 GGAATAGCAAAATGATATATAAATTAACTATT 53 156 0 ATGAATATAA 0.734866 -145 * *** ****** Masking position 5 Map Score: 31.4575 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 119 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 AAAAATATATACTTTATAATAGAAGCAAAAT 2 8 0 ATTATAATAA 0.79781 -83 ACTATTAACCATTCTACAATAAGAGTGTATCAAT 2 53 0 ATTACAATAA 0.536443 -38 AGCAACTAAAACTATTAAATTCAAGTATTATCTT 3 229 0 ATTTAAATTA 0.678959 -72 TAGCATTATTATTGTTTAATTGAATTGATATATA 4 40 1 ATTTTAATTA 0.919601 -119 ATTCACGAATATTTTACAATACTAACATCCTTCA 4 129 1 ATTACAATAA 0.536443 -30 GTCCCGTAAAAATCTATAAATTTATACATAAAAA 6 134 0 ATTATAAATA 0.473268 -111 TTTTGAATTTACTATATAATACAAATATAACTTT 7 28 1 ATTATAATAA 0.79781 -44 ATTCCTTATTATTTTATAATATCATACTAAAAAA 10 115 0 ATTATAATAA 0.79781 -29 AAGCAGTAACAATTTTAAATTAAATTAAAGTT 11 83 1 ATTTAAATTA 0.678959 -22 AAGACACTATAGTATTAAATTTTATTATTTTTAT 12 103 1 ATTTAAATTA 0.678959 -35 AACTATTCAATATAAAAATAATAAA 12 123 0 ATTTCAATAA 0.583305 -15 CATTATTGGCAGTCTATAATATTAGTTAAATAAT 15 14 1 ATTATAATAA 0.79781 -287 AAAATAGCAAATTTTTCAAGTTTAACTACGATAA 15 150 0 ATTTCAAGTA 0.48542 -151 GTAAAGGTGCAGTTTTTAATTATAGACAAATTAC 16 112 1 ATTTTAATTA 0.9196 -189 TACCAAGTTGATTGTATAAGTAGACTATGCAAAA 17 26 1 ATTATAAGTA 0.726705 -77 TTTAATCTTTAAGTGCAGTTGTTTATA 21 284 0 ATTTTAAGTA 0.762837 -17 AATATCCTTAACTTTTTAATTACAAAAAAATATA 24 15 1 ATTTTAATTA 0.9196 -98 ATGCAATATTTTTTAATTAAATATAAAAAAT 24 92 0 ATTTTAATTA 0.9196 -21 TACGTAGCTTATTGTATAAGTGGATCCACACTCA 27 83 0 ATTATAAGTA 0.726705 -48 TAAATATTTAAATGTTTAATTAGATATAAAGTGA 32 41 0 ATTTTAATTA 0.919601 -260 ATTTTTTAATATTTTATAATTTAAAAAATTTACT 34 65 0 ATTATAATTA 0.904358 -37 TTTATATTAAATTTTTAAATTATACGTTATATTC 36 25 1 ATTTAAATTA 0.678959 -221 AATAGTAATCAGTCTATAATACGAGGAGTAGAGT 37 107 0 ATTATAATAA 0.79781 -69 TATAGTAAAAAATCTATAATTTAAATCAGGTTAT 38 229 1 ATTATAATTA 0.904358 -26 TTTTTATTTGATTATTTAATTAAATCACTATGTA 43 42 0 ATTTTAATTA 0.9196 -108 TAATTTACAGAATCTTTAACTGTATTGCTTAG 44 9 0 ATTTTAACTA 0.477403 -135 CTACGTATGAAATGTTTAATTGCAATGATGATTA 44 100 1 ATTTTAATTA 0.919601 -44 TTTAATTAAAAATTTTTAAATACAAAGGAATAGC 53 180 0 ATTTTAAATA 0.520789 -121 TTATATATTAATTATTTAATTAAAAATTTTTAAA 53 194 0 ATTTTAATTA 0.9196 -107 TTAAATAATTAATATATAATAGAAAATTATATAA 53 209 1 ATTATAATAA 0.79781 -92 ATAATAGAAAATTATATAATTTAATATCGCTTGA 53 224 1 ATTATAATTA 0.904358 -77 * * ******* * Masking position 8 Map Score: 32.4476 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 126 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 ACTGTAAACAATATTAATCAACAGATTATTTAA 3 151 0 ATATTAATAA 0.755883 -150 AATACCATTAACATTATTGACTTTATTAAATGA 13 107 0 ACATTATTAT 0.848343 -52 TAACTTAAGCACATTATTAAGTAATTCAATACA 14 66 0 ACATTATTAA 0.862389 -68 TTGACTCTTTATATTATTTAACTAATATTATAG 15 27 0 ATATTATTAT 0.795815 -274 ACTCAGAATTACATTATTTATTATTAATGACAA 15 71 0 ACATTATTAA 0.862389 -230 GATAACTGTTACATTAATAACATTATAAAAAAA 18 68 1 ACATTAATAT 0.750488 -23 TTATATCACTACATTAATAAAAATAAAGTGAAA 20 11 0 ACATTAATAA 0.815303 -66 TACATTATTTATGTATGCAGTTTA 26 2 1 ACATTATTAT 0.796176 -208 AAAAATATCAATATTATTGATATTTTTAACTAA 26 133 1 ATATTATTAT 0.760405 -77 GTGATAAACTACATTAATTAACAGCAGTAACTA 28 190 0 ACATTAATAA 0.81632 -111 TCTACCTCAAATATTATTAAATATATAGTGTTT 30 203 1 ATATTATTAA 0.813658 -98 ATTATTAGTGACATTATTCACTTTCATTATTCA 32 11 1 ACATTATTAT 0.848343 -290 ACTCTTCAAGATATTATTTAGCATATAAATATT 32 67 0 ATATTATTAA 0.813682 -234 TGAAATTACGATATTAATAAGTTATCTCAAGCC 33 95 1 ATATTAATAT 0.732615 -53 TGCTATCATCATATTAATCATAAGGATGACACC 41 39 0 ATATTAATAA 0.754942 -49 AGCTATAATTATATTATTAATTAATAGTTAATT 53 134 1 ATATTATTAA 0.812346 -167 TTTCTATTATATATTAATTATTTAATTAAAAAT 53 201 0 ATATTAATAT 0.732615 -100 ******** * * Masking position 6 Map Score: 16.748 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 40 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 CATACTATGTTTGATCACAGTATTCACGAATAT 4 108 1 TGACACAGAT 0.935565 -51 AAACAGTAACTTGTCCACGGTATCGAAGGAAAA 8 79 0 TGTCACGGAT 0.937977 -85 CTATAGTGTCTTGACCATAGTATCAACTATAAA 12 82 0 TGACATAGAT 0.716313 -56 ATTCTCCTAATAAAATATGGAATATATCCTCAG 21 26 0 TAATATGGAT 0.681239 -275 TAAAAAATGATGATATACAGAATTTTTAAATTT 23 67 1 TATTACAGAT 0.726161 -234 ATAGCATGACTTATACACAGCATTTAGTTAAAA 26 104 1 TATCACAGAT 0.853502 -106 CGTAAATAATTAAAGTATGGCATAATACTGTAA 28 222 1 TAATATGGAT 0.681239 -79 ATGGCAATAATAATTTACAGTATTATGCCATAC 28 236 0 TATTACAGAT 0.726161 -65 AGATACAAAATCGACTACAGCATCAGTACGAAA 31 96 1 TGATACAGAT 0.868571 -205 TATCGTAGGCTTGACTACGGTATCTATAAAAAA 35 25 1 TGATACGGAT 0.935565 -104 ATGCAGCGGCTTGAACACGGCATCTAGTTAAAA 35 83 0 TGACACGGAT 0.969605 -46 TAACTTCTACAAATTTACGGGATGACGATAGTT 39 48 1 AATTACGGAT 0.437406 -65 AATACAATGCTAATTTACAGAATCTTTAACTGT 44 20 0 TATTACAGAT 0.726161 -124 TTTTAGTTTCTTGAGCATGGAATACAAAAAGTC 46 101 0 TGACATGGAT 0.847271 -52 CTACAATAATTTAAGCACAGGATGACAATAC 47 9 0 TAACACAGAT 0.924751 -105 CCCGTGATCAATAAACACGGGATAACACAGCAT 48 16 0 AAACACGGAT 0.782755 -93 ACCCCGTGTGTAAACCACGGGATTCATAAAAAA 48 64 0 TAACACGGAT 0.964285 -45 CTTGATCACGGTATGCGGTAAAAT 49 2 1 TGACACGGAT 0.969605 -85 ATCCAATGTATGAACCACGGGATCTAATATTGT 50 91 0 TAACACGGAT 0.964285 -46 * ** ***** ** Masking position 13 Map Score: 17.59 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 19 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 TTGATTAATATTGTTTACAGTAAACCTTGTAT 3 163 1 TTGTTACGTA 0.831147 -138 ATGCTATATTTTGACAATAGTAACAATAAAGA 4 14 0 TTGAAATGTA 0.773764 -145 CATACTATGTTTGATCACAGTATTCACGAATA 4 108 1 TTGACACGTA 0.96141 -51 AAACAGTAACTTGTCCACGGTATCGAAGGAAA 8 80 0 TTGTCACGTA 0.932884 -84 CCTAAATGATGTGAACATCGTAGTACTTTAGC 10 26 0 GTGACATGTA 0.648425 -118 CTATAGTGTCTTGACCATAGTATCAACTATAA 12 83 0 TTGACATGTA 0.939369 -55 AATAGCATTATTGTGTATTGAATTACTTAATA 14 53 1 TTGTTATGAA 0.432107 -81 AACAGAGTAATTGATCATTGAAGTCGGATAAC 15 223 0 TTGACATGAA 0.793939 -78 AGAATTATAGTTGACTACGGTACCTATAAAAC 23 168 1 TTGATACGTA 0.898195 -133 AGAAGTAAGATTGTTCAATGTAACAATCTTCG 23 254 1 TTGTCAAGTA 0.576743 -47 TATTATATTATTGTGTACCGTAGGTTATTATA 33 32 1 TTGTTACGTA 0.831147 -116 CTTAGCGATATTGTTAATAGTAAATTTTTTAA 34 47 1 TTGTAATGTA 0.656139 -55 TATCGTAGGCTTGACTACGGTATCTATAAAAA 35 25 1 TTGATACGTA 0.898195 -104 ATGCAGCGGCTTGAACACGGCATCTAGTTAAA 35 84 0 TTGACACGCA 0.784213 -45 TTTTAGTTTCTTGAGCATGGAATACAAAAAGT 46 102 0 TTGACATGAA 0.793939 -51 CTTGATCACGGTATGCGGTAAAA 49 2 1 TTGACACGTA 0.96141 -85 TTGAGTAAGATTGAGAATCGTAGATACAAGCT 49 34 1 TTGAAATGTA 0.773764 -53 **** *** *** Masking position 7 Map Score: 12.1641 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 19 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 ATACTCATACAAAAATAGCTAATAACAAAG 6 21 0 AAAAATAGCT 0.822139 -224 GTTAAGTGGTATAATTTGCTGCTAAAATTT 15 102 1 ATAATTTGCT 0.639638 -199 ATTTGCTGCTAAAATTTGATGTTCATCAAT 15 115 1 AAAATTTGAT 0.678494 -186 TTAAACTTGAAAAATTTGCTATTTTGTCTT 15 159 1 AAAATTTGCT 0.943437 -142 TGCTTTTTAAAAAGATTGCTTAGTATATTG 16 230 1 AAAGATTGCT 0.694271 -71 TAAAAAATTCAATAATTGCTTAAAATATGG 28 20 1 AATAATTGCT 0.605082 -281 ATTTATTGATAAAAAATGCTTTATTCAATA 31 249 1 AAAAAATGCT 0.605082 -52 CTAATAAAATAAAAATAGCTACCTAATAGC 32 124 0 AAAAATAGCT 0.822139 -177 TAGAACTCCAAAAATTTGCTAAGTCATCCT 36 177 0 AAAATTTGCT 0.943437 -69 GTTTAATATGAAAAATTGATACCAAGGTCC 37 49 1 AAAAATTGAT 0.645594 -127 AGTTTAATGTAAAATTAGCTATGTAGTAGC 38 55 1 AAAATTAGCT 0.842642 -200 TGGAATTTTAAAAATTTGCTGCGTCATCTT 42 43 0 AAAATTTGCT 0.943437 -30 GTGTGTATAGAAAATTTGCTCTATATCATC 45 19 1 AAAATTTGCT 0.943437 -155 ********** Masking position 1 Map Score: 8.85781 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 104 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 GCACCTTTACCATTACTGCACATGAGACAT 16 92 0 CATTACTGCA 0.863476 -209 ATGTTACCTGCATTATTGCAAGCAATATAC 16 252 0 CATTATTGCA 0.959698 -49 GATATTGAGTCATTATTGCACACAAAATTA 23 11 1 CATTATTGCA 0.959698 -290 AAACCTAAACCATCATTGCAAACAATCATA 38 91 1 CATCATTGCA 0.958916 -164 TTTTTTACTATATTATTGCACCGATACCTA 38 211 0 TATTATTGCA 0.72671 -44 AAATTGCTTTCCTTATTGCATTATGTTGTA 43 113 0 CCTTATTGCA 0.879909 -37 GATACCAAGTCTTCATTGCACGAAAGGACA 44 71 0 CTTCATTGCA 0.828931 -73 TTTAATTAATCATCATTGCAATTAAACATT 44 110 0 CATCATTGCA 0.958916 -34 ********** Masking position 5 Map Score: 5.84048 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 9 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 AGTTGCAGCCTTTTAATATATTAAATCCTTCT 3 48 1 TTTTATAATT 0.72 -253 CTTAAAATTGATTTTATACATTTTGTCTATAT 6 212 0 ATTTTTAATT 0.797858 -33 CTATTAATTGTTTTTCAATATTCCAGAACTGC 14 26 0 TTTTTAAATT 0.585219 -108 TTTTTTTATAATGTTATTAATG 18 79 0 TTTTTTAAAT 0.592239 -12 ATGAAAAAAGTTTTTACATATTCTAAAAGCTA 21 108 0 TTTTTCAATT 0.877527 -193 AATTTTTAAATTTTTCTATATTACTAAGTCAC 23 87 1 TTTTTTAATT 0.903392 -214 TTAACCTAATATTTTTTATATTTAATTAAAAA 24 82 1 ATTTTTAATT 0.797925 -31 CAATTATTGAATTTTTTATATTAAAAA 28 6 0 ATTTTTAATT 0.797925 -295 GTTTTCTATTTTTTTTCAAATTTTTTTTTGTC 28 84 1 TTTTTCAATT 0.877515 -217 GCAATTGTAATTTTTATAAATTTTATATTAAA 29 56 0 TTTTTTAATT 0.903302 -23 AAATTTTAAGTTTTTTCACATTTGTCGATAAA 30 60 1 TTTTTCAATT 0.877528 -241 ATATTAATGTTTTTTGTATAATCGTTTTTATG 31 162 1 TTTTTTAAAT 0.592202 -139 TGTGCTGGGTTTTTTACAAATTTACCATTATT 32 174 0 TTTTTCAATT 0.87744 -127 CGATAATGATTTTTATTATATTATTGTGTACC 33 19 1 TTTTATAATT 0.72 -129 TTAATAGTAAATTTTTTAAATTATAAAATATT 34 60 1 ATTTTTAATT 0.796998 -42 GTTTTGTTTATTTTTTAATATTTTATAATTTA 34 76 0 TTTTTAAATT 0.585219 -26 TATAGAAAGCTTTTATCATATTTCAATAGATT 36 213 1 TTTTACAATT 0.663336 -33 CTTGGTATCAATTTTTCATATTAAACAAGTAT 37 43 0 ATTTTCAATT 0.751593 -133 ACTGATTACTATTTTCCAAATTAAACTCCACC 37 128 1 ATTTTCAATT 0.751485 -48 AAGGTAAAGTTTTTTGTATAATAGTTTAATGT 38 33 1 TTTTTTAAAT 0.592202 -222 ATTATAGATTTTTTACTATATTATTGCACCGA 38 217 0 TTTTATAATT 0.72 -38 ATTATTCAAAATTTTGTAAATTGCTTTCCTTA 43 128 0 ATTTTTAATT 0.793219 -22 ATTGTATTTATTTTTCTAGATTGAAATGTCCT 44 45 1 TTTTTTAATT 0.903392 -99 TAAATATTTGTTTTACTAGATTTATCCTTTTG 45 108 1 TTTTATAATT 0.72 -66 ***** ** *** Masking position 4 Map Score: 29.6519 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 135 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 AATAAGAGTGTATCAATTTTATTTCAATAAAAA 2 37 0 TTCAATTATT 0.856835 -54 AGCAGCTTTCTATCATGATTATGAATTGTAG 3 9 0 TTCATTTATG 0.925855 -292 TGTCAAAATATAGCATTATTATTGTTTAATTGA 4 30 1 TGCATTTATT 0.61783 -129 TAATTACAATTATCATTTTTATGTATAAATTTA 6 119 1 TTCATTTATG 0.925856 -126 TATATTTGTATTTCTTGGTTATGAAGATAAGTT 12 25 0 TTCTTTTATG 0.700894 -113 AAATTCTGTATATCATCATTTTTTACTGTATTG 23 59 0 TTCATTTTTT 0.672968 -242 TTACTTCTTTTATCCTTGTTATGTGATCGCTGG 23 229 0 TTCCTTTATG 0.783768 -72 TAGTTAAAAATATCAATATTATTGATATTTTTA 26 128 1 TTCAATTATT 0.856835 -82 TTCTATTTTTTTTCAAATTTTTTTTTGTCAAAT 28 87 1 TTCAATTTTT 0.491387 -214 TTTTGTATCTTGTCAATATTATTTTATCACTAA 31 73 0 TTCAATTATT 0.856836 -228 ATGTAATTTCCTAATTATTGCGATAGCCT 32 282 0 TTCCTTTATT 0.787244 -19 ATATAATTCATTTCATTATTATTTTGTGGCTTG 33 122 0 TTCATTTATT 0.927261 -26 TGTATATTAGTATCATATTTATTTACCTTTTTA 34 12 1 TTCATTTATT 0.92726 -90 AAATCTAAGGTGTCATCCTTATGATTAATATGA 41 31 1 TTCATTTATG 0.925857 -57 ATTTGCTCTATATCATCCTTATTGATTACATGT 45 32 1 TTCATTTATT 0.927261 -142 GCAAGTCGTTTTTCTAGGTTATGTGCTTAAGTA 47 61 1 TTCTATTATG 0.523847 -53 * **** ***** Masking position 9 Map Score: 10.9243 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 97 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 TTTTCACTACAAATTACAATTTTTCGCAATT 6 87 0 AAATTAAATT 0.570961 -158 AAAATAATTACAATTATCATTTTTATGTATA 6 115 1 CAATTACATT 0.915955 -130 AGTTGTAATACCATTAACATTATTGACTTTA 13 115 0 CCATTACATT 0.564718 -44 AACCAATGTTAAATTACCATTGTTTATTTTT 17 57 0 AAATTACATT 0.905465 -46 TCTATCACTACAATTAATATTCTCCTAATAA 21 46 0 CAATTATATT 0.776823 -255 TATTTTAAGCAAATTACTATTTGCACTCATT 21 172 1 AAATTATATT 0.75364 -129 CAATAGTTCACAATTATCATCTATTAACTTT 21 217 1 CAATTACATC 0.564718 -84 ATAATACTGTAAATTATTATTGCCATCAATG 28 243 1 AAATTATATT 0.75364 -58 AAATTTATAAAAATTACAATTGCT 29 65 1 AAATTAAATT 0.570961 -14 ATTTCTACCTCAAATATTATTAAATATATAG 30 200 1 CAAATATATT 0.44602 -101 AGCAATAATAAAATTAACATTTAGTGATAAA 31 53 1 AAATTACATT 0.905465 -248 ATTTAGTGATAAAATAATATTGACAAGATAC 31 71 1 AAAATATATT 0.414372 -230 GTTTTTTACAAATTTACCATTATTAGCTATC 32 167 0 AATTTACATT 0.434806 -134 TAGTCATCAAAAATTATCAGTTTTGAAGTAA 38 182 0 AAATTACAGT 0.532755 -73 AAGATTCTGTAAATTAGCATTGTATTTATTT 44 27 1 AAATTACATT 0.905465 -117 AATTAAAAATCAAATAACATT 44 133 1 CAAATACATT 0.715978 -11 TCGAGATGAACAATTACCATTTCAAATGTGT 51 57 0 CAATTACATT 0.915955 -62 ****** **** Masking position 6 Map Score: 6.96524 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 50 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 TGCACTTTCTAAGCTCAGGACTTACAAAGA 42 17 1 AAGCTCAGGA 0.806256 -56 ACAATAATTTAAGCACAGGATGACAATAC 47 10 0 AAGCACAGGA 0.944034 -104 CGTGATCAATAAACACGGGATAACACAGCA 48 17 0 AAACACGGGA 0.948192 -92 CCCGTGTGTAAACCACGGGATTCATAAAAA 48 65 0 AACCACGGGA 0.986434 -44 TCGTATATGAAACCACGGGAGCCAATAAAA 50 58 1 AACCACGGGA 0.986434 -79 CCAATGTATGAACCACGGGATCTAATATTG 50 92 0 AACCACGGGA 0.986434 -45 ********** Masking position 2 Map Score: 4.16552 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 1 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 14 TGCGATATAAAAATGTACTTTAATTA 1 36 1 AAATGTCTTT 0.87824 -16 TTAGTTGCTATAAATACCTTTATTTTAAAGT 3 254 1 TAAATACTTT 0.471219 -47 AATTAAATTTCCTTTTTAAAGCTCT 9 5 1 AAATTTCTTT 0.699097 -94 GTTACCAGCTTAAAGAGCTTTAAAAAGGAAA 9 18 0 TAAAGACTTT 0.734274 -81 AAAAATAATTAAAAATGCTTTTTAAAAAGAT 16 215 1 AAAAATCTTT 0.708586 -86 AGTAGAACTTAAAAGTTCTTTATTGTGAAGA 28 141 1 AAAAGTCTTT 0.933361 -160 CTTATATAATAAATGTACTTTTAATATAAAA 29 37 1 AAATGTCTTT 0.87824 -42 CATTTGTCGATAAAGTACTTTATATTGTAAC 30 78 1 TAAAGTCTTT 0.8788 -223 TTTATTGATAAAAAATGCTTTATTCAATAAA 31 250 1 AAAAATCTTT 0.708586 -51 ATTGACATACAAATGACCTTTAGAAAGAGGC 32 242 1 AAATGACTTT 0.730445 -59 CAAAATTTTGTAAATTGCTTTCCTTATTGCA 43 123 0 TAAATTCTTT 0.7005 -27 TTCTAGATTGAAATGTCCTTTCGTGCAATGA 44 58 1 AAATGTCTTT 0.877046 -86 GGAATTCAAAAAAATAACTTTAATCTTGATA 45 70 1 AAAATACTTT 0.632703 -104 GTGCATATCTAAAACTACTTTTAAGAGACAA 51 90 1 AAAACTCTTT 0.671242 -29 CAAGTGTTGATAAAGTTCTTTAAATGCTGAG 52 150 1 TAAAGTCTTT 0.878805 -100 ****** **** Masking position 3 Map Score: 6.06072 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 80 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 TTATTTCAATAAAAATATATACTTTATAATAGAA 2 18 0 AAAAATATTT 0.552785 -73 TTAAATAAACAAAGACAAAGGCTTAATAAGCATA 3 83 0 AAAAAAAGTT 0.532237 -218 TTACTATTGTCAAAATATAGCATTATTATTGTTT 4 23 1 CAAAATAGTT 0.627716 -136 GTATGTCATTAAACACATAGAATTGTTGCGTGGA 4 79 0 AAAAATAGTT 0.930051 -80 TTGTAGTGAAAAATAATTACAATTATCATTTTTA 6 106 1 AAAATTACTT 0.63561 -139 TTTTATGTATAAATTTATAGATTTTTACGGGACA 6 135 1 AAATATAGTT 0.51918 -110 AGAAAATCATAAACAAATACTGTTGAATGTGTTT 6 171 1 AAAAATACTT 0.909498 -74 TTGCGATAAGAAACATATAGTTTTGACATGAGAA 19 43 0 AAAAATAGTT 0.906784 -41 AATTTGCTTAAAATATATACGCTTGTTCTACTCA 21 153 0 AAAAATACTT 0.909051 -148 AATTACAAAAAAATATATACATTTCTTGTATCAA 24 32 1 AAAAATACTT 0.88676 -81 AAATATTATTAAATATATAGTGTTTACAAAAATT 30 211 1 AAAAATAGTT 0.929594 -90 TTATAATTTAAAAAATTTACTATTAACAATATCG 34 52 0 AAAATTACTT 0.635583 -50 CAATCTAGAAAAATAAATACAATGCTAATTTACA 44 34 0 AAAAATACTG 0.56036 -110 GTTGGAATTCAAAAAAATAACTTTAATCTTGATA 45 67 1 AAAAATAATT 0.564715 -107 AACTTTACACAAAAATGTAGATTTTTCAAATAAA 46 11 0 AAAAGTAGTT 0.659491 -142 TTTACTGAAAAAATATATAGAATTTAGTAGATGA 52 107 0 AAAAATAGTT 0.929594 -143 *** * **** ** Masking position 9 Map Score: 6.17172 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 43 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802