AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00561_rpxx_reg_300.orf -o00561_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: RP409 21 unknown Input sequences: #1 RP009 300 UDP-3-O-[3-HYDROXYMYRISTOYL] GLUCOSAMINE N-ACYLTRANSFERASE (lpxD) #2 RP047 198 unknown #3 RP048 148 60 KD INNER-MEMBRANE PROTEIN (yidC) #4 RP238 75 ELONGATION FACTOR P (efp) #5 RP240 217 unknown #6 RP241 32 unknown #7 RP242 225 CDP-DIACYLGLYCEROL--SERINE O-PHOSPHATIDYLTRANSFERASE (pssA) #8 RP246 54 unknown #9 RP247 182 UDP-N-ACETYLMURAMATE--ALANINE LIGASE (murC) #10 RP249 115 D-ALANINE--D-ALANINE LIGASE (ddlB) #11 RP366 75 APOLIPOPROTEIN N-ACYLTRANSFERASE (lnt) #12 RP407 300 unknown #13 RP408 148 LIPOPROTEIN SIGNAL PEPTIDASE (lspA) #14 RP410 149 UDP-N-ACETYLMURAMOYLALANINE--D-GLUTAMATE LIGASE (murD) #15 RP411 74 CELL DIVISION PROTEIN FTSW (ftsW) #16 RP425 150 unknown #17 RP427 121 PETR PROTEIN (ompR) #18 RP441 86 unknown #19 RP442 57 GLYCEROL-3-PHOSPHATE DEHYDROGENASE (gpsA) #20 RP469 74 POSSIBLE 1-ACYL-SN-GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE (plsC) #21 RP719 300 unknown #22 RP750 80 PHOSPHATIDYLGLYCEROPHOSPHATASE A (pgpA) #23 RP825 300 UNDECAPRENYL-PHOSPHATE ALPHA-N-ACETYLGLUCOSAMINYLTRANSFERASE (mraY2) Motif number 1 AAATCAATATTATTAATTTAAATTTCTCAC 1 92 1 TATTAATTTA 0.917177 -209 ACTATATTAGTATTTTTATAGTCAAGTCAC 1 175 1 TATTTTTATA 0.851703 -126 TATTTTTATCAATAATTTTAACTCAAAAGC 2 119 0 AATAATTTTA 0.692759 -80 TACCTATTATTATTATTATAAAATACAAAT 2 175 0 TATTATTATA 0.884884 -24 TAAAATTTTTATAGAATATAATA 3 4 1 AATTTTTATA 0.655781 -145 TAAAATTAAGTATAAATATACAAATTATTT 4 36 0 TATAAATATA 0.487269 -40 ATTAGAGAAATATTTTTTTAGCGAAATAAG 5 51 1 TATTTTTTTA 0.902261 -167 ATAAGATTTTTATTATTTTTACTATATCTG 5 76 1 TATTATTTTT 0.677389 -142 ATTGTTAGAATATTATTATATAATTATTAA 5 187 1 TATTATTATA 0.884884 -31 ATTATATAATTATTAATTTATAAAGTT 5 201 1 TATTAATTTA 0.917177 -17 TAAATCTCCTTATTATTTTAA 6 2 0 TATTATTTTA 0.95129 -31 AAAATTATATATTTAAGAATATTAA 8 40 0 TATATATTTA 0.557476 -15 AAACGTTATAATTATAACAAGATCAA 9 7 1 TATAATTATA 0.495696 -176 TATGTAATACTATAATTTTGCTTACTTATT 9 79 0 TATAATTTTG 0.677792 -104 GTAGTGCATCAATTATTATACTTTATAACA 9 115 1 AATTATTATA 0.838967 -68 TTAAGTTTAATAATTTAAAATTGAATT 9 166 0 TAATAATTTA 0.669767 -17 AACATACTGATATTACTTTATCGCAACTTA 10 64 1 TATTACTTTA 0.689989 -52 TATCGCAACTTAATATTTTAGTCATACTAA 10 82 1 TAATATTTTA 0.814208 -34 TAGCATGATGTATTATTTTGTAAACAAATA 11 46 1 TATTATTTTG 0.827093 -30 AATAATTATATTCACCATTT 12 1 1 AATAATTATA 0.524675 -300 TACATTACAATATTTATTTAAAAAATATTA 12 30 1 TATTTATTTA 0.805306 -271 TTTTTGTATTTATAAATATATTAATTATCT 13 129 1 TATAAATATA 0.487269 -20 TATCATTCCGTATAATTTTATGCATAAAAA 16 24 1 TATAATTTTA 0.579502 -127 GTTTTTTGTTTATTTTTATGCATAAAATTA 16 36 0 TATTTTTATG 0.560636 -115 TCTAATCTAATATAAATATAACTTA 17 6 0 TATAAATATA 0.487269 -116 ATATTTATTTTATTATTTTATTCTTATAAC 18 56 0 TATTATTTTA 0.95129 -31 TATTATTTTTTTGATTATTA 19 1 1 TATTATTTTT 0.677389 -57 ATTTATAACATAATTTTATAATGAGTAAAA 20 25 0 TAATTTTATA 0.541679 -50 ATACCATTTTTATTAATATAATTATTTTAA 20 53 1 TATTAATATA 0.873466 -22 AATATATATTTTTACTGTATAAGT 22 5 1 TATATTTTTA 0.592665 -76 CTGTATAAGTTAAAATTTTATTATATAAGA 22 25 1 TAAAATTTTA 0.453315 -56 TTTTTAATTATTTTATTCTAGATTA 22 66 0 AATTATTTTA 0.877042 -15 CTAACTTGTTAATTTTTATATTACAGATTT 23 110 1 AATTTTTATA 0.655781 -191 ATTAGAGCAAAATTAATATATTTCATTGGT 23 169 0 AATTAATATA 0.695526 -132 GGTATTTCATTAATATTTTATTAGTCATAT 23 209 0 TAATATTTTA 0.814208 -92 ********** Masking position 7 Map Score: 33.0952 Number of sites scoring better than the average of aligned sites = 1269 Number in coding regions = 782 Number in noncoding regions = 487 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 2 TATTTAGAGATTACTTAGTATTCATAGATAC 1 15 0 TTACTAGTAT 0.738069 -286 TACTAAGAATTTTATTTTTATCAATAATTTT 2 130 0 TTTATTTTAT 0.706909 -69 TACAAATCATTTTTTTATTATTACTAAGAAT 2 151 0 TTTTTATTAT 0.941067 -48 TTTACCTATTATTATTATTATAAAATACAAA 2 176 0 ATTATATTAT 0.756776 -23 TACAAGATATATATTGATTATTTTCTCTAAA 3 75 1 ATATTATTAT 0.637258 -74 GCGAAATAAGATTTTTATTATTTTTACTATA 5 71 1 ATTTTATTAT 0.83709 -147 TAAGATTCGAATTTTTATTGTTAGAATATTA 5 171 1 ATTTTATTGT 0.473882 -47 ACTTTATAAATTAATAATTATATAATAATAT 5 196 0 TTAATATTAT 0.865602 -22 TTATATAGTATTTTTGAGTATTAAAATTGTT 7 117 1 TTTTTAGTAT 0.889367 -109 TTTTGCTTACTTATTAAGTATATGCCTTATC 9 63 0 TTATTAGTAT 0.854152 -120 ATTCTACTTTTTTATTAGTATGACTAAAATA 10 95 0 TTTATAGTAT 0.839952 -21 TTATTTACTCATTATATTTAAACTT 11 5 1 TTACTATTAT 0.842879 -71 TTTTATCGATTATTTGTTTACAA 11 63 0 TTATCATTAT 0.67028 -13 TTATCATAATATTCTATTTATGATGTTTTAG 12 57 1 ATTCTTTTAT 0.372172 -244 TGCTTTTTGTATTTTCAATATATATGTAACT 12 102 0 ATTTTAATAT 0.424739 -199 AATTTTACAATTTTTTATTGTAATTTCTTTA 12 220 1 TTTTTATTGT 0.73287 -81 TTTGAATCAATTTTTGATTATGAATAATATG 12 260 0 TTTTTATTAT 0.941067 -41 AACAGATCCTTTAATAAGTGTACACCGTATC 13 40 0 TTAATAGTGT 0.400605 -109 ATTTATAAATATATTAATTATCT 13 136 1 ATATTATTAT 0.637258 -13 TTAATAATGTTTTTTGTTTATTTTTATGCAT 16 43 0 TTTTTTTTAT 0.786847 -108 ATTAAAGTTGTTATTCTGTATACCGTGGTCA 16 69 1 TTATTTGTAT 0.57924 -82 TATGAATTTCTTTTTTAATATATAGACGCTT 18 13 1 TTTTTAATAT 0.694035 -74 AATTTAACTTAATATTTATTTTATTATTT 18 68 0 TTAATTTTAT 0.641088 -19 TATTATTTTTTTGATTATTATCTAATAG 19 8 1 TTTTTATTAT 0.941067 -50 CCTTTTTATTTTACTCATTATAAAATTATGT 20 17 1 TTACTATTAT 0.842879 -58 AAATACCATTTTTATTAATATAATTATTTTA 20 51 1 TTTATAATAT 0.596951 -24 GATGTAAGAGTTAATAATTATGGGAATTGTA 21 76 1 TTAATATTAT 0.865602 -225 GTGAGGTTAATTTATCAGTATACAAGGAAAA 21 178 1 TTTATAGTAT 0.839952 -123 ACATTTGCATTTTACGATTATATTAGATAAT 21 229 1 TTTACATTAT 0.641902 -72 TTTTTAATTATTTTATTCTAG 22 70 0 TTTTTATTAT 0.941067 -11 TCAGAAAATTTTTCCCATTATGAACTACTTC 23 39 1 TTTCCATTAT 0.573031 -262 AACTAACTTGTTAATTTTTATATTACAGATT 23 108 1 TTAATTTTAT 0.641088 -193 ATTAAATTTAATATTTATTATTACTGATCAT 23 271 0 ATATTATTAT 0.637258 -30 ***** ***** Masking position 9 Map Score: 28.7409 Number of sites scoring better than the average of aligned sites = 1016 Number in coding regions = 630 Number in noncoding regions = 386 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 3 AATGTGAGAAATTTAAATTAATAATATTGATTTA 1 91 0 ATAATAATAA 0.874786 -210 TAAATTTGAGATTCAAGTTATTAATTGAAGTAGA 1 131 0 ATAATATTAA 0.828922 -170 ATATAGTAATTTTAAACTAAATTTGAGATTCAAG 1 148 0 TTAAAAATTT 0.688491 -153 TTGCTGGAAATTACAAAGTAATTAATACAGTTTT 2 16 1 TTAATAATTA 0.748974 -183 TAAAATTTTTATAGAATATAATATGAGAATTATT 3 11 1 ATAATAATAT 0.896783 -138 AATTCTTGTGTTTAAAGGAAATAATTTGTATATT 4 18 1 TTAAAAATAA 0.857174 -58 AACTTTATAAATTAATAATTATATAATA 5 200 0 TTAATAATAA 0.908539 -18 ACATTTTTACTTTAAATGAAATAAAAAT 8 5 0 TTAAAAATAA 0.857174 -50 ACGAATTCAATTTTAAATTATTAAACTTAA 9 163 1 TTAATATTAA 0.874789 -20 ATGTATTATTTTGTAAACAAATAATCGATAAAA 11 53 1 TTAAAAATAA 0.857174 -23 CAATATTTATTTAAAAAATATTATCATAATATTC 12 37 1 TTAATATTAT 0.896243 -264 TTATGATGTTTTAGAACATATTATTCTTAGTTAC 12 74 1 TTAATATTAT 0.896787 -227 AATTAATTAAATATAAGTTAATTTTCATTAATAT 12 151 0 ATAATAATTT 0.72013 -150 TTTTATTGATTTAAAATTAATTAAATATAAGTTA 12 165 0 TTAAAATTAA 0.806258 -136 TATGAACTATATATAAAGAAATTACAATAAAAAA 12 230 0 ATAAAAATTA 0.552033 -71 CCGAAGATTATTTGAATCAATTTTTGATTATGAA 12 267 0 TTAAAATTTT 0.605153 -34 CTGAGTACCAATCTAATCAAATATTCTGAGATTC 15 23 0 ATAAAAATAT 0.838081 -52 CGGGATGAGTTTCTAATCTAATATAAATATAACT 17 13 0 TTAATAATAT 0.926091 -109 TGACCACGGGTTCAAAATTATTAATATCATAGTT 17 72 0 TTAATATTAA 0.874793 -50 TATTTTATTCTTATAACTTATTATTAGTTAAGCG 18 39 0 TTAATATTAT 0.895997 -48 AATTTAACTTAATATTTATTTTATT 18 72 0 ATAATAATAT 0.896791 -15 AAAATGGTATTTATAACATAATTTTATAATGAGT 20 29 0 TTAATAATTT 0.787713 -46 TATTAAAATAATTATATTAATAAAA 20 60 0 ATAAAATTAT 0.782097 -15 AATATGCTCATTTAAACGAAATATTAGTTAATGC 21 129 1 TTAAAAATAT 0.881855 -172 AAATTTTATTATATAAGATATTATAGCTCTAATC 22 37 1 ATAATATTAT 0.856716 -44 TTTAACACCAATGAAATATATTAATTTTGCTCTA 23 163 1 ATAATATTAA 0.828911 -138 AGTAACATAATTAAATTTAATATTTATTATTAC 23 278 0 ATAATAATAT 0.896795 -23 ** ** ****** Masking position 6 Map Score: 32.9861 Number of sites scoring better than the average of aligned sites = 754 Number in coding regions = 459 Number in noncoding regions = 295 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 4 TTTGCCATATAAAACTTACAATTTTATTGCATAATAA 1 225 1 AAATATTTAT 0.832329 -76 GCGATATTATATAAGTTATGCTTTTATTATGCAATAA 1 248 0 ATATCTTTAT 0.747838 -53 AACTGACTTAATCACTAGCGATATTATATAAGTTATG 1 265 0 ATATATTTAT 0.943467 -36 AAAAAACTGTATTAATTACTTTGTAATTTCCAGCAAC 2 15 0 ATATTTTAAT 0.711148 -184 TTTTTTTATTATTACTAAGAATTTTATTTTTATCAAT 2 136 0 ATATATTTAT 0.941534 -63 ATTATAAAATACAAATCATTTTTTTATTATTACTAAG 2 154 0 ACATTTTTAT 0.719636 -45 CAAAATGTACAATAATTCTCATATTATATTCTATAAA 3 18 0 AAATATTTAT 0.832473 -131 AGAGAAAATAATCAATATATATCTTGTATACCAAAAG 3 66 0 ATATATTTGT 0.695043 -83 TTTAAAGGAAATAATTTGTATATTTATACTTAATTTT 4 28 1 ATATTATTAT 0.481146 -48 ATATAGTAAAAATAATAAAAATCTTATTTCGCTAAAA 5 66 0 AAATATTTAT 0.832464 -152 GAAATGATTTAAGATTCGAATTTTTATTGTTAGAATA 5 162 1 AAATTTTTAT 0.892978 -56 AACTTTATAAATTAATAATTATATAATAATATTCTAA 5 191 0 ATATATTAAT 0.59432 -27 TTTAATCTCTATAAATCTCCTTATTATTTTAA 6 6 0 ATATTTTTAT 0.96526 -27 TGAGAGTTTCAAAATTGATCTTGTTATAATTATAACG 9 14 0 AAATTTTTAT 0.892946 -169 CGTCATAAAGATCATTACCTATGTTATAAAGTATAAT 9 129 0 ATATATTTAT 0.943467 -54 AATAAGATTTATAACTATGCTTTTTGTATTTTCAATA 12 113 0 ATATTTTTGT 0.790884 -188 CCTTTTTGGAATGATTAGACTTACTATTGTCCATTTT 13 76 1 ATATTTCTAT 0.675268 -73 TTTTGTATTTATAAATATATTAATTATCT 13 130 1 ATATTATTAT 0.458572 -19 CTGTGACTTAATACCTCCAGTTCTTATAGAATTAATT 14 39 0 ATCTTTTTAT 0.683705 -111 AACAAAAAACATTATTAAAGTTGTTATTCTGTATACC 16 56 1 ATATTTTTAT 0.963442 -95 AATATGAATTTCTTTTTTAATATATAGACG 18 4 1 ATATTTTTAA 0.58386 -83 AATTTAACTTAATATTTATTTTATTATTTTATTCTTA 18 60 0 AAATTTTTAT 0.892963 -27 TATTATTTTTTTGATTATTATCTAATAGTTT 19 5 1 ATTTTTTTAT 0.71998 -53 AAATTATGTTATAAATACCATTTTTATTAATATAATT 20 39 1 ATATTTTTAT 0.940933 -36 AGTCAAACATATTTATTGCTTTATTATCTAATATAAT 21 245 0 ATTTTTTTAT 0.71998 -56 TTTTTACTGTATAAGTTAAAATTTTATTATATAAGAT 22 19 1 ATATATTTAT 0.929029 -62 TATTAGTCATATGAATATCAATATTAGAGCAAAATTA 23 184 0 ATATATTTAG 0.553283 -117 AGTAACATAATTAAATTTAATATTTATTATTAC 23 278 0 ATATTTATAT 0.582428 -23 ** * * ** **** Masking position 6 Map Score: 32.8812 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 225 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 GCATCAATCTATAAAAAACTGTATTAATTAC 2 33 0 ATAAAAAATG 0.954966 -166 CTTAGTAATAATAAAAAAATGATTTGTATTT 2 154 1 ATAAAAAATG 0.954966 -45 TCTTATTTCGCTAAAAAAATATTTCTCTAAT 5 51 0 CTAAAAAATA 0.695377 -167 AGTCATACTAATAAAAAAGTAGAAT 10 101 1 ATAAAAAATA 0.930057 -15 TTTTAAATCAATAAAAAACTCATAACCCAGC 12 183 1 ATAAAAAATC 0.899477 -118 AGAAATTACAATAAAAAATTGTAAAATTTTG 12 217 0 ATAAAAAATG 0.954966 -84 ATTATTCATAATCAAAAATTGATTCAAATAA 12 263 1 ATCAAAAATG 0.880228 -38 TACAGTGAAGATAAAAAACTGTGACTTAATA 14 63 0 ATAAAAAATG 0.954966 -87 TACCAATCTAATCAAATATTCTGAGATTCCT 15 21 0 ATCAAATATC 0.524385 -54 AGTTATAAGAATAAAATAATAAAATAAATAT 18 55 1 ATAAAATATA 0.825408 -32 AATGAGTAAAATAAAAAGGTATTAA 20 5 0 ATAAAAAGTA 0.695377 -70 CATATGACTAATAAAATATTAATGAAATACC 23 208 1 ATAAAATATA 0.825408 -93 ******** ** Masking position 6 Map Score: 9.73947 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 150 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 TAGCTATTCAAAGATGAATCTCAAATAAATCAATATTAT 1 66 1 AATAACAATA 0.953657 -235 TTCAATTAATAACTTGAATCTCAAATTTAGTTTAAAATT 1 136 1 AATAACAATA 0.953658 -165 TATTATTATTATTATAAAATACAAATCATTTTTTTATTA 2 162 0 ATTAACAATT 0.677835 -37 ATCAATATATATCTTGTATACCAAAAGTAGCGAATATCC 3 54 0 ATTTACAAAA 0.556555 -95 AAAAATATCAAAATTTAAGACCTAATTAATA 3 128 1 AATAACAATA 0.953653 -21 TTTAAGACTTAAAATTAAGTATAAATATACAAATTATTT 4 36 0 AATAATAATA 0.653322 -40 TCTAATTATCAATTTAAATAACTAATACAGATAACCTTT 5 18 0 AATAACAATA 0.953659 -200 ATCATCACTAAACCTGTACCTCTAATAAAACTAATTCCA 7 164 1 AATTACAATA 0.958429 -62 CATAGGTAATGATCTTTATGACGAATTCAATTTTAAATT 9 143 1 GATTACAATA 0.732946 -40 TAAATATTGTAATGTAAATGGTGAATATAATTATT 12 7 0 AATAATAATA 0.65731 -294 ATTGTAGTTTAGTATCTAAGACAAATAGATAGAGATGAC 14 116 0 AGTTACAATA 0.898463 -34 ATTTCGTAACAAATTTTAATCCCAATACAATTCCCATAA 21 93 0 AATTACAATA 0.958429 -208 ATCTAATATAATCGTAAAATGCAAATGTTCTTCCGTATC 21 218 0 ATTAACAATT 0.677881 -83 AGTTTATGATTTACAGCAATTAAAAATAAAGTCA 21 277 0 ATTTACATTA 0.556555 -24 ATTATATAAGATATTATAGCTCTAATCTAGAATAAAATA 22 44 1 ATTTACAATA 0.939854 -37 TATTGTTATTATCGTCTATCACTAATAAAGACGTAAACT 23 73 1 ATTTACAATA 0.939854 -228 TAATAAGAGAAGAATTTAACACCAATGAAATATATTAAT 23 149 1 AGTTACAATA 0.898461 -152 ** * ** * *** * Masking position 8 Map Score: 13.9071 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 100 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 GTTCTTTTATTTAGAGATTACTTAGTATTCATA 1 20 0 TTAAGATATT 0.76702 -281 ATAAAAATACTAATATAGTAATTTTAAACTAAA 1 161 0 TAAATATATT 0.48135 -140 TTGCTGGAAATTACAAAGTAATTAATACAGTTT 2 16 1 TTAAAATATT 0.798838 -183 ATTTTACCTATTATTATTATTATAAA 2 183 0 TTACTATATA 0.895689 -16 AAATTAATAATTATATAATAATATTCTAACAAT 5 187 0 TTAATATATA 0.900011 -31 AACTTTATAAATTAATAATTATATAAT 5 201 0 TTAAAATATA 0.744727 -17 ATGATGTTCTTTATATAGTATTTTTGAGTATTA 7 107 1 TTAATATATT 0.924603 -119 AATTATAGTATTACATAGTATTTGTAGTGCATC 9 92 1 TTAATATATT 0.924605 -91 GATTATTTGTTTACAAAATAATACATCATGCTA 11 46 0 TTAAAATATA 0.744751 -30 TTTTATCGATTATTTGTTTACAAAA 11 61 0 TTACGATATT 0.7583 -15 CAATATTTATTTAAAAAATATTATCATAATATT 12 37 1 TTAAAATATA 0.744675 -264 TTAATGAAAATTAACTTATATTTAATTAATTTT 12 154 1 TTACTTTATT 0.455377 -147 ATTACATATTATTTCAAGCAATAG 15 61 0 TTAATATATT 0.924604 -14 GTACCTGGTATCATATAGTAGTTTGACCACGGT 16 90 0 TCAATATATT 0.579042 -61 ATATAGACGCTTAACTAATAATAAGTTATAAGA 18 32 1 TTACTATATA 0.89569 -55 TTTTTGATTATTATCTAATAGTTTAATCACCAG 19 18 1 TTACTATATT 0.921177 -40 ATTTCCTGCATTAACTAATATTTCGTTTAAATG 21 137 0 TTACTATATT 0.921177 -164 TATTGCTTTATTATCTAATATAATCGTAAAATG 21 236 0 TTACTATAAA 0.53326 -65 CTATAATATCTTATATAATAAAATTTTAACTTA 22 30 0 TTAATATAAA 0.545209 -51 *** *** ** ** Masking position 9 Map Score: 18.1201 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 108 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 8 ATATTATTAATTTAAATTTCTCACATTACATGTTCT 1 98 1 TTTATCTAAT 0.481349 -203 CAAATTTAGTTTAAAATTACTATATTAGTATTTTTA 1 157 1 TTAATCTTTT 0.562553 -144 TAATAAAAGCATAACTTATATAATATCGCTAGTGAT 1 256 1 ATAATATAAT 0.620321 -45 ATTTTAAGTCTTAAAATCTATAATAT 4 60 1 TTAATATAAT 0.935448 -16 TCTATAAGTTTTAAAGTACCTGATATTGTGACTTCT 5 120 1 TTAATCTAAT 0.940496 -98 TAAGACATTTTTACTTTAAATGAAATAAAAAT 8 7 0 TTACTATAAT 0.590505 -48 ATGTAATACTATAATTTTGCTTACTTATTAAGTATA 9 72 0 ATAATCTATT 0.384449 -111 GCATCAATTATTATACTTTATAACATAGGTAATGAT 9 120 1 TTATTATAAT 0.493144 -63 TTAAGTTTAATAATTTAAAATTGAAT 9 167 0 TTAATATATT 0.846122 -16 TACTTTTTTATTAGTATGACTAAAATATTAAGTTGC 10 86 0 TTAGTCTAAT 0.601749 -30 CTCATTATATTTAAACTTGCTGAAATGATAGCATGA 11 18 1 TTAATCTAAT 0.940496 -58 TTAATTTTCATTAATATAAATAAGATTTATAACTAT 12 132 0 TTAATATAAT 0.937795 -169 TTTTATTGATTTAAAATTAATTAAATATAAGTTAAT 12 163 0 TTAATATAAT 0.937688 -138 ATTTTGATAATTAACATTCCTTTTTTGTATTTATAA 13 108 1 TTAATCTTTT 0.562536 -41 TAGCAAATTTTTAAAGTGCATCAAATATA 14 4 0 TTAATATAAT 0.937826 -146 AATTTAACTTAATATTTATTTTATTATTTTATTC 18 63 0 TTAATATTAT 0.743041 -24 TACTGATAAATTAACCTCACTTAATTTTATTTCCTG 21 162 0 TTAATCTATT 0.852107 -139 CTGTATAAGTTAAAATTTTATTATATAAGATATTAT 22 25 1 TAAATATAAT 0.469695 -56 TCTTCTCTTATTAAGATTAATTAAATCTGTAATATA 23 126 0 TTAATATAAT 0.937688 -175 AGAGAAGAATTTAACACCAATGAAATATATTAATTT 23 154 1 TTAACATAAT 0.567614 -147 ATGAAATATATTAATTTTGCTCTAATATTGATATTC 23 173 1 TTAATCTTAT 0.779144 -128 ACTTTAAACATTAAGGTACATGATAATGTAATGATC 23 241 1 TTAATATAAA 0.620321 -60 ATAATTAAATTTAATATTTATTATTACTGATCATTA 23 269 0 TTAATATATA 0.372944 -32 **** * ** * ** Masking position 11 Map Score: 20.8349 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 131 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 9 TTGACTATAAAAATACTAATATAGTAATTT 1 170 0 AAATACTAAT 0.648052 -131 ATTACTAAGCAAATATAAATACTGTCATTA 2 82 0 AAATATAAAT 0.812282 -117 ATTTGCTTAGTAATACCAAATGCTTTTGAG 2 98 1 TAATACCAAA 0.590714 -101 TATTATTATAAAATACAAATCATTTTTTTA 2 165 0 AAATACAAAT 0.78023 -34 TAAGCTTCAAAAATATCAAAATTTAAGACC 3 120 1 AAATATCAAA 0.890553 -29 AAATATCAAAGGTTATCTGT 5 1 1 AAATATCAAA 0.890553 -217 ATATTTCTCTAATTATCAATTTAAATAACT 5 34 0 AATTATCAAT 0.532054 -184 TTCAATTTTAAATTATTAAACTTAA 9 168 1 AATTATTAAA 0.428812 -15 TATATATTGAAAATACAAAAAGCATAGTTA 12 109 1 AAATACAAAA 0.845985 -192 TAATTTTCATTAATATAAATAAGATTTATA 12 137 0 TAATATAAAT 0.483347 -164 AAGGAATGTTAATTATCAAAATGGACAATA 13 100 0 AATTATCAAA 0.637572 -49 ATATATTTATAAATACAAAAAAGGAATGTT 13 120 0 AAATACAAAA 0.845985 -29 GCAACATCTAAAATATAAAATA 16 139 1 AAATATAAAA 0.870047 -12 AATCTAATATAAATATAACTTA 17 3 0 AAATATAACT 0.486653 -119 ATTAAATCTGTAATATAAAAATTAACAAGT 23 113 0 TAATATAAAA 0.591415 -188 ATGACTAATAAAATATTAATGAAATACCAC 23 211 1 AAATATTAAT 0.691771 -90 AATATTAATGAAATACCACACTTTAAACAT 23 222 1 AAATACCACA 0.593908 -79 CAGTAATAATAAATATTAAATTTAATTATG 23 276 1 AAATATTAAA 0.776409 -25 ********** Masking position 4 Map Score: 12.7105 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 342 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 10 TCATATAGTAGTTTGACCACGGTATACAGA 16 83 0 GTTTGACCAC 0.991973 -68 TCATCCCGTGGTTTGACCACGAAAGCCAAA 17 39 1 GTTTGACCAC 0.991973 -83 ACATCTCGTGGTTTGACCACGGGTTCAAAA 17 89 0 GTTTGACCAC 0.991973 -33 TTATCTAATAGTTTAATCACCAGTTTTCAG 19 28 1 GTTTAATCAC 0.886814 -30 ********** Masking position 6 Map Score: 3.29187 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 1 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 TTTTGTGTAGTTCTTTTATTTAGAGATTAC 1 32 0 TTCTTTTATT 0.591918 -269 ATATAAGTTATGCTTTTATTATGCAATAAA 1 247 0 TGCTTTTATT 0.787719 -54 ACTTATAGAATGCTTTTTTACTACAGATAT 5 99 0 TGCTTTTTTA 0.957239 -119 ATTCTACTTTTTTATTAGTATGAC 10 102 0 TACTTTTTTA 0.77594 -14 TTTATAACTATGCTTTTTGTATTTTCAATA 12 113 0 TGCTTTTTGT 0.851629 -188 TAATTTCATATTCTTTTTGAAGTCATCTCT 14 95 1 TTCTTTTTGA 0.810504 -55 AATATGAATTTCTTTTTTAATATATAGAC 18 10 1 TTCTTTTTTA 0.897438 -77 ATATCTACACTGCTTTTTTAGCTTGTAATC 21 18 0 TGCTTTTTTA 0.957239 -283 ACATATTTATTGCTTTATTATCTAATATAA 21 246 0 TGCTTTATTA 0.779195 -55 ********** Masking position 5 Map Score: 3.90354 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 125 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 TTTAAATTAATAATATTGATTTATTTGAGA 1 84 0 TAATATTGAT 0.602695 -217 TATTATGCAATAAAATTGTAAGTTTTATAT 1 231 0 TAAAATTGTA 0.698262 -70 GCTTTTGAGTTAAAATTATTGATAAAAATA 2 119 1 TAAAATTATT 0.599164 -80 TTGATAAAAATAAAATTCTTAGTAATAATA 2 137 1 TAAAATTCTT 0.914861 -62 TAAAATTTTTATAGAATATA 3 1 1 TAAAATTTTT 0.675517 -148 AATTCTCATATTATATTCTATAAAAATTTT 3 12 0 TTATATTCTA 0.296639 -137 AAGATTAAATTCTTGTGTTTAAAG 4 5 1 TTAAATTCTT 0.706034 -71 TATTAGTTATTTAAATTGATAATTAGAGAA 5 30 1 TTAAATTGAT 0.399195 -188 GTAAAAATAATAAAAATCTTATTTCGCTAA 5 68 0 TAAAAATCTT 0.376874 -150 AATTATATAATAATATTCTAACAATAAAAA 5 182 0 TAATATTCTA 0.653851 -36 AGACAAATTTTACAATTCTTGCATAAAATT 7 41 0 TACAATTCTT 0.632469 -185 TTTTGAGTATTAAAATTGTTAAAAATTCGT 7 128 1 TAAAATTGTT 0.90523 -98 AAAAATGTCTTAATATTCTTAAATATATAA 8 31 1 TAATATTCTT 0.845755 -24 TTTAATAATTTAAAATTGAATTCGTCATAA 9 158 0 TAAAATTGAA 0.494036 -25 AATATTATGATAATATTTTTTAAATAAATA 12 40 0 TAATATTTTT 0.521847 -261 AATATTATCATAATATTCTATTTATGATGT 12 53 1 TAATATTCTA 0.653851 -248 TTTATTGATTTAAAATTAATTAAATATAAG 12 168 0 TAAAATTAAT 0.314444 -133 TAAAATTGCTCCGAAGATTA 12 291 0 TAAAATTGCT 0.666953 -10 GTACTCAGTTTACTATTGCTTGAAATAATA 15 49 1 TACTATTGCT 0.140515 -26 AAAACATTATTAAAGTTGTTATTCTGTATA 16 61 1 TAAAGTTGTT 0.447027 -90 TCCCAGTTAGTGAAATTCTTGAAAAGATGT 21 51 1 TGAAATTCTT 0.5197 -250 CTGTATAAGTTAAAATTTTATTATATAAGA 22 25 1 TAAAATTTTA 0.334544 -56 TTCATTGGTGTTAAATTCTTCTCTTATTAA 23 148 0 TTAAATTCTT 0.706034 -153 AATTTTGCTCTAATATTGATATTCATATGA 23 185 1 TAATATTGAT 0.602695 -116 ********** Masking position 7 Map Score: 8.77719 Number of sites scoring better than the average of aligned sites = 841 Number in coding regions = 593 Number in noncoding regions = 248 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 13 GTTCTACTTCAATTAATAACTTGAATCTCAAA 1 129 1 ATTAATAATT 0.309509 -172 TCTCAAATTTAGTTTAAAATTACTATATTAGT 1 154 1 ATTTAAAATA 0.334623 -147 ATGCAATAAAATTGTAAGTTTTATATGGCAAA 1 225 0 ATGTAAGTTT 0.241383 -76 CACTAGCGATATTATATAAGTTATGCTTTTAT 1 258 0 ATATATAATT 0.642063 -43 TGTATTAATTACTTTGTAATTTCCAGCAACTT 2 13 0 ATTTGTAATT 0.41882 -186 TCTATAAAAAACTGTATTAATTACTTTGTAAT 2 25 0 ATGTATTATT 0.661065 -174 AAAATATCAAAATTTAAGACCTAATTAATA 3 129 1 ATTTAAGACT 0.274851 -20 ATATTATAGATTTTAAGACTTAAAATTAAGT 4 55 0 ATTTAAGATT 0.831678 -21 AATATCAGGTACTTTAAAACTTATAGAATGCT 5 115 0 ATTTAAAATT 0.909898 -103 AACTTTATAAATTAATAATTATA 5 205 0 ATTTATAATT 0.820089 -13 TTATGCAAGAATTGTAAAATTTGTCTATCAAT 7 45 1 ATGTAAAATT 0.872527 -181 AATATTCTTAAATATATAATTTT 8 42 1 ATATATAATT 0.636054 -13 ATTCCTTGAGAGTTTCAAAATTGATCTTGTTA 9 25 0 ATTTCAAATT 0.436473 -158 CAATTATTATACTTTATAACATAGGTAATGAT 9 124 1 ATTTATAAAT 0.326738 -59 TTAAGTTTAATAATTTAAAATTGAA 9 168 0 ATTTAATATT 0.755669 -15 ACAATAAAAAATTGTAAAATTTTGATTGCTGG 12 209 0 ATGTAAAATT 0.872527 -92 TCAATTTTATAAATTGATGTTTTGT 13 4 1 ATTTATAATT 0.686695 -145 TATTTGATGCACTTTAAAAATTTGCTAATTAA 14 13 1 ATTTAAAATT 0.908634 -137 TTTTATCTTCACTGTATTAATTTCATATTCTT 14 78 1 ATGTATTATT 0.661065 -72 TATTTTATATTTTAGATGTTGCT 16 138 0 ATTTATATTT 0.471157 -13 CTTAATATTTATTTTATTATTTTATTCTTATA 18 58 0 ATTTATTATT 0.742188 -29 TTCTTGAAAAGATGTAAGAGTTAATAATTATG 21 66 1 GTGTAAGATT 0.198146 -235 AGTTTATGATTTACAGCAATTA 21 289 0 ATTTATGATT 0.821213 -12 ATATATTTTTACTGTATAAGTTAAAATTTTAT 22 14 1 ATGTATAATT 0.864164 -67 TTAAATCTGTAATATAAAAATTAACAAGTTAG 23 110 0 ATATAAAATT 0.651853 -191 GAAATACCACACTTTAAACATTAAGGTACATG 23 231 1 ATTTAAACTT 0.446077 -70 AACATAATTAAATTTAATATTTATTATTACTG 23 276 0 ATTTAATATT 0.755952 -25 * ******* ** Masking position 3 Map Score: 16.7852 Number of sites scoring better than the average of aligned sites = 752 Number in coding regions = 452 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 14 ********** No masking Map Score: 8.25894e-12 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: 8.25894e-12 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