AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_rpxx_reg_100.orf -o00190_rpxx_100.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 RP022 33 ATP SYNTHASE C CHAIN (atpE) #2 RP024 51 unknown #3 RP025 90 unknown #4 RP044 244 SUCCINATE DEHYDROGENASE IRON-SULFUR PROTEIN (sdhB) #5 RP115 163 NADH DEHYDROGENASE I CHAIN F (nuoF) #6 RP126 137 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT (sdhC) #7 RP127 158 SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN (sdhD) #8 RP128 133 SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT (sdhA) #9 RP191 300 CYTOCHROME C OXIDASE POLYPEPTIDE III (coxC) #10 RP265 102 ISOCITRATE DEHYDROGENASE (icd) #11 RP266 90 unknown #12 RP267 83 unknown #13 RP269 76 unknown #14 RP282 300 NADH DEHYDROGENASE I CHAIN N (nuoL3) #15 RP283 51 NADH DEHYDROGENASE I CHAIN L (nuoL2) #16 RP284 300 NADH DEHYDROGENASE I CHAIN N (nuoN2) #17 RP346 112 CYTOCHROME C OXIDASE ASSEMBLY FACTOR (ctaB) #18 RP353 66 NADH DEHYDROGENASE I CHAIN E (nuoE) #19 RP354 209 NADH DEHYDROGENASE I CHAIN D (nuoD) #20 RP357 130 NADH DEHYDROGENASE I CHAIN A (nuoA) #21 RP405 78 CYTOCHROME C OXIDASE POLYPEPTIDE I (coxA) #22 RP406 300 CYTOCHROME C OXIDASE POLYPEPTIDE II (coxB) #23 RP537 300 NADH DEHYDROGENASE I CHAIN N (nuoN1) #24 RP589 128 INORGANIC PYROPHOSPHATASE (ppa) #25 RP785 112 unknown #26 RP787 55 unknown #27 RP789 87 unknown #28 RP790 72 NADH DEHYDROGENASE I CHAIN J (nuoJ) #29 RP793 149 NADH DEHYDROGENASE I CHAIN M (nuoM) #30 RP796 143 NADH DEHYDROGENASE I CHAIN H (nuoH) #31 RP798 173 unknown #32 RP800 113 ATP SYNTHASE EPSILON CHAIN (atpC) #33 RP801 108 ATP SYNTHASE BETA CHAIN (atpD) #34 RP802 86 ATP SYNTHASE GAMMA CHAIN (atpG) #35 RP803 136 ATP SYNTHASE ALPHA CHAIN (atpA) #36 RP804 118 ATP SYNTHASE DELTA CHAIN (atpH) Motif number 1 TGGTTAATAGTCAAAAGGAATAAAT 3 76 1 TAAAAAAAAA 0.868917 -15 TATACGAAAGTTAAAATAATTAATAATTATTAAA 4 54 1 TAAAAATAAT 0.618827 -191 TTTGTAGTGAAAAATAATTACAATTATCATTTTT 4 105 1 AAATATAAAT 0.813472 -140 TTATGTCCCGTAAAAATCTATAAATTTATACATA 4 138 0 TAAAATAAAA 0.841853 -107 TCTGATATAGACAAAATGTATAAAATCAATTTTA 4 208 1 AAAAATAAAA 0.931433 -37 TATCGAAGGAAAAATAACTAAAAATACTAGTATT 5 58 0 AAATATAAAA 0.858563 -106 ACTATTCAATATAAAAATAATAAAATTTAATACT 6 113 0 AAAAAAAAAA 0.944183 -25 TACTATTTTTAAAAAATTAAAAATTCGTTTTATC 7 36 0 AAAAAAAAAT 0.923972 -123 ATATACCGTATCAAAAGTAAAAAATTAATTGA 8 112 1 TAAAAAAAAA 0.868917 -22 AGTATTAATTAGAAAATGATAAAATAAAACT 9 280 1 AAAAAATAAA 0.852216 -21 TAGACTATGCAAAAAATAAACAATGGTAATTTAA 10 46 1 AAAAAAAAAT 0.923972 -57 TATCACTACATTAATAAAAATAAAGTGAAA 13 7 0 TAATAAAAAA 0.747608 -70 TTAATAGGTTAAATTCTGAGGATA 14 1 1 TAATATTAAT 0.368123 -300 TTTAGCTTTTAGAATATGTAAAAACTTTTTTCAT 14 106 1 AAATATAAAA 0.858563 -195 TTAGTAATATAGAAAAATTTAAAAATTCTGTATA 16 80 0 AAAAATTAAA 0.822409 -221 TACGGTACCTATAAAACAATCAATAATTTAGTAT 16 183 1 AAAAAATAAT 0.80556 -118 ATTTTTTAATTAAATATAAAAAATATTAGGTTAA 17 82 0 TAATAAAAAT 0.680318 -31 CAGCATTTAGTTAAAAATATCAATATTATTGATA 19 121 1 TAAAAATAAT 0.618829 -89 GTTTTAGTTAAAAATATCAATAATATTGATATTT 19 135 0 AAATAAAAAT 0.844496 -75 ATATAAGTATAGAAAATCTAGAAATAAATAACAA 19 179 1 AAAAATAAAA 0.931433 -31 AATCTAGAAATAAATAACAAAAATACT 19 193 1 TAATAAAAAT 0.680318 -17 TACTTTTAATATAAAATTTATAAAAATTACAATT 21 52 1 AAAAATAAAA 0.931394 -27 GACAAATGTGAAAAAACTTAAAATTTTTGCTCGT 22 52 0 AAAAATAAAT 0.907059 -249 ACTAATGCAGATAAAATTAATAAATGCCAAAGTA 22 136 1 AAAAAAAAAA 0.944183 -165 TTTGTTAAAGTAAAAATCAATAAATTTTTGTAAA 22 233 0 TAAAAAAAAA 0.868917 -68 AATACTACATACAATAAAAATAAAATTATTTCGC 23 194 0 AAATAAAAAA 0.883164 -107 TACGGTATCTATAAAAAATTTAAAGTATCAGTTG 24 40 1 AAAAATTAAA 0.82233 -89 CCGCTGCATGACAAAAAAAATAAAACAAAAAC 24 107 1 AAAAAAAAAA 0.944183 -22 ATTGTTGCTTACAAAATAAAAAAAACATTATATA 26 31 0 AAAAAAAAAA 0.944183 -25 TGTAGTAATAATAAAAACTATAAATGCGCATTTT 29 72 0 AAAAATAAAA 0.931394 -78 AAAGCAATTTACAAAATTTTGAATAAT 29 133 1 AAAAATTAAT 0.768895 -17 TCAATCTAGAAAAATAAATACAATGCTAATTTAC 30 35 0 AAATATAAAT 0.813472 -109 GGAATTCAAAAAAATAACTTTAATCTTGATATAG 31 70 1 AAATATTAAT 0.597859 -104 CACGGGATTCATAAAAAATAAAAAAGACTGGCCC 33 48 0 AAAAATAAAA 0.931433 -61 TGTTAACAATAGAAAACTAACAAACTAT 34 69 1 AAAAAAAAAA 0.944183 -18 ACGGGAGCCAATAAAAGTAACAATATTAGATCCC 35 72 1 AAAAAAAAAT 0.923972 -65 * **** ** *** Masking position 6 Map Score: 48.9638 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 516 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 2 ACAAACCTAACTTTTAATTAATCAAAATAACAA 1 10 0 ATTTTATTAA 0.945557 -24 AGAGTGTATCAATTTTATTTCAATAAAAATATATA 3 31 0 ATTTTATTAA 0.945557 -60 TCGCAATTTTAATAATTATTAATTATTTTAACTTT 4 60 0 ATAATTTTAA 0.650721 -185 TGATAATTGTAATTATTTTTCACTACAAATTACAA 4 99 0 ATTATTTTAA 0.828048 -146 CACATTCAACAGTATTTGTTTATGATTTTCTTATG 4 167 0 ATATTTTTAA 0.795999 -78 GGCAGTCTATAATATTAGTTAAATAATATAAAGAG 9 21 1 ATATTATTAA 0.870453 -280 GAATTACATTATTTATTATTAATGACAACTAAAAT 9 64 0 ATTATTTTAA 0.828048 -237 TAACTACGATAATTATTATTGATGAACATCAAATT 9 127 0 ATTATTTTAA 0.828048 -174 AGTTTTATTTTATCATTTTCTAATT 9 286 0 ATTTTATTAA 0.945557 -15 TTATTAATAAATTTTTTTTTGAGAAAATAT 13 57 1 ATTTTTTTAA 0.909794 -20 TACTGTATAGAATTATAGTTGACTACGGTACCTAT 16 160 1 ATTATATTAA 0.892387 -141 AAATGTATATATTTTTTTGTAATTAAAAAGTTAAG 17 21 0 ATTTTTGTAA 0.741396 -92 AAATATAAAAAATATTAGGTTAAAAATCAATGATT 17 70 0 ATATTAGTAA 0.656356 -43 ATGCAATATTTTTTAATTAAATATAAAAA 17 94 0 ATATTTTTAA 0.795999 -19 TGACGGTTTAATTTTTAGTTAAGTAAACTGCATAC 19 23 0 ATTTTATTAA 0.945557 -187 GATTTTCTATACTTATATTTTATCACATGTTTTAG 19 162 0 ATTATATTAA 0.892387 -48 TGTTTTTATTATTTATATGTTACTACGTAGCTTAT 20 105 0 ATTATAGTAA 0.702133 -26 AATTTTTATAAATTTTATATTAAAAGTACATTTAT 21 45 0 ATTTTAATAA 0.554087 -34 AAATTTATTGATTTTTACTTTAACAAAAATGCATA 22 240 1 ATTTTATTAA 0.945557 -61 GTATCTTGTCAATATTATTTTATCACTAAATGTTA 23 67 0 ATATTATTAA 0.870453 -234 ATAAATGCGCATTTTTATTTGATTATTTAATTAAA 29 52 0 ATTTTATTAA 0.945557 -98 ATGTTATTTGATTTTTAATTAATCATCATTGCAAT 30 118 0 ATTTTATTAA 0.945557 -26 * ***** ** * * Masking position 6 Map Score: 29.5459 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 200 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 ATCTAATGAACAAATTACGGTATAATTAGTTGT 5 16 0 CAATACGGAT 0.722269 -148 AAACAGTAACTTGTCCACGGTATCGAAGGAAAA 5 79 0 TGTCACGGAT 0.932881 -85 CTATAGTGTCTTGACCATAGTATCAACTATAAA 6 82 0 TGACATAGAT 0.616339 -56 AACACTTAACTTAAGCACATTATTAAGTAATTC 8 72 0 TAACACATAT 0.645728 -62 ATTCTCCTAATAAAATATGGAATATATCCTCAG 14 26 0 TAATATGGAT 0.732354 -275 TAAAAAATGATGATATACAGAATTTTTAAATTT 16 67 1 TATTACAGAT 0.732011 -234 AGAATTATAGTTGACTACGGTACCTATAAAACA 16 168 1 TGATACGGAC 0.672636 -133 ATAGCATGACTTATACACAGCATTTAGTTAAAA 19 104 1 TATCACAGAT 0.842683 -106 TATTTTTAACTAAAACATGTGATAAAATATAAG 19 153 1 TAACATGTAT 0.387734 -57 AGATACAAAATCGACTACAGCATCAGTACGAAA 23 96 1 TGATACAGAT 0.874076 -205 TATCGTAGGCTTGACTACGGTATCTATAAAAAA 24 25 1 TGATACGGAT 0.953347 -104 ATGCAGCGGCTTGAACACGGCATCTAGTTAAAA 24 83 0 TGACACGGAT 0.975654 -46 TAACTTCTACAAATTTACGGGATGACGATAGTT 25 48 1 AATTACGGAT 0.517637 -65 AATACAATGCTAATTTACAGAATCTTTAACTGT 30 20 0 TATTACAGAT 0.732011 -124 CTACAATAATTTAAGCACAGGATGACAATAC 32 9 0 TAACACAGAT 0.939189 -105 GGTTATGTGCTTAAGTACGTTATGTGACATTAA 32 77 1 TAATACGTAT 0.732354 -37 CCCGTGATCAATAAACACGGGATAACACAGCAT 33 16 0 AAACACGGAT 0.85851 -93 ACCCCGTGTGTAAACCACGGGATTCATAAAAAA 33 64 0 TAACACGGAT 0.97848 -45 CTTGATCACGGTATGCGGTAAAAT 34 2 1 TGACACGGAT 0.975654 -85 ATCCAATGTATGAACCACGGGATCTAATATTGT 35 91 0 TAACACGGAT 0.97848 -46 * ** ***** ** Masking position 7 Map Score: 17.6996 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 54 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 ATTAGCTATTTTTGTATGAGTATTTTTATACGAAAGTTA 4 28 1 TTTTTATTAT 0.970749 -217 ACAATTATCATTTTTATGTATAAATTTATAGATTTTTAC 4 124 1 TTTTTATTAT 0.970749 -121 CATTATTGACTTTATTAAATGATTTTTATTTCATTTCAG 7 90 0 TTTTAATTAT 0.891926 -69 TTTTTTTATAATGTTATTAATGTAACAGTTA 11 70 0 TTTTTTTTAT 0.852063 -21 GTCATCTTATTTTATATCACTACATTAATAAAAATAAAG 13 16 0 TTTTTATTAT 0.970749 -61 TACATTATTTATGTATGCAGTTTACTTAACTAAAAA 19 8 1 TTTTTATTCT 0.892317 -202 TAAAAGTACATTTATTATATAAGGTTGATCTATTGTTCT 21 21 0 TTTTAATTAT 0.891926 -58 ATTTATTAATTTTATCTGCATTAGTTTATTTATTAACGG 22 122 0 TTTTTTTTAT 0.852063 -179 TCAATATTATTTTATCACTAAATGTTAATTTTATTATTG 23 55 0 TTTTAATTAT 0.891926 -246 ATTAATGTTTTTTGTATAATCGTTTTTATGGCGAAATAA 23 164 1 TTTTTGTTAT 0.828797 -137 AATAAAGCATTTTTTATCAATAAATTGATATATCATATT 23 235 0 TTTTTATTAT 0.970749 -66 CATTGTATTATTGCTATCATCATATTAATCATAAGGATG 27 44 0 TTGTTATTAT 0.892317 -44 TAGCATTGTATTTATTTTTCTAGATTGAAATGTCCTTTC 30 41 1 TTTTTATTAA 0.739555 -103 GAAGTAAATATTTGTTTTACTAGATTTATCCTTTTGCAG 31 104 1 TTTTTATTAT 0.970749 -70 GATTTTTCTGTAAAGGTTTATAACCCCGTGT 33 88 0 TTTTTATTAT 0.970749 -21 TTCATTGCTGTTGATATTATTATGTTACTTTCCATTTAT 36 16 0 TTGTTATTCT 0.674173 -103 *** * * * ** ** Masking position 5 Map Score: 15.6706 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 61 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 AATAATTATTAATTATTTTAACTTTCGTATAAAA 4 51 0 AATATTTATT 0.656076 -194 TAAAATTGCGAAAAATTGTAATTTGTAGTGAAAA 4 84 1 AAAATGTATT 0.927207 -161 TTCAGTTCAAAATACTAGTATTTTTAGTTATTTT 5 48 1 AAACTGTATT 0.822456 -116 TTAGTTTCAGAAAATTATTATATTTGTATTTCTT 6 42 0 AAATTTTATT 0.810568 -96 TCAACTATAAAAAACTCTTAGTTTCAGAAAATTA 6 59 0 AAACTTTATT 0.906522 -79 TTAATTTTTTAAAAATAGTATGTTTATATTTGCG 7 50 1 AAAATGTATT 0.927191 -109 GCAAAAAATAAACAATGGTAATTTAACATTGGTT 10 54 1 AAAATGTATT 0.927207 -49 TTGACGAAACAATCTTAAGATGTTTTATATG 12 8 1 AAAATTTAAT 0.656076 -76 GTAGTTTTATAAAACTTTTAGCTTTTAGAATATG 14 90 1 AAACTTTATT 0.906522 -211 GGATCGAGTTAACAATACTAAATTATTGATTGTT 16 197 0 AAAATCTATT 0.783437 -104 TGTTACATTGAACAATCTTACTTCTTTTATCCTT 16 245 0 AAAATTTATC 0.846244 -56 CTTAATTACGAAGATTGTTACATTGAACAATCTT 16 260 0 AAATTTTATT 0.811464 -41 ATTAAATATAAAAAATATTAGGTTAAAAATCAAT 17 74 0 AAAATTTATT 0.96385 -39 TGTAATTTTTATAAATTTTATATTAAAAGTACAT 21 49 0 ATAATTTATT 0.656076 -30 ATTAACGAGCAAAAATTTTAAGTTTTTTCACATT 22 48 1 AAAATTTATT 0.963851 -253 TTTATGGCGAAATAATTTTATTTTTATTGTATGT 23 188 1 AAAATTTATT 0.96385 -113 ATGTTCCCATAATAATATTAGTTTAT 23 285 1 AAAATTTATT 0.96385 -16 TATTCACGTAAAAAATTTTAACTTCTACAAATTT 25 30 1 AAAATTTATT 0.963851 -83 CAATAAAAGTAACAATATTAGATCCCGTGGTTCA 35 80 1 AAAATTTATC 0.846244 -57 ** *** *** ** Masking position 6 Map Score: 23.4465 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 93 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 ATATATTTTTATTGAAATAAAATTGATACACT 3 32 1 ATGAATAAAA 0.927625 -59 GTATAAAAATACTCATACAAAAATAGCTAATA 4 27 0 ATCAACAAAA 0.681502 -218 TTCAGTGTAAAGTGAGATAAAACGAATTTTTA 7 21 1 ATGAATAAAA 0.927625 -138 ATTGTTCTGAAATGAAATAAAAATCATTTAAT 7 84 1 ATGAATAAAA 0.927625 -75 TGATCATTGAAGTCGGATAACAGAGCGTATCT 9 212 0 ATCGATAACA 0.575144 -89 TTGACATGAGAATCATATAAAACATCTTAAGA 12 23 0 ATCAATAAAA 0.950191 -61 TTATTAATGTAGTGATATAAAATAAGATGACT 13 24 1 ATGAATAAAA 0.927624 -53 GTGTGTTTAGAGTCATATAACAACATCGACAA 15 13 1 ATCAATAACA 0.93086 -39 TAGGTACCGTAGTCAACTATAATTCTATACAG 16 162 0 ATCACTATAA 0.331908 -139 TCGATCCAGCGATCACATAACAAGGATAAAAG 16 224 1 GTCAATAACA 0.575144 -77 GTGGATCCACACTCAGATAACACCACAATCAA 20 66 0 ATCAATAACA 0.930861 -65 AAATAAACTAATGCAGATAAAATTAATAAATG 22 130 1 AGCAATAAAA 0.657313 -171 GAATGAACTAAAACAATTTCAAC 23 2 1 ATGACTAAAA 0.725703 -299 TTATCAATAAATTGATATATCATATTGTATTT 23 229 0 ATGAATATCA 0.532974 -72 ATATCAATTTATTGATAAAAAATGCTTTATTC 23 243 1 ATGAAAAAAA 0.631051 -58 CTCGTAACTTATTCACGTAAAAAATTTTAACT 25 21 1 ATCAGTAAAA 0.681502 -92 TTAATTAAATAATCAAATAAAAATGCGCATTT 29 53 1 ATCAATAAAA 0.950191 -97 ATTAATTAAAAATCAAATAACATT 30 130 1 ATCAATAACA 0.930861 -14 CTTTTGCAGGAGTGACATAAAATGCTGTGTGA 31 134 1 ATGAATAAAA 0.927625 -40 AAACCACGGGATTCATAAAAAATAAAAAAGAC 33 54 0 ATCAAAAAAA 0.717973 -55 * *** ****** Masking position 9 Map Score: 19.7464 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 54 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 AAAGTATATATTTTTATTGAAATAAAATTGA 3 27 1 TTTTATTGAA 0.821658 -64 AAAAATTCTCGTTATTGCTTTAATAAGTT 5 145 0 TCTTATTGCT 0.935813 -19 ACTACGATAATTATTATTGATGAACATCAAA 9 129 0 TTTTATTGAT 0.76994 -172 AACTATATGTTTCTTATCGCAATGACGTTTT 12 55 1 TTTTATCGCA 0.682815 -29 GATATTGAGTCATTATTGCACACAAAATTA 16 10 1 TCTTATTGCA 0.952541 -291 ATCAGTTTATCATTGATCTTAATTACG 16 284 0 TTTCATTGAT 0.651685 -17 AATGTTAATTTTATTATTGCTGATAACTTAC 23 43 0 TTTTATTGCT 0.901079 -258 AATAATTTTATTTTTATTGTATGTAGTATTA 23 198 1 TTTTATTGTA 0.583392 -103 TAAATTGCTTTCCTTATTGCATTATGTTGTA 29 113 0 TCTTATTGCA 0.952541 -37 AGATACCAAGTCTTCATTGCACGAAAGGACA 30 71 0 TCTCATTGCA 0.918171 -73 TTTTAATTAATCATCATTGCAATTAAACATT 30 110 0 TCTCATTGCA 0.918171 -34 CTCTATATCATCCTTATTGATTACATGTGAG 31 37 1 TCTTATTGAT 0.842682 -137 ** ******** Masking position 6 Map Score: 7.53031 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 70 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 AACTTTCGTATAAAAATACTCATACAAAAA 4 36 0 TAAAAATACT 0.964422 -209 TAGATTCAGTTCAAAATACTAGTATTTTTA 5 44 1 TCAAAATACT 0.849696 -120 GAAAAATAACTAAAAATACTAGTATTTTGA 5 54 0 TAAAAATACT 0.964422 -110 CTATTCAATATAAAAATAATAAAATTTAAT 6 116 0 TAAAAATAAT 0.68111 -22 ATCGCAAATATAAACATACTATTTTTAAAA 7 56 0 TAAACATACT 0.836196 -103 ATTAAAATACTCTCATCTTTT 10 92 0 TTAAAATACT 0.792283 -11 AAAAGTTTTATAAAACTACTCGTGTTATAT 14 79 0 TAAAACTACT 0.912309 -222 TAGAAAAATTTAAAAATTCTGTATATCATC 16 75 0 TAAAAATTCT 0.774992 -226 TGGATCGAGTTAACAATACTAAATTATTGA 16 202 0 TAACAATACT 0.836196 -99 AAATAAATAACAAAAATACT 19 200 1 CAAAAATACT 0.836196 -10 TGTGCATATCTAAAACTACTTTTAAGAGAC 36 89 1 TAAAACTACT 0.912309 -30 ********** Masking position 3 Map Score: 7.42317 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 65 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 TAATTAAAGTACATTTTTATATCGCAA 2 35 0 AGTACATTTT 0.844555 -17 ACACTATAGTATTAAATTTTATTATTTTTA 6 106 1 ATTAAATTTT 0.707185 -32 ACTTAACTTAAGCACATTATTAAGTAATTC 8 72 0 AGCACATTAT 0.706738 -62 AAATTTTAGCAGCAAATTATACCACTTAAC 9 102 0 AGCAAATTAT 0.874271 -199 ATTGATGAACATCAAATTTTAGCAGCAAAT 9 115 0 ATCAAATTTT 0.769414 -186 AAGACAAAATAGCAAATTTTTCAAGTTTAA 9 159 0 AGCAAATTTT 0.955868 -142 GACTATTATTAATAAATTTTTTTTTGAGAA 13 52 1 AATAAATTTT 0.707178 -25 TTGTATTTGGAGTAAATAATGAGTGCAAAT 14 190 0 AGTAAATAAT 0.506889 -111 AATTCTATACAGTAGATTTTCTTAGTATAC 16 144 0 AGTAGATTTT 0.74698 -157 AGTAAAAATCAATAAATTTTTGTAAACACT 22 229 0 AATAAATTTT 0.707178 -72 AAGATGACGCAGCAAATTTTTAAAATTCCA 28 43 1 AGCAAATTTT 0.955868 -30 GATGATATAGAGCAAATTTTCTATACACAC 31 19 0 AGCAAATTTT 0.955868 -155 TGATATAGGAAGTAAATATTTGTTTTACTA 31 96 1 AGTAAATATT 0.762005 -78 ********** Masking position 6 Map Score: 5.95272 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 238 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 10 AATTGCGAAAAATTGTAATTTGTAGTGAAAA 4 87 1 AATTTAATTT 0.749374 -158 TATACATAAAAATGATAATTGTAATTATTTT 4 115 0 AATGTAATTG 0.965137 -130 TAAAGTCAATAATGTTAATGGTATTACAACT 7 115 1 AATGTAATGG 0.826161 -44 AAAAATAAACAATGGTAATTTAACATTGGTT 10 57 1 AATGTAATTT 0.945344 -46 TTATTAGGAGAATATTAATTGTAGTGATAGA 14 46 1 AATATAATTG 0.82716 -255 AATGAGTGCAAATAGTAATTTGCTTAAAATA 14 172 0 AATATAATTT 0.749375 -129 AAAGTTAATAGATGATAATTGTGAACTATTG 14 217 0 GATGTAATTG 0.826161 -84 AGCAATTGTAATTTTTATAAATTT 21 65 0 AATTTAATTT 0.749374 -14 TTTATCACTAAATGTTAATTTTATTATTGCT 23 53 0 AATGTAATTT 0.945343 -248 AAATAAATACAATGCTAATTTACAGAATCTT 30 27 0 AATGTAATTT 0.945344 -117 AATGTTATTTGATTTTTAATT 30 133 0 AATGTATTTG 0.762274 -11 ACACATTTGAAATGGTAATTGTTCATCTCGA 36 57 1 AATGTAATTG 0.965137 -62 **** ****** Masking position 7 Map Score: 10.6994 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 40 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 TAATTATTTTTCACTACAAATTACAATTTT 4 95 0 TCACTACAAA 0.956649 -150 TTATTTTATATCACTACATTAATAAAAATA 13 19 0 TCACTACATT 0.956649 -58 ATATTCTCTATCACTACAATTAATATTCTC 14 53 0 TCACTACAAT 0.969344 -248 ATTGTGAGGATCACTACATAGTGATTTAAT 29 28 1 TCACTACATA 0.939026 -122 TTACTTTCAGTCACTACAATAATTTAAGCA 32 25 0 TCACTACAAT 0.969344 -89 ********** Masking position 5 Map Score: 3.14831 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 12 TGTTATTTTGATTAATTAAAAGTTAGGTTT 1 12 1 ATTAATTAAA 0.612984 -22 AGTCTATAATATTAGTTAAATAATATAAAG 9 24 1 ATTAGTTAAA 0.852597 -277 TCCTTAACTTTTTAATTACAAAAAAATATA 17 19 1 TTTAATTACA 0.626322 -94 ATTTTTTATATTTAATTAAAAAATATTGCA 17 92 1 TTTAATTAAA 0.492869 -21 CGGTTTAATTTTTAGTTAAGTAAACTGCAT 19 25 0 TTTAGTTAAG 0.74153 -185 ATACACAGCATTTAGTTAAAAATATCAATA 19 116 1 TTTAGTTAAA 0.8284 -94 TATCACATGTTTTAGTTAAAAATATCAATA 19 147 0 TTTAGTTAAA 0.8284 -63 GAGGATCGTGTTTTGTTACAATATAAAGTA 22 93 0 TTTTGTTACA 0.567693 -208 AGATATGCATTTTTGTTAAAGTAAAAATCA 22 248 0 TTTTGTTAAA 0.788092 -53 GAACACGGCATCTAGTTAAAAATGTTGCAA 24 74 0 TCTAGTTAAA 0.74153 -55 TACATAGTGATTTAATTAAATAATCAAATA 29 42 1 TTTAATTAAA 0.492869 -108 TGCAATGATGATTAATTAAAAATCAAATAA 30 120 1 ATTAATTAAA 0.612984 -24 AATTCTTGCCTTTAGTTATATACA 35 5 0 TTTAGTTATA 0.699174 -132 ********** Masking position 8 Map Score: 7.52649 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 157 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 ATATCGCAATCAAGTCGCGGCATGAAGTTATTA 2 7 0 CAAGTCGTAG 0.783616 -45 GTTATGAAGATAAGTTACATGATGATATTA 6 4 0 TAAGTCATAA 0.740777 -134 ATAATGTGCTTAAGTTAAGTGTTAACAGAGATATACC 8 82 1 TAAGTAGTAA 0.809646 -52 TCATCAATAATAATTATCGTAGTTAAACTTGAAAAAT 9 137 1 TAATTCGTAA 0.581971 -164 AGCTATAGTTCGAGTCACGCTTTGATAATAATCTAC 11 10 0 CGAGTCGTAA 0.877531 -81 ATGCTGTGTATAAGTCATGCTATGACACTCATTAGAT 19 90 0 TAAGTTGTAA 0.907212 -120 TTATGATATTCGAGCACTGATCTCATATCTATATCTA 20 23 0 CGAGCTGTAA 0.700474 -108 ACACCACAATCAAGTTGCGTTATGATATTCGAGCACT 20 42 0 CAAGTCGTAA 0.963887 -89 ACTTATACAATAAGCTACGTAGTAACATATAAATAAT 20 96 1 TAAGCCGTAA 0.952849 -35 ATGCCGTGTTCAAGCCGCTGCATGACAAAAAAAATAA 24 93 1 CAAGCCTTAA 0.59082 -36 TTTACGTGAATAAGTTACGAGATAAAAGAGT 25 5 0 TAAGTCGTAA 0.960944 -108 GTCATCTTTGTAAGTCCTGAGCTTAGAAAGTGCAAAT 28 14 0 TAAGTTGTAA 0.907212 -59 TGTTGTACAATAAGTGTAGTAATAATAAAAACTATAA 29 83 0 TAAGTAGTAA 0.809646 -67 CTAAGCAATACAGTTAAAGATTCTGTAA 30 2 1 TAAGCTATAA 0.482585 -142 ATCGTAGATACAAGCTATGTGTTAACAATAGAAAACT 34 50 1 CAAGCTGTAA 0.897027 -37 ***** ** * * * Masking position 3 Map Score: 4.59478 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 85 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 14 CAAAATGTATAAAATCAATTTTAAGAGAGT 4 219 1 AAAATCAATT 0.815172 -26 GTATCGAAGGAAAAATAACTAAAAATACTA 5 63 0 AAAAATAACT 0.603125 -101 TGGAATATTGAAAAACAATTAATAGCATTA 8 33 1 AAAAACAATT 0.833715 -101 AAAATATACGAAAATCAACTTAGAACAGAG 9 248 0 AAAATCAACT 0.925673 -53 GTCTACTTATACAATCAACTTGGTAACAAA 10 21 0 ACAATCAACT 0.662652 -82 TATGCAAAAAATAAACAATGGTAATTTAAC 10 51 1 ATAAACAATG 0.284588 -52 GAATAGAAGTATAAACAACTGCACTTAAAG 14 275 1 ATAAACAACT 0.726532 -26 GTATACTAAGAAAATCTACTGTATAGAATT 16 144 1 AAAATCTACT 0.590585 -157 TATTAGGTTAAAAATCAATGATTGACTTTG 17 63 0 AAAATCAATG 0.65093 -50 GACAAGATACAAAATCGACTACAGCATCAG 23 92 1 AAAATCGACT 0.851438 -209 ATTTCGCCATAAAAACGATTATACAAAAAA 23 171 0 AAAAACGATT 0.697637 -130 TATGAATTATAAAAACAACGAGCATCAAGA 25 84 1 AAAAACAACG 0.856856 -29 TGATTAATTAAAAATCAAATAACATT 30 128 1 AAAATCAAAT 0.52109 -16 TGGAATTCAAAAAAATAACTTTAATCTTGA 31 69 1 AAAAATAACT 0.603125 -105 CATAACCTAGAAAAACGACTTGCTATTTAT 32 54 0 AAAAACGACT 0.866937 -60 ********** Masking position 4 Map Score: 4.69015 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 168 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 15 TTTTGCTTCTATTATAAAGTATATATTTTT 3 12 1 ATTATAAAGT 0.790015 -79 TTAGTTAAATAATATAAAGAGTCAAGAGGA 9 35 1 AATATAAAGA 0.792543 -266 TACATTAATAAAAATAAAGTGAAA 13 5 0 AAAATAAAGT 0.792543 -72 ATGTACTTTTAATATAAAATTTATAAAAAT 21 49 1 AATATAAAAT 0.701953 -30 GTTTTGTTACAATATAAAGTACTTTATCGA 22 84 0 AATATAAAGT 0.954467 -217 AATATTATTAAATATATAGTGTTTACAAAA 22 212 1 AATATATAGT 0.789205 -89 AAAAAACATTAATATAAAGTGCTATATAGC 23 147 0 AATATAAAGT 0.954467 -154 ATCTATAAAAAATTTAAAGTATCAGTTGTT 24 46 1 AATTTAAAGT 0.789205 -83 ********** Masking position 6 Map Score: 2.04933 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 18 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802