AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_rpxx_reg_300.orf -o00230_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: RP636 23 30S RIBOSOMAL PROTEIN S11 (rpsK) RP655 24 30S RIBOSOMAL PROTEIN S19 (rpsS) Input sequences: #1 RP053 300 ADP,ATP CARRIER PROTEIN (tlc1) #2 RP054 72 GLYCEROL-3-PHOSPHATE TRANSPORTER (glpT) #3 RP055 162 NUCLEOSIDE DIPHOSPHATE KINASE (ndk) #4 RP064 249 DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE (dgtP) #5 RP140 300 DNA-DIRECTED RNA POLYMERASE BETA CHAIN (rpoB) #6 RP141 156 DNA-DIRECTED RNA POLYMERASE BETA PRIME CHAIN (rpoC) #7 RP171 300 DNA-BINDING PROTEIN HU (hupA) #8 RP172 110 DNA POLYMERASE III, DELTA SUBUNIT (holB) #9 RP215 297 unknown #10 RP216 172 CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT I (cydA) #11 RP217 93 CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT II (cydB) #12 RP218 259 unknown #13 RP219 138 MITOCHONDRIAL PROTEASE (mpp) #14 RP220 133 PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE (purC) #15 RP303 89 RNA POLYMERASE SIGMA-32 FACTOR (rpoH) #16 RP415 300 DIAMINOPIMELATE EPIMERASE (dapF) #17 RP417 106 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (pheS) #18 RP501 215 TRNA PSEUDOURIDINE 55 SYNTHASE (truB) #19 RP503 21 30S RIBOSOMAL PROTEIN S15 (rpsO) #20 RP504 154 POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE (pnp) #21 RP512 164 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE BETA CHAIN (nrdB) #22 RP513 300 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE ALPHA CHAIN (nrdA) #23 RP541 62 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE (ubiX) #24 RP637 57 30S RIBOSOMAL PROTEIN S13 (rpsM) #25 RP641 24 50S RIBOSOMAL PROTEIN L30 (rpmD) #26 RP649 60 50S RIBOSOMAL PROTEIN L14 (rplN) #27 RP658 241 50S RIBOSOMAL PROTEIN L4 (rplD) #28 RP660 93 30S RIBOSOMAL PROTEIN S10 (rpsJ) #29 RP661 300 ELONGATION FACTOR TU (tuf) #30 RP730 300 unknown #31 RP765 116 GUANYLATE KINASE (gmk) #32 RP766 300 unknown #33 RP774 93 unknown #34 RP775 191 CELL DIVISION PROTEIN FTSY (ftsY) #35 RP776 153 DNA POLYMERASE I (polA) #36 RP778 127 DNA POLYMERASE III, ALPHA CHAIN (dnaE) #37 RP779 245 UDP-GLUCOSE 6-DEHYDROGENASE (udg) #38 RP864 66 unknown #39 RP865 149 DNA POLYMERASE III SUBUNITS GAMMA AND TAU (dnaX) Motif number 1 TTTAGTGAACTTTAAATTGTAAAGGCTTATTTG 1 95 0 TTTAATTTAA 0.581342 -206 TTTACTTAATTTTGATTTCTATATATTAACTGT 1 146 0 TTTGTTTTAA 0.895086 -155 TAGAAGCTTTTTTATATTTTTTTACAAATT 2 8 0 TTTAATTTTT 0.719921 -65 AATCTAATAATTTATTATATATAAAGGTTATAA 3 138 1 TTTATATTAA 0.498662 -25 AATTTAAATTATTATATTTTAAACAGTAAAGCT 5 64 0 ATTAATTTAA 0.620834 -237 AATATAATAATTTAAATTTTATATAGAACCTAG 5 79 1 TTTAATTTAA 0.947703 -222 AATAACAATTTTTAAATTATACAACAAGACAAA 6 33 0 TTTAATTTAA 0.947703 -124 ATGTTATTATATTAATTTATAGAAAAATGTAGC 7 110 0 ATTATTTTAA 0.672526 -191 ATTTACAAAGTTTAAAATATATATGTTATTATA 7 132 0 TTTAAATTAA 0.588505 -169 GAAGTTGGTATTTATTTTTTATAAAAACATCAA 7 238 1 TTTATTTTAA 0.923823 -63 TTAACTGTAATTTGTATTTTATTTGGTATTATT 9 17 0 TTTGATTTAT 0.804388 -281 TAAAATTAAGATTACTTTATTAACTGTAATTTG 9 36 0 ATTATTTTTA 0.474198 -262 AGCTTAGGTATTTATTTTTTAAAATTTGATAAA 9 65 0 TTTATTTTAA 0.910812 -233 TTTATTAAAATTTTTTTTGTAAAAATATACCTC 9 180 1 TTTTTTTTAA 0.585819 -118 ATATAAAAAATTTGCTTTTTATATATTTTCCGG 10 75 1 TTTGTTTTAA 0.895086 -98 TTTGTATTATACAGCAATTTGCT 11 1 1 TTTGATTTAA 0.945763 -93 TAGTTATTTTTTTAAATTTTTTAGAAATTTTCA 12 17 0 TTTAATTTTA 0.91603 -243 AATTTATTTTTATTTTCTAAATAATCATTTT 13 118 0 TTTATTTTAA 0.910812 -21 AATACAAATTTTTAATATGTAAAACATT 16 283 1 TTTATATTAA 0.44137 -18 AATTATTTTTTGTTTTTAGATTTTATCTCA 17 87 0 TTTTTTTTAA 0.586748 -20 GATATACTCGTTTAATTTTAAAATTGGCTAAGT 18 77 1 TTTATTTAAA 0.570117 -139 ATAGACACAGTTTAATTTCAACAAGAGCAAAAA 18 166 0 TTTATTTAAA 0.571081 -50 GTCTATCAATTTTGCATTTTATATCATATATTC 18 193 1 TTTGATTTAA 0.945763 -23 CATTTCATAATTTATATTCTATTAAAGATATCA 20 122 0 TTTAATTTAT 0.851996 -33 TATTACTAATATTACATTGTTTAAAGGTTTTTT 21 138 0 ATTAATTTTA 0.648772 -27 CTTTTGTATTATTTTTTTCAACAAT 22 3 1 TTTGATTTTT 0.643614 -298 TTTATTTTTTTTTAGATTTTTGACTTGACAAAA 22 158 0 TTTAATTTTA 0.91603 -143 AAATAAAATATTTATATTGAATAAATTATTATT 22 184 1 TTTAATTAAA 0.730454 -117 TTTTATATTGTTTTTATTATATACTAAATTTAA 23 22 1 TTTTATTTAA 0.74294 -41 ATCAAAGATTTTTATATTATTTTCTAGTTACTA 24 15 1 TTTAATTTTT 0.719921 -43 AAATAAACAATTTACATTATTAAGTCAAAAG 26 9 0 TTTAATTTTA 0.903131 -52 ATAATAGGTATTTGTATTTTAATATCTGAAAAA 28 40 1 TTTGATTTAT 0.802225 -54 GCTGTTGCTCTTTGTATTGTTGACTCATTGTTC 30 16 0 TTTGATTTTA 0.884707 -285 TTATTTTACCTTTACATTTTAATTAAATTCAGG 30 210 0 TTTAATTTAT 0.685496 -91 GAATTCTAGATTTATATTAAAAATTGGCTTATA 30 243 1 TTTAATTAAA 0.620062 -58 ACAAGTGAATTTTGTATTATTAATGCATTTGAC 31 19 1 TTTGATTTTA 0.884606 -98 CTTCCAGGGCTTTGCATTTTAAATTCATCTTGT 31 58 1 TTTGATTTAA 0.931125 -59 ACAAATACTTTTTAATTTATTTAGCGAGGCTAA 33 13 0 TTTATTTTTA 0.842091 -81 GGTCATATCATTTGCATTGTAGATTTCAGCTAT 35 112 0 TTTGATTTAA 0.945763 -42 TTTAGATTTTATTTATATAGGTC 35 141 0 TTTAATTTAT 0.851996 -13 TGATTTTTATATTAAATTTTTAAATTATACGTT 37 214 0 ATTAATTTTA 0.646575 -32 AAATACTTTAATTATATTATTAAAACAAATATT 38 13 0 ATTAATTTTA 0.646575 -54 TTTTATTGTTTTGTATTTTAAATTATGTTTAA 38 45 0 TTTGATTTAA 0.931125 -22 **** *** ** * Masking position 8 Map Score: 43.4612 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 346 Number in noncoding regions = 246 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 2 TCTTATGACAATACAAAATATTGAAGGTAAA 1 44 0 ATAAAAATAT 0.925794 -257 CTTCAAATAAATAGAAAATTTAATT 1 286 1 ATAAAAATTT 0.88747 -15 AATTTGTAAAAAAATATAAAAAAGCTT 2 7 1 TAAAAAATAT 0.731028 -66 TAGGCTCAAGATATAAATTTTAACACAGAGA 3 13 0 ATAAAATTTT 0.914346 -150 CCTTTATATATAATAAATTATTAGATTTACT 3 134 0 TAAAAATTAT 0.786283 -29 TGTAAAAATCTTATAAATTATATAATATATC 4 23 1 TTAAAATTAT 0.914352 -227 ATTTATTATAAATTATAAGTAATTTA 5 6 1 TTAAAATTAT 0.914352 -295 CCTAGGTTCTATATAAAATTTAAATTATTAT 5 82 0 ATAAAAATTT 0.887464 -219 TTATACAACAAGACAAATTATGTACAACATA 6 19 0 AGAAAATTAT 0.767213 -138 TTATTGTCAGTAACAAATTATC 7 2 0 TAAAAATTAT 0.786283 -299 TAACGGGGTTTTAGAAATTATCAGTACTATA 8 26 0 TTAAAATTAT 0.914352 -85 TATTTTTACAAAAAAAATTTTAATAAACTAA 9 176 0 AAAAAATTTT 0.786278 -122 GCAAAAATATATAAAAAATTTGCTTTTTATA 10 67 1 ATAAAAATTT 0.887462 -106 TTTAAATTTTTTAGAAATTTTCACAGAAC 12 9 0 TTAAAATTTT 0.870942 -251 TGCAATTGCAATATAAAATAT 12 249 1 ATAAAAATAT 0.925776 -11 GATTTTATTTAAAAAAATTATAGAAAAAGTT 15 16 1 AAAAAATTAT 0.853361 -74 AACTAGTATTTTAAAAAATTTGCAGTAAGAC 16 164 0 TTAAAAATTT 0.832924 -137 ATTTGCTATAATACAAATTTTTAATATGTAA 16 274 1 ATAAAATTTT 0.914352 -27 CTTTAATAGAATATAAATTATGAAATGAGAT 20 128 1 ATAAAATTAT 0.944079 -27 ATCGTGAGCTAGAGAAATTATAGAATAATTT 21 107 0 AGAAAATTAT 0.767213 -58 AACAGTTTTTTTAAAAAATTTTGATATCTCG 22 49 1 TTAAAAATTT 0.832924 -252 ATCTAAAAAAAAATAAAATATTTATATTGAA 22 174 1 AAAAAAATAT 0.811294 -127 AATAAAAACAATATAAAATATATTTATAT 23 9 0 ATAAAAATAT 0.925776 -54 TTATAATTTCTTATAAATTATCTATAATAAT 32 98 1 TTAAAATTAT 0.914352 -203 ATCTATAATAATAAAAATTTTTTTTGTATTA 32 117 1 ATAAAATTTT 0.914344 -184 GATTAGGTGCATAAAAAATATTTAGTATTTT 34 54 0 ATAAAAATAT 0.925769 -138 *** ******* Masking position 9 Map Score: 28.0278 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 332 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 3 TTGACTTCTATCATATATTTTAGTATAATGTT 1 251 1 TATATTTTTA 0.817548 -50 TAATATATCTTAATATTTTTCAAGATGGTGTT 4 45 1 TATATTTTCA 0.674998 -205 TTCAAGATGGTGTTGTTTTGTAGTTTAGAAAT 4 63 1 TTTGTTTGTA 0.809551 -187 TCTTTAAAATTCTTGTATTTTAAGTTGCTTTA 4 161 1 TTTGTTTTTA 0.79647 -89 AAATTTAAATTATTATATTTTAAACAGTAAAG 5 66 0 TTTATTTTTA 0.894095 -235 AGTGTATATATGTTGTACATAATTTGT 6 6 1 AATATTTGTA 0.791844 -151 TGAGCCATAATGTTATTTTGTATTTAAGCTAT 6 90 1 TTTATTTGTA 0.901682 -67 ATATAATAACATATATATTTTAAACTTTGTAA 7 131 1 AATATTTTTA 0.777881 -170 AGAAGTTGGTATTTATTTTTTATAAAAACATC 7 237 1 ATTATTTTTA 0.868396 -64 ATTAACTGTAATTTGTATTTTATTTGGTATTA 9 19 0 ATTGTTTTTA 0.753597 -279 TAGCTTAGGTATTTATTTTTTAAAATTTGATA 9 67 0 ATTATTTTTA 0.868396 -231 AAGGCTTGTTTATTATTTTTCAATAGATTTAA 9 219 0 TTTATTTTCA 0.79647 -79 ATATTACTCAAAATATATTGTATTGGATGCAA 11 45 1 AATATTTGTA 0.791844 -49 ATATTTTATATTGCAATTGCAAGGA 12 245 0 TTTATTTGCA 0.809551 -15 AATTTATTTTTATTTTCTAAATAATCATT 13 120 0 TTTATTTCTA 0.622304 -19 AATCATAGGATATTGTTTTGCAGACTGTATCT 14 47 1 TTTGTTTGCA 0.663322 -87 TTATATATTGTATACAGGATCA 17 1 1 TATATTTGTA 0.829567 -106 TATTTAGCAAAGTTATGTTGTAACAATGTTGA 17 58 1 ATTATTTGTA 0.877564 -49 TGATCTCATTATATATATTGCAATATGAGATT 20 69 1 AATATTTGCA 0.638098 -86 ATATAAATATATTTTATATTGTTTTT 23 5 1 AATATTTTTA 0.777878 -58 AAGATTTTTATATTATTTTCTAGTTACTAGTA 24 19 1 TTTATTTCTA 0.622304 -39 ACGATAATTTAATTATTTTGCACTATAAATCA 27 95 0 ATTATTTGCA 0.768633 -147 TACAAATACCTATTATTTTTTAATAATAGGTA 28 24 0 TTTATTTTTA 0.894101 -70 AATAATAGGTATTTGTATTTTAATATCTGAAA 28 39 1 ATTGTTTTTA 0.753597 -55 TTAAACAGCAAGATGTTTTTCAGATATTAAAA 28 56 0 AATGTTTTCA 0.429336 -38 TAGATTTATATGTTATTTTTTATAATCTGAAA 29 85 1 TTTATTTTTA 0.894101 -216 ATTTTATGTTTTAGTTCATAGAG 31 104 0 TTTATTTTTA 0.894101 -13 TAGAAGATCAATATATTTTTTAGTTGTTATAT 32 199 1 AATATTTTTA 0.777881 -102 CAAAAATACTAAATATTTTTTATGCACCTAAT 34 52 1 AATATTTTTA 0.777881 -140 ATCTAGTCTGTTTTATGTTTTACACAGTAAAA 35 13 0 TTTATTTTTA 0.894101 -141 AGATTTCAGCTATTATATTGTATCTTGACCAT 35 93 0 TTTATTTGTA 0.901682 -61 TTTTATTGTTTTGTATTTTAAATTA 38 52 0 TTTGTTTGTA 0.809551 -15 * **** ***** Masking position 6 Map Score: 37.6198 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 214 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 4 AGAAAACAATTTTTACTTAATTTTGATTTCTATATAT 1 153 0 TTTTATTTTT 0.856088 -148 TATCATATATTTTAGTATAATGTTTATCTTCAAATAA 1 259 1 TTTAGTTTTT 0.311583 -42 TTTTATAACCTTTATATATAATAAATT 3 146 0 TTTTAATTAT 0.767634 -17 TTTATAAGATTTTTACAAGGTAATTTTAA 4 3 0 TTTTAATATT 0.337078 -247 CTATATAAAATTTAAATTATTATATTTTAAACAGTAA 5 68 0 TTTAATTTAT 0.677791 -233 AACATATATATTTTAAACTTTGTAAATAACTGGCATT 7 138 1 TTTTACTTAT 0.467189 -163 GTAATTTGTATTTTATTTGGTATTATTCCAGCA 9 7 0 TTTTATTTTT 0.856088 -291 AAAGCAAATTTTTTATATATTTTTGCTTCCTGACGCC 10 56 0 TTTTATTTTT 0.856088 -117 TCTACATTACTTTTAACTTATATAGTTAAATTAGTGT 12 103 1 TTTTATTTAT 0.905931 -157 CGTTCACAAATTTTACTTCTTTAAAATATCATTCTCA 12 140 0 TTTTATTAAT 0.705857 -120 AAAAAGTTTATTTTAGATCATATATATGTTAGTATAA 15 39 1 TTTTATTTAT 0.905921 -51 TGAATTGATTTTATTTCATGTTGTTAGTGCTAAAA 16 9 1 TTTTATTTTT 0.856088 -292 AAACACGTCTTTTTAAGTATTGGTGTTTTATTAGACT 16 50 1 TTTTATTGTT 0.59232 -251 AATGTTTTACATATTAAAAATTTGTATTATA 16 280 0 TTTTATTAAT 0.705854 -21 CTTTTGTATTATTTTTTTCAACAATAAT 22 2 1 TTTTGTTTTT 0.674491 -299 TAAACAGTTTTTTTAAAAAATTTTGATATCTCGTATC 22 47 1 TTTTAATTTT 0.671115 -254 AAGATTGGTATTTTATTAGATCTAGATACGAGATATC 22 71 0 TTTTAATTAT 0.767634 -230 TTTTATTTTTTTTTAGATTTTTGACTTGACAAAAATA 22 155 0 TTTTATTGAT 0.701683 -146 TATAAATATATTTTATATTGTTTTTATTATATACTAA 23 12 1 TTTTATTTTT 0.856088 -51 GCTTTGTTAATTTTAAATCCTAAATCTGAATAACATC 27 152 0 TTTTATTAAT 0.705858 -90 AAATCTATCTTTTAAATAGATATATTTCCCTGAACCA 29 55 0 TTTAAATTAT 0.419142 -246 AGTGCATTTTTTTTGCTAAATTTATTTGTTACCACTA 29 233 0 TTTTGATTAT 0.535041 -68 AAATTTAATTTTATCTAGATTTTATTAAAA 33 74 0 TTTAATTTAT 0.677791 -20 TTGGTGTTATTTTTACTTCATTATAATTCCATCATAC 34 139 0 TTTTATTATT 0.597146 -53 ATTAGCTAGTTTTTGTTTTATGTATGTTGGTGTTATT 34 165 0 TTTTGTTTAT 0.770357 -27 TTGATTAGATTTTTAGGTTCTCTACGTTCTTGGACAC 36 75 1 TTTTATTTAT 0.905931 -53 AGCTTCAGCTTTTTATATTATGGATCTTTGGTTCTTT 37 122 1 TTTTATTGAT 0.701683 -124 AATTTTTTGTGATTTTTATATTAAATTTTTA 37 225 0 TTTTGATTAT 0.535041 -21 TTAAATTATGTTTAAAATACTTTAATTATATTATTAA 38 23 0 TTTAATTTAT 0.677791 -44 ***** * * ** * Masking position 11 Map Score: 24.6708 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 361 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 5 TTATCTTCAAATAAATAGAAAATTTAATT 1 282 1 ATAAAAAAAT 0.648477 -19 AGTTTATGCAGTAAATCTAATAATTTATTATATA 3 125 1 GTAAACAAAT 0.753428 -38 TACAAGAATTTTAAAGATAAAAGTTGATTATCTA 4 144 0 TTAAAAAAAT 0.781747 -106 AGGCAATATTTTAAAGCGAAAATTAATACGATTT 5 141 1 TTAAACAAAT 0.941947 -160 AATCAAGTGATTAAAACCAAAAATTCATTATTAC 7 42 0 TTAAACAAAT 0.941947 -259 TTAAAATTTGATAAAATTAAGATTACTTTATTAA 9 46 0 ATAAATAAAT 0.706064 -252 TTAAATCAAATACTGTCTTGATGT 10 1 1 TTAAACAAAT 0.941947 -172 TAAGACAAAAATAAAGATAATAATCATTGCTAAA 16 136 0 ATAAAAAAAT 0.648477 -165 AGATAAAATCTAAAAACAAAAAATAATT 17 89 1 TAAAACAAAT 0.5813 -18 GTACTGCATGTTAAACTCAAAAATTTGGTGTAAG 21 61 1 TTAAATAAAT 0.823445 -104 TACATGAGAGTTAAAATAAACAATTTACATTATT 26 21 0 TTAAATAAAT 0.823445 -40 TCATTAAACCTAATATTTAAACAGCAA 28 77 0 TTAAACAAAT 0.941947 -17 ATAACTTGTATTAAACCTAAAAATTGTAGAGAGT 29 271 1 TTAAACAAAT 0.941947 -30 GCCTCGCTAAATAAATTAAAAAGTATTTGTCAAA 33 16 1 ATAAATAAAT 0.706064 -78 ACCAACATACATAAAACAAAAACTAGCTAAT 34 171 1 ATAAACAAAT 0.893125 -21 AATTATATTATTAAAACAAATATTTT 38 3 0 TTAAACAAAT 0.941947 -64 ***** * ** * * Masking position 9 Map Score: 17.225 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 62 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 6 ATCTATGTACTGCAGTATGAGGTATGTGATGTC 3 65 1 TGCATATAGT 0.918176 -98 GTGATTAAGCTGCAATAAAAATTGGAGCTACAT 4 197 1 TGCATAAAAT 0.956615 -53 TAGTTTGGCTTGCAATAACAATTTTTAAATTAT 6 46 0 TGCATAAAAT 0.956615 -111 GCAATTTGCTTGCAGTATAAAATATTACTCAAA 11 24 1 TGCATATAAT 0.974785 -70 TCCTTGCAATTGCAATATAAAATAT 12 245 1 TGCATATAAT 0.974785 -15 GTAGTACTCATGCATTAATAATGCTCCTTGCAT 18 126 1 TGCATAAAAG 0.791021 -90 TAATGCTCCTTGCATTATAAACTTTTTGCTCTT 18 144 1 TGCATATAAT 0.974785 -72 TTATATATATTGCAATATGAGATTAAGTGTTTG 20 77 1 TGCATATAGT 0.918176 -78 ATAAACAATTTACATTATTAAGTCAAAAG 26 7 0 TACATATAAT 0.701781 -54 TTAATTATTTTGCACTATAAATCACTAAATATT 27 86 0 TGCATATAAC 0.869051 -156 CAAAGCGTCATGCAATATTAAATGATTTATATA 27 183 1 TGCATATAAT 0.974785 -59 GCAAAAAAAATGCACTAATAACTTGTATTAAAC 29 254 1 TGCATAAAAT 0.956615 -47 ATAGGTCAAATGCATTAATAATACAAAATTCAC 31 23 0 TGCATAAAAA 0.718618 -94 TCCAGGGCTTTGCATTTTAAATTCATCTTGTCT 31 60 1 TGCATTTAAT 0.791879 -57 **** *** ** * Masking position 4 Map Score: 16.8033 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 44 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 CTATCATATATTTTAGTATAATGTTTATCTT 1 258 1 TTTTATATAA 0.543395 -43 AAATCTAATAATTTATTATATATAAAGGTTA 3 137 1 ATTTATATAT 0.763661 -26 ATTTATTATAAATTATAAGTA 5 1 1 ATTTATATAA 0.908632 -300 ATAAAATTTAAATTATTATATTTTAAACAGT 5 70 0 AATTATATAT 0.571841 -231 TTTTTCTATAAATTAATATAATAACATATAT 7 116 1 AATTATATAA 0.804013 -185 GTTGGTATTTATTTTTTATAAAAACATCAAT 7 241 1 ATTTTTATAA 0.633364 -60 TTGTAGCATTATTTAATGTAAGAAGCAAGGC 9 246 0 ATTTATGTAA 0.738862 -52 ATAACATTTTAATTGATATATAAATAAGTAT 16 106 0 AATTGTATAT 0.40688 -195 AGAAGCATGAAATTAGTATAATAGTCTATAT 16 209 1 AATTATATAA 0.804013 -92 ATTTCTTTAAATTTACTATAATGAATTGAGG 16 245 0 ATTTATATAA 0.908632 -56 ATTTAAAGAAATTTGCTATAATACAAATTTT 16 264 1 ATTTGTATAA 0.836399 -37 CCGCAACTTAAATTAGTGTAAGCACGTAACT 20 30 1 AATTATGTAA 0.538349 -125 ACAAATTACGATTTGGTATATGATTTATGTA 21 20 0 ATTTGTATAT 0.624681 -145 AAACTCAAAAATTTGGTGTAAGATTACATGC 21 73 1 ATTTGTGTAA 0.592377 -92 AATTCATTAAATTTAGTATATAATAAAAACA 23 30 0 ATTTATATAT 0.763661 -33 TTTATATGTTATTTTTTATAATCTGAAAAAT 29 89 1 ATTTTTATAA 0.633364 -212 ATAAGCCAATTTTTAATATAAATCTAGAATT 30 244 0 TTTTATATAA 0.543395 -57 CATTCTAAACATTTATTATAAGCCAATTTTT 30 261 0 ATTTATATAA 0.908632 -40 TGGTATTATAATTTCTTATAAATTATCTATA 32 93 1 ATTTCTATAA 0.727678 -208 TACGTTTCCTAATTCATATAACAAGGTTGGT 32 261 1 AATTCTATAA 0.524109 -40 TAATTTAAAAATTTAATATAAAAATCACAAA 37 220 1 ATTTATATAA 0.908632 -26 ***** ***** Masking position 7 Map Score: 15.2785 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 189 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 8 GTCAAACAAATTGATTTTTTCTAGAAAGAA 1 226 0 TTGATTTTTT 0.753459 -75 AAGTTATGATTCGATTTTATAGGCTCAAGA 3 33 0 TCGATTTTAT 0.698276 -130 TTAATATGTATTGATGTTTTTATAAAAAAT 7 251 0 TTGATGTTTT 0.793851 -50 TCTTATGATTTTGAAGTTATTTTCTGAATT 9 277 0 TTGAAGTTAT 0.569886 -21 AAATACTGTCTTGATGTTATTGTATGTAAT 10 18 1 TTGATGTTAT 0.939338 -155 TTCTAGTTTTTTGTTTTTATCACATCGCTT 14 17 1 TTGTTTTTAT 0.782446 -117 TGTTTGATTTTATTTAAAAAAAT 15 4 1 TTGATTTTAT 0.924751 -86 TGAATTGATTTTATTTCATGTTGT 16 5 1 TTGATTTTAT 0.924751 -296 TTTTTAAGTATTGGTGTTTTATTAGACTTT 16 59 1 TTGGTGTTTT 0.548859 -242 TTTTTGTTTTTAGATTTTATCTCAACATTG 17 81 0 TAGATTTTAT 0.863562 -26 ATATTTTATATTGTTTTTATTATATACTAA 23 19 1 TTGTTTTTAT 0.782446 -44 AATAATCTCTTAGATGTTATTCAGATTTAG 27 140 1 TAGATGTTAT 0.888583 -102 ATATATTTTTTAGTTGTTATATACTGTTAA 32 209 1 TAGTTGTTAT 0.700064 -92 TAATTTTATCTAGATTTTATTAAAAGATTA 33 69 0 TAGATTTTAT 0.863562 -25 TTTATGTATGTTGGTGTTATTTTTACTTCA 34 156 0 TTGGTGTTAT 0.830282 -36 TTTAGATTTTATTTATATAGGT 35 142 0 TAGATTTTAT 0.863562 -12 ********** Masking position 7 Map Score: 12.5748 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 86 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 TATAGTTAATAAAATGTTTATTGAGTTCTTT 1 201 1 AAAATGTTAT 0.879435 -100 AAAAAATATAAAAAAGCTTCTAAAACCTGAA 2 19 1 AAAAAGTTCT 0.603244 -54 ATTACCTTGTAAAAATCTTATAAATTATATA 4 16 1 AAAAATTTAT 0.857237 -234 ATATAAAATTTAAATTATTATATTTTAAACA 5 72 0 TAAATTTTAT 0.685397 -229 ACTTTTTCAAAAAAATCTTATGATTTACAGC 5 188 1 AAAAATTTAT 0.857237 -113 GTATAATTTAAAAATTGTTATTGCAAGCCAA 6 44 1 AAAATTTTAT 0.870585 -113 TTGGAAAATTCTTATTTACAGAATT 13 5 1 AAAATTTTAT 0.870585 -134 ATTTTTCTGTAAAATGATTATTTAGAAAATA 13 108 1 AAAATGTTAT 0.879427 -31 GATTTTATTTAAAAAAATTATAGAAAAAGTT 15 16 1 AAAAAATTAT 0.596955 -74 AAAATTATAGAAAAAGTTTATTTTAGATCAT 15 29 1 AAAAAGTTAT 0.866865 -61 ATATATCAATTAAAATGTTATTTAGCAATGA 16 116 1 TAAAATTTAT 0.660403 -185 CAACAAGAGCAAAAAGTTTATAATGCAAGGA 18 150 0 AAAAAGTTAT 0.866865 -66 TTACATGCAAAAAATTATTCTATAATTTCTC 21 96 1 AAAATTTTCT 0.610565 -69 AAAAAAAAATAAAATATTTATATTGAATAAA 22 178 1 AAAATATTAT 0.624028 -123 TTATATTGAATAAATTATTATTCTCGTGTCT 22 195 1 TAAATTTTAT 0.685397 -106 TAATACAAAAAAAATTTTTATTATTATAGAT 32 117 0 AAAATTTTAT 0.870133 -184 TAGATTTTATTAAAAGATTATAATATACTTC 33 58 0 TAAAAGTTAT 0.678411 -36 ****** **** Masking position 4 Map Score: 13.8688 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 223 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 10 TACATAGATATAAGTTATGATTCGATTTTATAG 3 41 0 TAATTATATC 0.813995 -122 TATTGCCTAATATAATATTAATCAAAAGTGTTC 5 116 0 TATATATATC 0.813995 -185 ACTCCTACTCTAAAATGTTACTCCATAGCTTAA 6 113 0 TAAATGTATC 0.77166 -44 GCTTGCAGTATAAAATATTACTCAAAATATATT 11 31 1 TAAATATATC 0.955409 -63 TTTACTTCTTTAAAATATCATTCTCAACACTAA 12 133 0 TAAATATATC 0.955409 -127 TATTAGACTTTATTATATCAATCTTAGGATACT 16 78 1 TATATATATC 0.813995 -223 AGAAAATCTTTAATATATAATTCTAGCCAATAG 18 30 0 TAAATATATC 0.955409 -186 ATATTCTATTAAAGATATCATTCAGTAATCATC 20 109 0 AAAATATATC 0.695134 -46 CTAGATCTAATAAAATACCAATCTTTATGGAGA 22 83 1 TAAATACATC 0.80139 -218 TTATATTGAATAAATTATTATTCTCGTGTCTAC 22 195 1 TAATTATATC 0.813995 -106 AACTAGAAAATAATATAAAAATCTTTGATGAAG 24 11 0 TAAATAAATC 0.827604 -47 TTATAAAAAATAACATATAAATCTATCTTTTAA 29 77 0 TAAATATATC 0.955409 -224 TTTAAAAATTTAATATAAAAATCACAAAAAATT 37 223 1 TAAATAAATC 0.827604 -23 *** **** * ** Masking position 10 Map Score: 11.224 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 14 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TTCTTATGACAATACAAAATATTGAAGGTAA 1 45 0 AATACAAATA 0.852354 -256 ATTATACAACAAGACAAATTATGTACAACAT 6 20 0 AAGACAATTA 0.693336 -137 CCATAGCTTAAATACAAAATAACATTATGGC 6 93 0 AATACAAATA 0.852354 -64 ACATACTGCAAATGCCAGTTATTTACAAAGT 7 154 0 AATGCAGTTA 0.540989 -147 TAAAAACATCAATACATATTAACCCATAACC 7 259 1 AATACTATTA 0.908646 -42 TGCTGGAATAATACCAAATAAAATACAAAT 9 10 1 AATACAAATA 0.852354 -288 TACCAAATAAAATACAAATTACAGTTAATAA 9 22 1 AATACAATTA 0.946887 -276 ACTAACAATTAACACAAATTAATATTTAAGA 9 150 0 AACACAATTA 0.693336 -148 AATTTTTTAAAATACTAGTTATTGTGAAGTA 16 175 1 AATACAGTTA 0.908263 -126 AATTTGCTATAATACAAATTTTTAATATGTA 16 273 1 AATACAATTT 0.588802 -28 TTATTTTACAAATACCTATTATTAAAAAATA 28 12 1 AATACTATTA 0.908646 -82 TTAAAATACAAATACCTATTATTTTTTAATA 28 31 0 AATACTATTA 0.908646 -63 TTTTAGGTTTAATACAAGTTATTAGTGCATT 29 262 0 AATACAGTTA 0.908263 -39 TAATTTGACAAATACTTTTTAATTTATTTAG 33 22 0 AATACTTTTA 0.514203 -72 ATCCCAATACAATACTTGTTAGATCCAAATA 34 21 0 AATACTGTTA 0.846713 -171 TGGGATCAAAAATACTAAATATTTTTTATGC 34 46 1 AATACAAATA 0.852354 -146 TTGGACACTGAATACTTATTAAATTAATTTT 36 104 1 AATACTATTA 0.908646 -24 ***** ***** Masking position 2 Map Score: 14.9696 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 60 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 ATCTAGTGTTTTAAGCCAAGGTATAATGAATAT 4 99 0 TTAAGCAGTA 0.919941 -151 TAAATCTACATTTAGCTTAGGTATTTATTTTTT 9 78 0 TTTAGCTGTA 0.889126 -220 TATCCTATGATTAAGCGATGTGATAAAAACAAA 14 26 0 TTAAGCAGGA 0.68394 -108 TAAAATGTTATTTAGCAATGATTATTATCTTTA 16 126 1 TTTAGCAGTT 0.785662 -175 CACTGGACTATTTAGCAAAGTTATGTTGTAACA 17 50 1 TTTAGCAGTA 0.966498 -57 TGAAAAATGATATAGCACTGTTATATATTTAAT 29 112 1 TATAGCCGTA 0.798958 -189 CGTTTATTACTATAGCTATATTAGCACCAAATA 30 172 1 TATAGCAATA 0.572688 -129 GTTGATAATATATAGCATGGCTAATTAAAAACA 32 53 0 TATAGCTGTA 0.825425 -248 TTTTAATTTATTTAGCGAGGCTAATA 33 4 0 TTTAGCAGTA 0.966498 -90 CTTGACCATGTATAGCGATGCTATGTTTGAATC 35 69 0 TATAGCAGTA 0.944473 -85 TATTAATTGGTTAAGCAATGATACTAGTAATGA 39 101 0 TTAAGCAGTA 0.919941 -49 ****** * * ** Masking position 4 Map Score: 4.29318 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 24 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 GTGCATAGAGCCTAATCAAACTTAAATACG 5 253 1 CCTAATCAAA 0.94544 -48 TATAATAAAGTCTAATAAAACACCAATACT 16 65 0 TCTAATAAAA 0.875354 -236 CGTATCTAGATCTAATAAAATACCAATCTT 22 78 1 TCTAATAAAA 0.875354 -223 ATCAAAACAATCTAATCAAATAT 27 4 0 TCTAATCAAA 0.962578 -238 GTATCTAATCAAAACAAGACTAG 32 4 1 TCTAATCAAA 0.962578 -297 TTTTTATGCACCTAATCAACAATCTACATA 34 68 1 CCTAATCAAC 0.842077 -124 AACCTAAAAATCTAATCAAACAGTATAAAA 36 64 0 TCTAATCAAA 0.962578 -64 ********** Masking position 5 Map Score: 4.57551 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 6 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 TTCTTATGACAATACAAAATATTGAAGGTAAAA 1 43 0 ATCAAATATT 0.735553 -258 CAATTTAAAGTTCACTAAATTTTCATTTAGTTA 1 109 1 TCCAAATTTT 0.52368 -192 AAATACTTTTCCCTAAAAATTACTCCTACTC 6 136 0 TCCAAAAATT 0.789769 -21 TCAAGTGATTAAAACCAAAAATTCATTATTACA 7 41 0 AACAAAAATT 0.735554 -260 GTAAAAATATACCTCAAAATATTAAATCTATTG 9 198 1 ACCAAATATT 0.952425 -100 CTGCATGTTAAACTCAAAAATTTGGTGTAAGAT 21 64 1 ACCAAAATTT 0.854203 -101 AAATAATCTCCAAATTTTACTAGTAACT 24 40 0 ACCAAATTTT 0.854203 -18 TGCACTATAAATCACTAAATATTTATAGTATTT 27 76 0 ACCAAATATT 0.952425 -166 AACTTGTATTAAACCTAAAAATTGTAGAGAGTA 29 273 1 AACAAAAATT 0.735553 -28 ATACTCGATGAACTTCAAAAATTTGCTGCGTCG 30 87 0 ACTAAAAATT 0.549267 -214 TAGCTATATTAGCACCAAATATTATGCCTGAAT 30 184 1 ACCAAATATT 0.952425 -117 TGGGATCAAAAATACTAAATATTTTTTATGCAC 34 46 1 ATCAAATATT 0.735496 -146 ACTCAGATAGAACTCCAAAAATTTGCTAAGTCA 37 53 1 ACCAAAAATT 0.952425 -193 TAATATAAAAATCACAAAAAATT 37 233 1 ACCAAAAATT 0.952425 -13 * * * ******* Masking position 7 Map Score: 9.44718 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 69 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 GGTATAATGAATATGGCAATTTCTAAACTACA 4 81 0 ATAGCAATTT 0.923234 -169 TAATCACAGTATAAAGCAACTTAAAATACAAG 4 172 0 ATAGCAACTT 0.917953 -78 TATAAAAAATAAATACCAACTTCTGGTAAATA 7 229 0 AAACCAACTT 0.561874 -72 GAAAATATATAAAAAGCAAATTTTTTATATAT 10 73 0 AAAGCAAATT 0.386851 -100 TTTGTATTATACAGCAATTTGCTTGCAGTA 11 9 1 ATAGCAATTT 0.931134 -85 CTACATTGTCATAATGCAATTTGCATCCAATA 11 65 0 ATAGCAATTT 0.923234 -29 ATATTTTATATTGCAATTGCAAGGAAATT 12 241 0 ATAGCAATTG 0.817429 -19 TATTATACTTATACCGCAACTTAAATTAGTGT 20 17 1 ATAGCAACTT 0.917953 -138 CTCATTATATATATTGCAATATGAGATTAAGT 20 73 1 ATAGCAATAT 0.424368 -82 AACATTTATTATAAGCCAATTTTTAATATAAA 30 253 0 ATACCAATTT 0.874049 -48 CTAAATAAGCCAAGTTGTAATTAGAT 36 5 1 ATACCAAGTT 0.797151 -123 ATTATACGTTATATTCCAAGTGTATACCTCAA 37 192 0 ATACCAAGTG 0.57662 -54 *** ******* Masking position 8 Map Score: 3.65608 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 44 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987