AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_rpxx_reg_100.orf -o00130_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 RP115 163 NADH DEHYDROGENASE I CHAIN F (nuoF) #2 RP282 300 NADH DEHYDROGENASE I CHAIN N (nuoL3) #3 RP283 51 NADH DEHYDROGENASE I CHAIN L (nuoL2) #4 RP284 300 NADH DEHYDROGENASE I CHAIN N (nuoN2) #5 RP353 66 NADH DEHYDROGENASE I CHAIN E (nuoE) #6 RP354 209 NADH DEHYDROGENASE I CHAIN D (nuoD) #7 RP357 130 NADH DEHYDROGENASE I CHAIN A (nuoA) #8 RP478 103 unknown #9 RP479 77 OCTAPRENYL-DIPHOSPHATE SYNTHASE (ispB) #10 RP537 300 NADH DEHYDROGENASE I CHAIN N (nuoN1) #11 RP541 62 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE (ubiX) #12 RP680 185 UBIQUINONE/MENAQUINONE BIOSYNTHESIS METHLYTRANSFERASE UBIE (ubiE) #13 RP686 300 4-HYDROXYBENZOATE OCTAPRENYLTRANSFERASE (ubiA) #14 RP785 112 unknown #15 RP787 55 unknown #16 RP789 87 unknown #17 RP790 72 NADH DEHYDROGENASE I CHAIN J (nuoJ) #18 RP793 149 NADH DEHYDROGENASE I CHAIN M (nuoM) #19 RP796 143 NADH DEHYDROGENASE I CHAIN H (nuoH) #20 RP798 173 unknown #21 RP860 270 unknown #22 RP876 300 PROBABLE LIPOATE-PROTEIN LIGASE B (lipB) Motif number 1 CAAATTACGGTATAATTAGTTGTAAATT 1 5 0 TAATAGTTTA 0.580017 -159 CAGTTCAAAATACTAGTATTTTTAGTTATTTTTC 1 50 1 TATTATTTTA 0.871604 -114 GAGGATATATTCCATATTTTATTAGGAGAATATT 2 28 1 TCATTTTATA 0.658998 -273 ATTAGGAGAATATTAATTGTAGTGATAGAGAATA 2 48 1 TATTTGTATG 0.766062 -253 TCGAATTTTGTCGATGTTGTTATATGACTCTAAA 3 18 0 TCATTGTTTA 0.471663 -34 AATACTAAATTATTGATTGTTTTATAGGTACCGT 4 184 0 TATTTGTTTA 0.884588 -117 ATATCAATAATATTGATATTTTTAACTAAATGCT 6 122 0 TATTATTTTA 0.878759 -88 ATATCAATATTATTGATATTTTTAACTAAAACAT 6 137 1 TATTATTTTA 0.878759 -73 AATCATATGCTACTTGTTTTACTAAAATCTAATT 8 32 1 TATTTTTATA 0.94336 -72 CACTAAATGTTAATTTTATTATTGCTGATAACTT 10 45 0 TATTATTATG 0.816696 -256 CACTTTATATTAATGTTTTTTGTATAATCGTTTT 10 156 1 TATTTTTTTA 0.950895 -145 GTTTTTTGTATAATCGTTTTTATGGCGAAATAAT 10 170 1 TATTTTTTTG 0.905933 -131 TATGGCGAAATAATTTTATTTTTATTGTATGTAG 10 190 1 TATTATTTTA 0.911878 -111 ATATATTTTATATTGTTTTTATTATATACTAAAT 11 17 1 TATTTTTATA 0.94336 -46 TGACTGTCATTATTATTTTTACTAATTAATCATG 13 193 1 TATTTTTATA 0.941932 -108 AAAAATCTAGTAGATTTATTTTTGTTGCGTATTT 13 244 1 TAATATTTTG 0.662256 -57 TTCTTGATGCTCGTTGTTTTTATAATTCATAATA 14 81 0 TCTTTTTTTA 0.855796 -32 AGGGGATATATAATGTTTTTTTTATTTTGTAAGC 15 25 1 TATTTTTTTA 0.950895 -31 TTTCCTTATATCATTGTATTATTGCTATCATCAT 16 60 0 TCTTATTATG 0.577235 -28 AATGCGCATTTATAGTTTTTATTATTACTACACT 18 74 1 TAATTTTATA 0.863127 -76 ATTAGCATTGTATTTATTTTTCTAGATTGAAATG 19 39 1 TATTTTTTTA 0.950455 -105 AGGAAGTAAATATTTGTTTTACTAGATTTATCCT 20 102 1 TATTTTTATA 0.94336 -72 TGTATAGATTTAGTAATTTTAGTATACTATTTTC 21 20 1 TATTTTTATA 0.861568 -251 TGATTGACTGTATATTTTGTTGTATTGTGGCAAG 21 147 1 TAATTGTTTA 0.744461 -124 TTATACTCGTTAAATCTATTACTACAATATTAAT 22 33 0 TAATATTATA 0.738447 -268 TCATAATTAGTAATGTTTTTAGTGATTTAGATGT 22 222 1 TATTTTTATG 0.892296 -79 ** * ***** ** Masking position 7 Map Score: 30.0783 Number of sites scoring better than the average of aligned sites = 1055 Number in coding regions = 684 Number in noncoding regions = 371 Number of orfs with sites within 600 bp upstream = 178 Fraction of orfs with sites within 600 bp upstream = 0.0285898 Motif number 2 TATACCGTAATTTGTTCATTAGATTCAGTTCAAAATACTAGTAT 1 25 1 TTTAATATAA 0.926379 -139 GATATACAGAATTTTTAAATTTTTCTATATTACTAAGTCACTAT 4 78 1 ATTTTTATAT 0.688816 -223 AAAATATCAATATTATTGATATTTTTAACTAAAACATGTGATAA 6 134 1 TTTATTATAA 0.941787 -76 TGTTATTTAGTATAGATATAGATATGAGATCAGTGCTCG 7 6 1 TTTAATATAA 0.794599 -125 ATGTTTTTATTATTTATATGTTACTACGTAGCTTA 7 106 0 TTTATTATAT 0.926363 -25 AAACTAATATTATTATGGGAACATAGATTTTATTGAATAAAGCA 10 265 0 TTTAATATAT 0.902357 -36 TTAAATTTCTTTAATTCATTAAATTTAGTATATAATAAA 11 34 0 TTTTATATAT 0.814236 -29 ATACACTTTTTTACAGTTGTAAATAACTAAATGCGGAT 13 5 1 ATTATTATAT 0.821928 -296 AAAATCATCCAATAATCAATAATTGTAATTTATATCCTATTACA 13 65 1 ATTATTATAA 0.861255 -236 CAAAAATAAATCTACTAGATTTTTATAGCTAAAAACTCAAGCAT 13 224 0 TTTTTTATAA 0.89034 -77 GTAGATTTATTTTTGTTGCGTATTTTATTTAAATTATCTGTATT 13 253 1 TTTTTTATAT 0.856436 -48 AAATGCGCATTTTTATTTGATTATTTAATTAAATCACTATGTAG 18 41 0 TTTTATATAT 0.813259 -109 GTTTAATTGCAATGATGATTAATTAAAAATCAAATAACATT 19 113 1 ATTATTATAA 0.742472 -31 AGATTAAAGTTATTTTTTTGAATTCCAACTCACATGTAATCAAT 20 52 0 TTTATTATAA 0.940698 -122 AAAACAAATATTTACTTCCTATATCAAGATTAAAGTTATTTTTT 20 78 0 TTTAATATAA 0.923397 -96 TCATCATGTAATTTATTATGAGATCCATGTAAAAATACAAATTT 21 206 0 ATTAATATAA 0.823539 -65 TACACCAATGTTTCCTTGTAAATTTTACATGATAATGGAAATTG 22 77 1 TTTATTATAA 0.940698 -224 TGAAAATCCATTTTCTTTCATTTTAGAGTTTAAAATTCCTGTAG 22 181 0 TTTTTTATAA 0.890295 -120 CTAAAATTGCTATGGTTTCAACATCTAAATCACTAAAAACATTA 22 232 0 TTTAATATAT 0.899889 -69 * * * * ** * * * * Masking position 14 Map Score: 19.0688 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 200 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 3 CGAAGGAAAAATAACTAAAAATACTAGTAT 1 59 0 ATAACTAAAA 0.838667 -105 TATATTCTCTATCACTACAATTAATATTCT 2 54 0 ATCACTACAA 0.734783 -247 ACATATTCTAAAAGCTAAAAGTTTTATAAA 2 95 0 AAAGCTAAAA 0.570755 -206 TCGAGTTAACAATACTAAATTATTGATTGT 4 198 0 AATACTAAAT 0.795494 -103 ATTCAATTGATTTACTACAAGATGAGGAAG 5 23 1 TTTACTACAA 0.730619 -44 TGCAGTTTACTTAACTAAAAATTAAACCGT 6 26 1 TTAACTAAAA 0.777811 -184 ATTGATATTTTTAACTAAATGCTGTGTATA 6 115 0 TTAACTAAAT 0.815812 -95 ATTGATATTTTTAACTAAAACATGTGATAA 6 148 1 TTAACTAAAA 0.777811 -62 TATCTATATCTATACTAAATAACA 7 5 0 TATACTAAAT 0.723717 -126 TGCTACTTGTTTTACTAAAATCTAATTTTT 8 39 1 TTTACTAAAA 0.838337 -65 GATATTTTTTATTGCTAAATTCCAGTATTA 9 58 0 ATTGCTAAAT 0.861924 -20 ATATTATTTTATCACTAAATGTTAATTTTA 10 61 0 ATCACTAAAT 0.870167 -240 ATTGTATTTTAATACTACATACAATAAAAA 10 208 0 AATACTACAT 0.670451 -93 GTTTTTATTATATACTAAATTTAATGAATT 11 31 1 TATACTAAAT 0.723717 -32 ACTATTGATCTATGCTAAAAAAGCTTAATG 12 101 1 TATGCTAAAA 0.570158 -85 ACAGTTGTAAATAACTAAATGCGGATATAT 13 23 1 ATAACTAAAT 0.868026 -278 TTTAAAATGCTTAGCTAAATAATAAAAACT 13 147 1 TTAGCTAAAT 0.739432 -154 CTAGATTTTTATAGCTAAAAACTCAAGCAT 13 224 0 ATAGCTAAAA 0.769083 -77 CATTGTGAGGATCACTACATAGTGATTTAA 18 27 1 ATCACTACAT 0.778043 -123 GTATACTAAAATTACTAAATCTATACAATA 21 17 0 ATTACTAAAT 0.906918 -254 TATCTAGGGAAACACTAAATAATTAAAAAG 21 108 0 AACACTAAAT 0.727948 -163 TTACTAATTTATTGCTACATACAGTTTTCA 21 247 0 ATTGCTACAT 0.765527 -24 CGTTAAATCTATTACTACAATATTAATTTA 22 30 0 ATTACTACAA 0.801096 -271 TGTAATACATTTTGCTAAATACTGCAATAT 22 130 0 TTTGCTAAAT 0.80783 -171 CAACATCTAAATCACTAAAAACATTACTAA 22 228 0 ATCACTAAAA 0.841198 -73 ********** Masking position 6 Map Score: 26.3811 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 377 Number in noncoding regions = 203 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 CTATCACTACAATTAATATTCTCCTAATAAA 2 45 0 AATAATATTC 0.77875 -256 AGGATAAAAGAAGTAAGATTGTTCAATGTAA 4 246 1 AATAAGATTG 0.870093 -55 TTAAAAATATCAATAATATTGATATTTTTAA 6 131 0 CATAATATTG 0.761476 -79 TTTAAATTAACATTGATGTATGATT 8 89 0 AATAACATTG 0.959304 -15 ATAGTATGACAACTAATACTGGAATTTAGCA 9 45 1 AATAATACTG 0.840821 -33 GCAATAATAAAATTAACATTTAGTGATAAAA 10 54 1 AATAACATTT 0.589459 -247 TTTAGTGATAAAATAATATTGACAAGATACA 10 72 1 AATAATATTG 0.957351 -229 ATAAACTAATATTATTATGGGAAC 10 287 0 AATAATATTA 0.703768 -14 AGTTTTACCTACATAACATTGAGGTATTTAG 12 73 0 ACTAACATTG 0.74949 -113 TAATTAGTAAAAATAATAATGACAGTCAAAT 13 190 0 AATAATAATG 0.767236 -111 AGATTCTGTAAATTAGCATTGTATTTATTTT 19 28 1 AATAGCATTG 0.749469 -116 AAATTATATTGTATAGATTTA 21 1 1 AATTATATTG 0.769174 -270 ATACTATTTTCAATAATATTGATTTCAGCAA 21 43 1 CATAATATTG 0.761476 -228 TAAAGTAATAAATTAATATTGTAGTAATAGA 22 22 1 AATAATATTG 0.973346 -279 AAATTGATATAATCAATATTGCAGTATTTAG 22 115 1 AACAATATTG 0.831902 -186 ATTTTAGATGCATTAATATTGGAAATGTTAA 22 269 1 CATAATATTG 0.913424 -32 ** ******** Masking position 8 Map Score: 13.1652 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 78 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 5 AAACATGAACTTATTAAAGCAATAACGAGAATTTT 1 138 1 TTAAGCAAAA 0.942533 -26 TTTTTACATATTCTAAAAGCTAAAAGTTTTATAAA 2 95 0 TTAAGCTAAA 0.760479 -206 TTGGAGTAAATAATGAGTGCAAATAGTAATTTGCT 2 179 0 TTATGCAATA 0.763355 -122 TACTAGGTAATTTTGTGTGCAATAATGACTCAATA 4 13 0 TTTTGCAAAA 0.947595 -288 TAGATTTTCTTAGTATACGCAACAATGCTTTATGA 4 127 0 TTTCGCAAAA 0.808608 -174 ATTTGCTAGTTTATAATTGCAAGAAAAATTAGATT 8 57 0 TTATGCAAAA 0.924269 -47 TTAATTAGTAAGTTATCAGCAATAATAAAATTAAC 10 36 1 ATTAGCAAAA 0.756389 -265 CTTGTCAATATTATTTTATCACTAAATGTTAATTT 10 63 0 TTTATCACAA 0.439345 -238 TGATAAAAAATGCTTTATTCAATAAAATCTATGTT 10 255 1 TTTTTCAAAA 0.746849 -46 TATTGTAAGCAAATATTACATGCGT 12 1 1 TTTAGCAATA 0.866726 -185 GTAAAACTATTGATCTATGCTAAAAAAGCTTAATG 12 96 1 TTTTGCTAAA 0.775672 -90 ATCTACTAGATTTTTATAGCTAAAAACTCAAGCAT 13 224 0 TTAAGCTAAA 0.760546 -77 GTTTTTTTTATTTTGTAAGCAACAATA 15 39 1 TTTAGCAAAA 0.960941 -17 ATGATTAATATGATGATAGCAATAATACAATGATA 16 51 1 TTAAGCAAAA 0.943226 -37 AATAATACAATGATATAAGGAAAAAAT 16 71 1 TTTAGGAAAA 0.604139 -17 AGATACCAAGTCTTCATTGCACGAAAGGACATTTC 19 67 0 TTATGCACAA 0.704331 -77 TTTTAATTAATCATCATTGCAATTAAACATTTCAT 19 106 0 TTATGCAATA 0.763355 -38 ATTCCAACTCACATGTAATCAATAAGGATGATATA 20 40 0 ATTATCAAAA 0.336257 -134 AATTTTAGTATACTATTTTCAATAATATTGATTTC 21 34 1 TTTTTCAAAA 0.74686 -237 TCAATAATATTGATTTCAGCAAGTATATTTGTAAT 21 52 1 TTTAGCAATA 0.866655 -219 * * * ***** ** Masking position 4 Map Score: 16.6812 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 263 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 TTACAACTAATTATACCGTAATTTGTTCATTAGATTC 1 14 1 TATCGAATTT 0.969363 -150 TCATTGATCTTAATTACGAAGATTGTTACATTGAACA 4 265 0 TATCGAGTTT 0.85629 -36 TGCTCGAATATCATAACGCAACTTGATTGTGGTGTTA 7 44 1 TATCGAATTT 0.969363 -87 GTATGACAACTAATACTGGAATTTAGCAATAAAAAAT 9 48 1 TATTGAATTC 0.824219 -30 ACTTACTAATTAATAGTTGAAATTGTTTTAGTTCATT 10 12 0 TATTTAATTT 0.662139 -289 AATTGATATATCATATTGTATTTTAATACTACATACA 10 215 0 TATTGATTTT 0.776311 -86 ACTCTTTTATCTCGTAACTTATTCACGTAAAAA 14 7 1 TATCGAATTT 0.969363 -106 TAAACTATCGTCATCCCGTAAATTTGTAGAAGTTAAA 14 46 0 TATCGAATTT 0.969363 -67 ATTATTCAAAATTTTGTAAATTGCTTTCCTTATTG 18 125 0 AATTGAATTT 0.759825 -25 CATACAGTTTTCATCATGTAATTTATTATGAGATCCA 21 223 0 TATTGAATTT 0.964681 -48 AAATTTTACATGATAATGGAAATTGATATAATCAATA 22 96 1 TATTGAATTT 0.964681 -205 AAAACATTACTAATTATGAAAATCCATTTTCTTTCAT 22 204 0 TATTGAATCT 0.824219 -97 * ** ** ** ** * Masking position 10 Map Score: 9.70224 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 30 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 TTTAAACAAAGTATTGCTTTACCTGCACTA 1 109 1 GTATTGCTTT 0.823998 -55 AAAATTCTCGTTATTGCTTTAATAAGTTCA 1 143 0 TTATTGCTTT 0.927913 -21 ATTTTTTACTGTATTGCTGAGTTGAATTAC 4 45 0 GTATTGCTGA 0.789984 -256 TCATAAAGCATTGTTGCGTATACTAAGAAA 4 127 1 TTGTTGCGTA 0.759059 -174 AATATCAATATTATTGATATTTTTAACTAA 6 136 1 TTATTGATAT 0.69615 -74 GATATTTTTTATTGCTAAATTCCAGTAT 9 60 0 TTATTGCTAA 0.938892 -18 GTTAATTTTATTATTGCTGATAACTTACTA 10 41 0 TTATTGCTGA 0.911832 -260 ATATATCAATTTATTGATAAAAAATGCTTT 10 241 1 TTATTGATAA 0.840683 -60 AACATAGATTTTATTGAATAAAGCATTTTT 10 260 0 TTATTGAATA 0.734969 -41 TAAATTACAATTATTGATTATTGGATGATT 13 67 0 TTATTGATTA 0.911592 -234 AGATTTATTTTTGTTGCGTATTTTATTTAA 13 255 1 TTGTTGCGTA 0.759059 -46 TATTGTTGCTTACAAAATAAAA 15 44 0 TTGTTGCTTA 0.915637 -12 TATCATTGTATTATTGCTATCATCATATTA 16 56 0 TTATTGCTAT 0.868931 -32 ATTGCTTTCCTTATTGCATTATGTTGTACA 18 111 0 TTATTGCATT 0.775842 -39 ATCTTTAACTGTATTGCTTAG 19 2 0 GTATTGCTTA 0.915637 -142 TATATCATCCTTATTGATTACATGTGAGTT 20 40 1 TTATTGATTA 0.911592 -134 GAAATCAATATTATTGAAAATAGTATACTA 21 39 0 TTATTGAAAA 0.58817 -232 ********** Masking position 5 Map Score: 14.29 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 244 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 8 GTGTGTTTAGAGTCATATAACAACATCGACAA 3 13 1 ATCAATAACA 0.968457 -39 TCACTATACTAATCATAAAGCATTGTTGCGTA 4 115 1 ATCAAAAGCA 0.799764 -186 TCGATCCAGCGATCACATAACAAGGATAAAAG 4 224 1 GTCAATAACA 0.852608 -77 GTGGATCCACACTCAGATAACACCACAATCAA 7 66 0 ATCAATAACA 0.968471 -65 TAAACTAGCAAATCATACATCAATGTTAATTT 8 79 1 ATCAACATCA 0.828626 -25 TTATCAATAAATTGATATATCATATTGTATTT 10 229 0 ATGAATATCA 0.728241 -72 TAATAATGACAGTCAAATAGCAGCTATAAGGA 13 176 0 ATCAATAGCA 0.96203 -125 TTAATTAAATAATCAAATAAAAATGCGCATTT 18 53 1 ATCAATAAAA 0.825549 -97 ATTAATTAAAAATCAAATAACATT 19 130 1 ATCAATAACA 0.968471 -14 CTTTTGCAGGAGTGACATAAAATGCTGTGTGA 20 134 1 ATGAATAAAA 0.530011 -40 GTACCTCTTTATTCACACAGCATTTTATGTCA 20 146 0 ATCAACAGCA 0.915926 -28 * *** ****** Masking position 7 Map Score: 6.81258 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 15 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 CTGAGTTGAATTACTAGGTAATTTTGTGTG 4 29 0 TTACTAGGTA 0.862692 -272 TTTTTCTATATTACTAAGTCACTATACTAA 4 97 1 TTACTAAGTC 0.931062 -204 ATGCCATTGCTTACTAATAATGACGGTTTA 6 48 0 TTACTAATAA 0.777264 -162 TATTTATATGTTACTACGTAGCTTATTGTA 7 101 0 TTACTACGTA 0.863645 -30 TGCTGATAACTTACTAATTAATAGTTGAAA 10 27 0 TTACTAATTA 0.959853 -274 ATTATTATTTTTACTAATTAATCATGCTTG 13 201 1 TTACTAATTA 0.959853 -100 TATACTAAAATTACTAAATCTATACAATAT 21 16 0 TTACTAAATC 0.772693 -255 AAAATTACTAATTTATTGCTACAT 21 257 0 TTACTAATTT 0.834738 -14 ACTAAAAACATTACTAATTATGAAAATCCA 22 215 0 TTACTAATTA 0.959853 -86 ********** Masking position 5 Map Score: 4.12511 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 36 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 TTGCTTAAAATATATACGCTTGTTCTACTCAA 2 152 0 TATATACCTG 0.817629 -149 AAAAATTCTGTATATCATCATTTTTTACTGTA 4 62 0 TATATCACTT 0.901691 -239 TCTTACTTCTTTTATCCTTGTTATGTGATCGC 4 232 0 TTTATCCTTT 0.888987 -69 GCTTAACCGCTATATCCATATTTTGTGATCAG 9 12 0 TATATCCTTT 0.938507 -66 TTTATGCTAATATATCCGCATTTAGTTATTTA 13 30 0 TATATCCCTT 0.978982 -271 AAAAACATTATATATCCCCTTTATTTATGGTC 15 13 0 TATATCCCTT 0.978982 -43 AAATTTGCTCTATATCATCCTTATTGATTACA 20 30 1 TATATCACTT 0.901691 -144 TTTTACTAGATTTATCCTTTTGCAGGAGTGAC 20 118 1 TTTATCCTTG 0.796512 -56 AGGGTTTTGGTTTATACTCGTTAAATCTATTA 22 46 0 TTTATACCTT 0.827922 -255 ******* * ** Masking position 5 Map Score: 3.11229 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 38 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 ATACTAGTATTTTTAGTTATTTTTCCTTCG 1 59 1 TTTTAGTTAT 0.778656 -105 ATATCATCATTTTTTACTGTATTGCTGAGT 4 53 0 TTTTTACTGT 0.617805 -248 AGTATTTTTGTTATTTATTTCTAG 6 196 0 TTTTTGTTAT 0.87282 -14 ATGTTTTTATTATTTATATGTTA 7 118 0 TTTTTATTAT 0.93492 -13 GATATTTTTTATTGCTAAATTCCAG 9 63 0 TTTTTATTGC 0.452837 -15 CTAAATGTTAATTTTATTATTGCTGATAAC 10 47 0 ATTTTATTAT 0.520881 -254 AATAATTTTATTTTTATTGTATGTAGTATT 10 198 1 TTTTTATTGT 0.880647 -103 TTTTATATTGTTTTTATTATATACTAAATT 11 22 1 TTTTTATTAT 0.93492 -41 TGTGCAAGCTTTTTTATGATAATGCTTGCA 12 129 1 TTTTTATGAT 0.77026 -57 CTATAAGGAGTTTTTATTATTTAGCTAAGC 13 155 0 TTTTTATTAT 0.93492 -146 ATGCTTGAGTTTTTAGCTATAAAAATCTAG 13 224 1 TTTTAGCTAT 0.435246 -77 GCGTATTTTATTTAAATTATCTGTATTTAT 13 270 1 TTTAAATTAT 0.357852 -31 ATGCTCGTTGTTTTTATAATTCATAATAAA 14 79 0 TTTTTATAAT 0.551406 -34 TATAATGTTTTTTTTATTTTGTAAGCAACA 15 33 1 TTTTTATTTT 0.585732 -23 GCATTTATAGTTTTTATTATTACTACACTT 18 79 1 TTTTTATTAT 0.93492 -71 AAATAAGCCTTTTTAATTATTTAGTGTTTC 21 100 1 TTTTAATTAT 0.880435 -171 AATTTGAGTATTTTAATTGTTATCTAGACA 21 181 0 TTTTAATTGT 0.790889 -90 TTAGTAATGTTTTTAGTGATTTAGATGTTG 22 228 1 TTTTAGTGAT 0.450858 -73 ********** Masking position 3 Map Score: 13.4969 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 175 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 12 TTTTAGTTATTTTTCCTTCGATACCGTGGACA 1 69 1 TTTTCTTCGT 0.452375 -95 AAAGTATTGCTTTACCTGCACTAAACATGAAC 1 116 1 TTTACTGCAT 0.925701 -48 TTTAATCTTTAAGTGCAGTTGTTTATACT 2 282 0 TTTAATGCAT 0.914933 -19 TATCATCATTTTTTACTGTATTGCTGAGTTGA 4 50 0 TTTTATGTAT 0.773695 -251 TAGTATTACTGCATTGTGGATAATC 8 4 1 TATTATGCAT 0.64986 -100 AAAATCTAATTTTTCTTGCAATTATAAACTAG 8 55 1 TTTTCTGCAT 0.956226 -49 GTTGAAATTGTTTTAGTTCATTC 10 2 0 TTTTATTCAT 0.830179 -299 TTAAATTTCTTTAATTCATTAAATTTAGTA 11 43 0 CTTTATTCAT 0.586601 -20 TTACAGAATCTTTAACTGTATTGCTTAG 19 7 0 TTTAATGTAT 0.661009 -137 TTGAAATGTCCTTTCGTGCAATGAAGACTTGG 19 65 1 CTTTCTGCAT 0.863773 -79 GTATGAAATGTTTAATTGCAATGATGATTAAT 19 104 1 TTTAATGCAT 0.914933 -40 TGACTGTATATTTTGTTGTATTGTGGCAAGTG 21 151 1 TTTTGTGTAT 0.625626 -120 TGAAAATCCATTTTCTTTCATTTTAGAGTTTA 22 193 0 TTTTCTTCAT 0.849915 -108 CCATAGCAATTTTAGATGCATTAATATTGGAA 22 261 1 TTTAGTGCAT 0.840187 -40 ***** **** * Masking position 7 Map Score: 6.15787 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 153 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 ATTTTTAAATTTTTCTATATTACTAAGTCAC 4 88 1 TTTCTATATT 0.844455 -213 TTTGTTATTTATTTCTAGATTTTCTATACTT 6 183 0 ATTCTAGATT 0.938524 -27 TGATGTATGATTTGCTAGTTTATAATTGCAA 8 70 0 TTTCTAGTTT 0.879309 -34 GATATTTTTTATTGCTAAATTCCAGTATTAG 9 57 0 ATTCTAAATT 0.702538 -21 CAAAAATAAATCTACTAGATTTTTATAGCTA 13 237 0 TCTCTAGATT 0.915241 -64 TTGTATTTATTTTTCTAGATTGAAATGTCCT 19 46 1 TTTCTAGATT 0.972294 -98 AAATATTTGTTTTACTAGATTTATCCTTTTG 20 109 1 TTTCTAGATT 0.972294 -65 *** ******* Masking position 7 Map Score: 1.90073 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 20 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 AGTACGATATAGTTTTCTTCCTCATCTTGTAG 5 37 0 AGTTCTTCCT 0.821151 -30 TTCCAGTATTAGTTGTCATACTATAGCTTAAC 9 37 0 AGTTCATACT 0.936837 -41 TATATAGCTTAGTTCTAATCATCTGTTTTCGT 10 123 0 AGTTAATCAT 0.874325 -178 ATGACACCTTAGATTTCATAATATTTCACAGA 16 15 0 AGTTCATAAT 0.947321 -73 ATGAAATCTAAGGTGTCATCCTTATGATTAAT 16 28 1 AGTTCATCCT 0.966817 -60 ATTGTATTATTGCTATCATCATATTAATCATA 16 50 0 TGTTCATCAT 0.863604 -38 GTGTTTCCCTAGATATAATAATTGTGATTGAC 21 123 1 AGTTAATAAT 0.779788 -148 ATTTTTACATGGATCTCATAATAAATTACATG 21 214 1 GGTTCATAAT 0.826881 -57 TGCTACATACAGTTTTCATCATGTAATTTATT 21 233 0 AGTTCATCAT 0.972473 -38 ** * ******* Masking position 6 Map Score: 3.83516 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 24 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 CACGAGTAGTTTTATAAAACTTTTAGCTTTTAGA 2 85 1 TTTAAAATTT 0.730091 -216 GCTTTTAGAATATGTAAAAACTTTTTTCATGTGC 2 110 1 TATGAAATTT 0.807102 -191 AAAATGATGATATACAGAATTTTTAAATTTTTCT 4 70 1 TATAAGATTT 0.954949 -231 ACTATAATTCTATACAGTAGATTTTCTTAGTATA 4 145 0 TATAAGATTT 0.954949 -156 AGAACTAAGCTATATAGCACTTTATATTAATGTT 10 139 1 TATAAGATTA 0.69285 -162 GATTTTATTGAATAAAGCATTTTTTATCAATAAA 10 250 0 AATAAGATTT 0.69285 -51 ATAAAAACAATATAAAATATATTTATAT 11 5 0 TATAAAATTT 0.929794 -58 TTGTTTTTATTATATACTAAATTTAATGAATTAA 11 29 1 TATAACATTT 0.802959 -34 ATAAAGGGGATATATAATGTTTTTTTTATTTTGT 15 21 1 TATAAAGTTT 0.676255 -35 ACAATGCTAATTTACAGAATCTTTAACTGTATTG 19 16 0 TTTAAGATTT 0.812362 -128 ATAAGGATGATATAGAGCAAATTTTCTATACACA 20 20 0 TATAAGATTT 0.954949 -154 TTACTAAATCTATACAATATAATTT 21 2 0 TATAAAAATT 0.584953 -269 TACAGCTCTATATGTAATACATTTTGCTAAATAC 22 138 0 TATGAAATTT 0.807102 -163 **** ** * *** Masking position 6 Map Score: 4.93978 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 84 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467