AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00051_rpxx_reg_300.orf -o00051_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 RP008 190 (3R)-HYDROXYMYRISTOYL-[ACYL CARRIER PROTEIN] DEHYDRATASE (fabZ) #2 RP009 300 UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE (lpxD) #3 RP053 300 ADP,ATP CARRIER PROTEIN (tlc1) #4 RP054 72 GLYCEROL-3-PHOSPHATE TRANSPORTER (glpT) #5 RP055 162 NUCLEOSIDE DIPHOSPHATE KINASE (ndk) #6 RP060 171 ABC TRANSPORTER ATP-BINDING PROTEIN (abcT1) #7 RP061 60 unknown #8 RP062 34 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE (kdsA) #9 RP379 300 3-DEOXY-MANNO-OCTULOSONATE CYTIDYLYLTRANSFERASE (kdsB) #10 RP407 300 unknown #11 RP408 148 LIPOPROTEIN SIGNAL PEPTIDASE (lspA) #12 RP409 21 unknown #13 RP410 149 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (murD) #14 RP411 74 CELL DIVISION PROTEIN FTSW (ftsW) #15 RP501 215 TRNA PSEUDOURIDINE 55 SYNTHASE (truB) #16 RP503 21 30S RIBOSOMAL PROTEIN S15 (rpsO) #17 RP504 154 POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE (pnp) #18 RP505 184 KPSF PROTEIN (kpsF) #19 RP508 68 ABC TRANSPORTER ATP-BINDING PROTEIN (abcT2) #20 RP509 92 PHOSPHOMANNOMUTASE (exoC) #21 RP825 300 UNDECAPRENYL-PHOSPHATE ALPHA-N-ACETYLGLUCOSAMINYLTRANSFERASE (mraY2) Motif number 1 AGATAACAATAAAAATTGATTCATACAACAA 1 26 0 AAAAATTATT 0.775769 -165 TCCAGAAAAATATATTTAATTGGGTCCCGTG 1 75 1 TATATTTATT 0.879968 -116 TCTGTTATTCAATTATTTATTCACGGGACCC 1 96 0 AATTATTATT 0.788796 -95 TAATAAAGGCAAATTTATATTAAACAAGAGA 1 161 1 AAATTTAATT 0.769636 -30 TTTAAATTAATAATATTGATTTATTTGAGAT 2 83 0 TAATATTATT 0.730802 -218 GTAATGTGAGAAATTTAAATTAATAATATTG 2 96 0 AAATTTAATT 0.768036 -205 CTTGAATCTCAAATTTAGTTTAAAATTACTA 2 148 1 AAATTTATTT 0.572986 -153 AAAGTTCACTAAATTTTCATTTAGTTAGTTA 3 115 1 AAATTTTATT 0.926494 -186 AATTTTTACTTAATTTTGATTTCTATATATT 3 152 0 TAATTTTATT 0.892106 -149 AAAATTAAGTAAAAATTGTTTTCTTTTTCAC 3 166 1 AAAAATTTTT 0.570032 -135 AAATAAATAGAAAATTTAATT 3 290 1 AAAATTTATT 0.909477 -11 GAAGCTTTTTTATATTTTTTTACAAATT 4 8 0 TATATTTTTT 0.737477 -65 CAGTAAATCTAATAATTTATTATATATAAAG 5 133 1 AATAATTATT 0.761193 -30 AATGAATATATTAAATTATAAAAGCTT 6 7 1 TATATTAATT 0.670694 -165 ATAACGATTGAATATTTCTTTTTTAGTCTTG 6 49 0 AATATTTTTT 0.810744 -123 TACAATGTTTAATTTTAAATTTAATGTCTAT 6 86 1 AATTTTAATT 0.762854 -86 AAATTTTGTTTCCTTATTATT 6 161 0 AAATTTTTTT 0.828473 -11 CAAATATTATTAATTTTATTTGTATGGATAT 7 25 1 TAATTTTTTT 0.759965 -36 AACTCTTATATTTAATTATTGAATGAG 8 18 0 TATATTTATT 0.879968 -17 ATCTGTCAACAATTATTTTTTAATTTTAAAT 9 269 1 AATTATTTTT 0.608721 -32 TTTACATTACAATATTTATTTAAAAAATATT 10 28 1 AATATTTTTT 0.802408 -273 AATATTATGATAATATTTTTTAAATAAATAT 10 39 0 TAATATTTTT 0.509667 -262 AAATATAAGTTAATTTTCATTAATATAAATA 10 146 0 TAATTTTATT 0.892106 -155 AAAATTAACTTATATTTAATTAATTTTAAAT 10 160 1 TATATTTATT 0.879968 -141 AAAAATTGTAAAATTTTGATTGCTGGGTTAT 10 204 0 AAATTTTATT 0.926494 -97 AAAATTTTACAATTTTTTATTGTAATTTCTT 10 218 1 AATTTTTATT 0.921836 -83 TATTTGAATCAATTTTTGATTATGAATAATA 10 262 0 AATTTTTATT 0.930331 -39 GGAATCTCAGAATATTTGATTAGATTGGTAC 14 22 1 AATATTTATT 0.917833 -53 TATTGGCTAGAATTATATATTAAAGATTTTC 15 31 1 AATTATAATT 0.505572 -185 TCTCATTTCATAATTTATATTCTATTAAAGA 17 127 0 TAATTTAATT 0.696651 -28 GCAAAATTAATATATTTCATTGGTGTTAAAT 21 162 0 TATATTTATT 0.88006 -139 GTATTTCATTAATATTTTATTAGTCATATGA 21 207 0 AATATTTATT 0.909454 -94 TAATAAATATTAAATTTAATTATGTTACT 21 282 1 TAAATTTATT 0.873601 -19 ******* *** Masking position 6 Map Score: 38.0565 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 586 Number in noncoding regions = 369 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 2 AGTTCTTTTATTTAGAGATTACTTAGTATTCATAGATACGATA 2 11 0 TTAGATTTAT 0.894397 -290 AAAATACTAATATAGTAATTTTAAACTAAATTTGAGATTCAAG 2 148 0 TTAGATTATT 0.879126 -153 CTAGCGATATTATATAAGTTATGCTTTTATTATGCAATAAAAT 2 245 0 TTATGTTAAT 0.907745 -56 AATACTGCATTGTATGGGATGAAATTTTAATATTTTACCTTCA 3 11 1 TTATGTTAAT 0.907795 -290 GACCCCAAGAAATATCAAATAAGCCTTTACAATTTAAAGTTCA 3 80 1 ATATATTAAT 0.73742 -221 TAAATTTTCATTTAGTTAGTTAACAGTTAATATATAGAAATCA 3 124 1 TTAGATTAAT 0.907795 -177 CAATAAACATTTTATTAACTATAGGATGTGAAAAAGAAAACAA 3 181 0 TTATATTTAA 0.766918 -120 AATTAAATTTTCTATTTATTTGAAGATAAACATTATACTAAAA 3 268 0 TTATATTAAT 0.951921 -33 AGATTCAGGTTTTAGAAGCTTTTTTATATTTTTTTACAAATT 4 10 0 TTAGGTTTTT 0.756762 -63 ATAACTTATATCTATGTACTGCAGTATGAGGTATGTGATGTCT 5 56 1 TTATATTATA 0.738603 -107 TTATAACCTTTATATATAATAAATTATTAGATTTACTGCATAA 5 128 0 TTATATTATT 0.936005 -35 ATTCAATCGTTATAGAAATTACAATGTTTAATTTTAAATTTAA 6 67 1 TTAGATTTTT 0.862195 -105 AAATTTAATGTCTATAGAATAATAAATGTATATACTTAGTAGT 6 102 1 TTATATTTAT 0.944543 -70 TATTTTTGAATATATTCAATATTCGATCTGTTTAAAGAATGGC 9 198 0 TTATATTTTT 0.926373 -103 TTATGAGTTTTTTATTGATTTAAAATTAATTAAATATAAGTTA 10 165 0 TTATATTAAA 0.792323 -136 GTAATTTCTTTATATATAGTTCATATTATTCATAATCAAAAAT 10 239 1 TTATATTTAT 0.944543 -62 TATATTTGATGCACTTTAAAAATTTGCTAATTA 13 1 1 TTATGTTAAT 0.907795 -149 TTATCTTCACTGTATTAATTTCATATTCTTTTTGAAGTCATCT 13 80 1 TTATATTTTT 0.926373 -70 TTGACTTAAATGTAGAAAATCTTTAATATATAATTCTAGCCAA 15 33 0 TTAGATTTAA 0.620663 -183 TGCTCCTTGCATTATAAACTTTTTGCTCTTGTTGAAATTAAAC 15 147 1 ATATATTTTT 0.641143 -69 TTAAACTGTGTCTATCAATTTTGCATTTTATATCATATATTC 15 184 1 TTATATTTAT 0.944543 -32 TTGATCTCATTATATATATTGCAATATGAGATTAAGTGTTTGA 17 68 1 TTATATTATT 0.936004 -87 GTTTATTAACTATATCTAGTACATATTTAGTATTAGGAGTATT 18 129 0 TTATATTAAT 0.951921 -56 GACCATTGGCTCTATGCGTTATTAAATTTGTATTTTGGACAAA 19 29 0 TTATGTTTAT 0.894397 -40 GCTATGTTATTATGTGTTAGGTTGTCATATTATGCTTGACC 20 9 1 ATATGTTATT 0.50806 -84 ACCAATGAAATATATTAATTTTGCTCTAATATTGATATTCATA 21 169 1 TTATATTATT 0.933815 -132 * *** * * * * ** Masking position 10 Map Score: 30.8756 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 261 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 3 TATCGTATCTATGAATACTAAGTAATCTCTA 2 10 1 TATGAAACAA 0.563941 -291 AAATCAATATTATTAATTTAAATTTCTCACAT 2 92 1 TATTAATTAA 0.507781 -209 TTTAGTGAACTTTAAATTGTAAAGGCTTATTT 3 96 0 TTTAAATGAA 0.813074 -205 ACAGTTAATATATAGAAATCAAAATTAAGTAA 3 146 1 TATAGAATAA 0.689243 -155 TTTCTATTTATTTGAAGATAAACATTATACTA 3 271 0 TTTGAAATAA 0.658757 -30 TCTCCTCAACTATAAAAAGTAAGATTCAGGTT 4 42 0 TATAAAAGAA 0.924015 -31 AGGCTCAAGATATAAATTTTAACACAGAGATT 5 11 0 TATAAATTAA 0.906669 -152 ATCTTGAGCCTATAAAATCGAATCATAACTTA 5 32 1 TATAAATCAA 0.761101 -131 TAAACTATCTTATAAAGAGGAATTTGAATTGG 5 99 0 TATAAAAGAA 0.924015 -64 AGAAAAAGCTTTTATAATTTAATATATTCATT 6 11 0 TTTATATTAA 0.543522 -161 AGACATTAAATTTAAAATTAAACATTGTAATT 6 83 0 TTTAAATTAA 0.788892 -89 TTTATTATTCTATAGACATTAAATTTAAAATT 6 96 0 TATAGAATAA 0.689243 -76 TATGTAGCAATATGAAGATCAATTTTAAAAAG 9 97 1 TATGAAATAA 0.802108 -204 AGATCAATTTTAAAAAGAGCAAAGAGTTTATC 9 112 1 TAAAAAAGAA 0.368413 -189 ACTGCCTATATTTAAAATTAAAAAATAATTGT 9 277 0 TTTAAATTAA 0.788892 -24 CTTAGTTACATATATATTGAAAATACAAAAAG 10 99 1 TATATATGAA 0.695098 -202 ATATGAACTATATATAAAGAAATTACAATAAA 10 233 0 TATATAAGAA 0.751868 -68 TTAATATATTTATAAATACAAAAAAGGAATGT 11 121 0 TATAAAACAA 0.805246 -28 TTTAAATATAAAGGTATTTAA 12 1 1 TTTAAAATAA 0.575391 -21 CTTAGCCAATTTTAAAATTAAACGAGTATATC 15 77 0 TTTAAATTAA 0.788892 -139 GAGCAAAAAGTTTATAATGCAAGGAGCATTAT 15 143 0 TTTATATGAA 0.524402 -73 GAATATATGATATAAAATGCAAAATTGATAGA 15 194 0 TATAAATGAA 0.901751 -22 GATCTCATTATATATATTGCAATATGAGATTA 17 70 1 TATATATGAA 0.695764 -85 AAATCTGTAATATAAAAATTAACAAGTTAGTT 21 108 0 TATAAAATAA 0.929708 -193 ATTCTTCTCTTATTAAGATTAATTAAATCTGT 21 132 0 TATTAAATAA 0.577989 -169 TTATTAGTCATATGAATATCAATATTAGAGCA 21 190 0 TATGAAATAA 0.80207 -111 AATACCACACTTTAAACATTAAGGTACATGAT 21 233 1 TTTAAAATAA 0.863909 -68 GATCAGTAATAATAAATATTAAATTTAATTAT 21 273 1 AATAAAATAA 0.38819 -28 ****** ** ** Masking position 6 Map Score: 24.8151 Number of sites scoring better than the average of aligned sites = 655 Number in coding regions = 375 Number in noncoding regions = 280 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 ATCTCTGTTATTCAATTATTTATTCACGGGACCC 1 96 0 TTAATTTTAT 0.582214 -95 ATTTCTATATATTAACTGTTAACTAACTAAATGA 3 131 0 ATAATTTAAT 0.697574 -170 CCTATAGTTAATAAAATGTTTATTGAGTTCTTTC 3 199 1 ATAATTTTAT 0.930801 -102 GTACTGCAGTATGAGGTATGTGATGTCTCCAATT 5 71 1 ATAGTTGTGT 0.824858 -92 TTTATATATAATAAATTATTAGATTTACTGCATA 5 129 0 ATAATTTAGT 0.559879 -34 TCCTCAATTGATAAACTCTTTGCTCTTTTTAAAA 9 119 0 ATAATTTTGT 0.881273 -182 CGTTGTCTTAATAAAGTTTGTAGTTTTTTGTGTT 9 162 0 ATAATTGTAT 0.948619 -139 TATTTTTTAAATAAATATTGTAATGTAAATGGTG 10 23 0 ATAAATGTAT 0.656548 -278 TTGCTGGGTTATGAGTTTTTTATTGATTTAAAAT 10 182 0 ATAGTTTTAT 0.861587 -119 GATTATTTGAATCAATTTTTGATTATGAATAATA 10 262 0 ATAATTTGAT 0.575071 -39 AGAATATTTGATTAGATTGGTACTCAGTTTACTA 14 30 1 ATAGTGGTAT 0.415596 -45 ACTTAAATGTAGAAAATCTTTAATATATAATTCT 15 39 0 AGAATTTTAT 0.537766 -177 AGTTGTCTTAATAAGCTCTGTAGTACTCATGCAT 15 107 1 ATAGTTGTAT 0.895162 -109 TCCTTGCATTATAAACTTTTTGCTCTTGTTGAAA 15 150 1 ATAATTTTGT 0.881142 -66 AACTGTGTCTATCAATTTTGCATTTTATATCATA 15 187 1 ATAATTGCAT 0.649906 -29 GCAATATGAGATTAAGTGTTTGATGATTACTGAA 17 88 1 ATAATTTTGT 0.879113 -67 TGATTACTGAATGATATCTTTAATAGAATATAAA 17 111 1 ATATTTTTAT 0.490534 -44 TTAATAGAATATAAATTATGAAATGAGATAAATA 17 130 1 ATAATTGAAT 0.759888 -25 GTAAGAAGTTTTAAGCTGTGTGGTAATCAAATGA 18 21 1 TTAGTTGTGT 0.327797 -164 TACTCCTAATACTAAATATGTACTAGATATAGTT 18 131 1 ACAATTGTAT 0.604762 -54 TCTATGCGTTATTAAATTTGTATTTTGGACAAAA 19 28 0 ATAATTGTAT 0.948309 -41 ATTAAGATTAATTAAATCTGTAATATAAAAATTA 21 119 0 ATAATTGTAT 0.945635 -182 GTGGTATTTCATTAATATTTTATTAGTCATATGA 21 207 0 ATAAATTTAT 0.582074 -94 ACATAATTAAATTTAATATTTATTATTACTGATC 21 273 0 ATTATTTTAT 0.418183 -28 ** ** * **** * Masking position 14 Map Score: 17.2043 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 183 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 CGGGACCCAATTAAATATATTTTTCTGGATCTAA 1 70 0 TTAAATATTT 0.529399 -121 GAAATTTAAATTAATAATATTGATTTATTTGAGA 2 84 0 TTAATAATGT 0.600094 -217 TCTACTTCAATTAATAACTTGAATCTCAAATTTA 2 131 1 TTAATAATAT 0.718961 -170 CATCCTATAGTTAATAAAATGTTTATTGAGTTCT 3 196 1 TTAATAATTT 0.934 -105 TGCAGTAAATCTAATAATTTATTATATATAAAGG 5 131 1 CTAATAATTA 0.475255 -32 TTTTATAACCTTTATATATAATAAA 5 148 0 TTTATAATTT 0.730169 -15 ACAAATAAAATTAATAATATTTGTGTAAAAGACA 7 14 0 TTAATAATTT 0.933999 -47 CATTCCTCAATTGATAAACTCTTTGCTCTTTTTA 9 122 0 TTGATAATTT 0.613496 -179 CTACGTTGTCTTAATAAAGTTTGTAGTTTTTTGT 9 165 0 TTAATAATTT 0.934 -136 CATATTATTCTTAGTTACATATATATTGAAAATA 10 90 1 TTAGTTATTT 0.474201 -211 TTCATTAATATAAATAAGATTTATAACTATGCTT 10 128 0 TAAATAATTT 0.61679 -173 TAACTTATATTTAATTAATTTTAAATCAATAAAA 10 165 1 TTAATTATTA 0.629149 -136 TATTTATAAATATATTAATTATCT 11 135 1 TATATTATTT 0.177145 -14 TTAAATACCTTTATATTTAAA 12 8 0 TTAAATATTT 0.529595 -14 TAAAAATTTGCTAATTAATTCTATAAGAACTGGA 13 27 1 CTAATTATTT 0.787042 -123 CTAAGTTGTCTTAATAAGCTCTGTAGTACTCATG 15 104 1 TTAATAATTT 0.934 -112 TTTATCTCATTTCATAATTTATATTCTATTAAAG 17 128 0 TTCATAATTT 0.613496 -27 TTCACCGTGGTTTATTAACTATATCTAGTACATA 18 147 0 TTTATTATTT 0.654313 -38 CGTAAATCTACTAATAATTTTACTTGATTCCGTG 20 53 1 CTAATAATAT 0.488531 -40 CTTATTAAGATTAATTAAATCTGTAATATAAAAA 21 122 0 TTAATTATTT 0.908245 -179 ATTCATATGACTAATAAAATATTAATGAAATACC 21 205 1 CTAATAATTA 0.475255 -96 AATATTAAATTTAATTATGTTACT 21 287 1 TTAATTATAT 0.641502 -14 ******* * * * Masking position 10 Map Score: 11.2859 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 378 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 6 AATCAACGCGTTCTCGTAATAAAGGCAAATT 1 145 1 TTCTCTAATA 0.946626 -46 TAATTTAAATTTCTCACATTACATGTTCTAC 2 105 1 TTCTCCATTA 0.716426 -196 ATATTTTGTATTGTCATAAGAATATTGACCC 3 54 1 TTGTCTAAGA 0.904272 -247 AATGGCTACGTTGTCTTAATAAAGTTTGTAG 9 173 0 TTGTCTAATA 0.956463 -128 TTAAAAAATATTATCATAATATTCTATTTAT 10 47 1 TTATCTAATA 0.772653 -254 ATTGGCTAAGTTGTCTTAATAAGCTCTGTAG 15 99 1 TTGTCTAATA 0.956463 -117 TATCAACAAATACTCCTAATACTAAATATGT 18 121 1 TACTCTAATA 0.831366 -64 ATGTGTTAGGTTGTCATATTATGCTTGACCA 20 22 1 TTGTCTATTA 0.937521 -71 TGTTAAATTCTTCTCTTATTAAGATTAATTA 21 139 0 TTCTCTATTA 0.923747 -162 AATATTTTATTAGTCATATGAATATCAATAT 21 197 0 TAGTCTATGA 0.642032 -104 ***** ***** Masking position 4 Map Score: 6.46155 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 38 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 CTATAACTTTATTGTTGTATGAATCAATTTTT 1 15 1 ATTGTGATGA 0.932209 -176 CTTATATTTAATTATTGAATGAGACACAAA 8 9 0 ATTATGATGA 0.965674 -26 TTAAAAAATAATTGTTGACAGATTAGCCTTTT 9 260 0 ATTGTGCAGA 0.818177 -41 AAGGAGCATTATTAATGCATGAGTACTACAGA 15 123 0 ATTATGATGA 0.965674 -93 CGCAACTTAAATTAGTGTAAGCACGTAACTTG 17 31 1 ATTATGAAGC 0.890086 -124 GTGTTTGATGATTACTGAATGATATCTTTAAT 17 103 1 ATTATGATGA 0.965674 -52 GACCATTATTGTAAGAAGTTTTAAGC 18 5 1 ATTATGAAGA 0.971957 -180 TTACGTCTTTATTAGTGATAGACGATAATAAC 21 77 0 ATTATGTAGA 0.861328 -224 CTAATAAAATATTAATGAAATACCACACTTTA 21 215 1 ATTATGAATA 0.772617 -86 **** ** **** Masking position 6 Map Score: 5.63945 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 24 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 8 AGATAACAATAAAAATTGATTCATACAACA 1 27 0 AAAAATTGAT 0.574231 -164 ATAACAGAGATAAAATTGCTCTATGCAATC 1 119 1 TAAAATTGCT 0.948628 -72 TTTAAATTAATAATATTGATTTATTTGAGA 2 84 0 TAATATTGAT 0.91978 -217 AAATTTAGTTTAAAATTACTATATTAGTAT 2 158 1 TAAAATTACT 0.510968 -143 ATAACTTATATAATATCGCTAGTGATTAAG 2 266 1 TAATATCGCT 0.787083 -35 AATTTTTACTTAATTTTGATTTCTATATAT 3 153 0 TAATTTTGAT 0.665543 -148 AAATTGATCTTCATATTGCTACATATTTAA 9 92 0 TCATATTGCT 0.879725 -209 TTGCTCTTTTTAAAATTGATCTTCATATTG 9 104 0 TAAAATTGAT 0.885989 -197 ATTCATAATCAAAAATTGATTCAAATAATC 10 266 1 AAAAATTGAT 0.574231 -35 TAAAATTGCTCCGAAGATTA 10 291 0 TAAAATTGCT 0.948628 -10 GTACTCAGTTTACTATTGCTTGAAATAATA 14 49 1 TACTATTGCT 0.787083 -26 ACTCATGCATTAATAATGCTCCTTGCATTA 15 131 1 TAATAATGCT 0.71381 -85 ACACTTAATCTCATATTGCAATATATATAA 17 77 0 TCATATTGCA 0.401046 -78 TGAAATATATTAATTTTGCTCTAATATTGA 21 174 1 TAATTTTGCT 0.825436 -127 AATTTTGCTCTAATATTGATATTCATATGA 21 185 1 TAATATTGAT 0.91978 -116 ********** Masking position 6 Map Score: 10.6462 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 345 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 TCGTATCTATGAATACTAAGTAATCTCTAA 2 13 1 GAATACTAAG 0.801673 -288 AATGTCTATAGAATAATAAATGTATATACT 6 108 1 GAATAATAAA 0.59871 -64 TAGCAGTGTAAAATAATAAGGAAACAAAAT 6 150 1 AAATAATAAG 0.832993 -22 ATCATAAATAGAATATTATGATAATATTTT 10 51 0 GAATATTATG 0.838688 -250 ATGTAACTAAGAATAATATGTTCTAAAACA 10 80 0 GAATAATATG 0.96668 -221 TTTTGATTATGAATAATATGAACTATATAT 10 250 0 GAATAATATG 0.96668 -51 ATGACTTCAAAAAGAATATGAAATTAATAC 13 91 0 AAAGAATATG 0.689594 -59 CTATTGCTTGAAATAATATGTAAT 14 61 1 AAATAATATG 0.904838 -14 ACGTGGTCAAGCATAATATGACAACCTAAC 20 26 0 GCATAATATG 0.871441 -67 ********** Masking position 5 Map Score: 3.69131 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 68 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 ********** No masking Map Score: 4.85601e-13 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 11 TTATTCAATTATTTATTCACGGGACCCAAT 1 93 0 ATTTATTCAC 0.455409 -98 AAAGGCAAATTTATATTAAACAAGAGACCT 1 165 1 TTATATTAAA 0.664913 -26 AAAAATACTAATATAGTAATTTTAAACTAA 2 162 0 ATATAGTAAT 0.646211 -139 TTTGATTTCTATATATTAACTGTTAACTAA 3 139 0 ATATATTAAC 0.89771 -162 TTATAATTTAATATATTCATT 6 2 0 ATATATTCAT 0.897462 -170 CGAATATTGAATATATTCAAAAATATGTTT 9 216 1 ATATATTCAA 0.821156 -85 AATAATTATATTCACCATTTACATT 10 6 1 TTATATTCAC 0.719643 -295 TAAATCTTATTTATATTAATGAAAATTAAC 10 139 1 TTATATTAAT 0.790906 -162 GTATTTATAAATATATTAATTATCT 11 134 1 ATATATTAAT 0.914062 -15 GGCTAGAATTATATATTAAAGATTTTCTAC 15 35 1 ATATATTAAA 0.848046 -181 CACCAATGAAATATATTAATTTTGCTCTAA 21 168 1 ATATATTAAT 0.914062 -133 ATGACTAATAAAATATTAATGAAATACCAC 21 211 1 AAATATTAAT 0.552048 -90 ********** Masking position 5 Map Score: 5.84973 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 130 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 12 ACATGTTCTACTTCAATTAATAACTTGAATCTC 2 125 1 CTCAATTTAA 0.974266 -176 TATAAACTCTCCTCAACTATAAAAAGTAAGATT 4 48 0 CTCAACTAAA 0.707475 -25 AAGCTGCATTCCTCAATTGATAAACTCTTTGCT 9 129 0 CTCAATTTAA 0.974267 -172 TGCAACAAAACATCAATTTATAAAATTGA 11 7 0 CTCAATTTAA 0.974267 -142 ATGAAACCATCATCAATTCCTAAGATTATGTGT 18 51 1 CTCAATTTAA 0.974267 -134 TTGTTATTATCGTCTATCACTAATAAAGACGTA 21 75 1 CTCTATCTAA 0.835197 -226 GTGTTAAATTCTTCTCTTATTAAGATTAATTAA 21 138 0 CTCTCTTTAA 0.835197 -163 * ****** *** Masking position 12 Map Score: 0.462276 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 25 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 ********** No masking Map Score: 4.85601e-13 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: 4.85601e-13 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: 4.85601e-13 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