AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_mjan_reg_300.orf -o00190_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MJ0086 36 unspecified methyltransferase MJ0087 23 hemin permease (hemU) Input sequences: #1 MJ0030 300 coenzyme F420-reducing hydrogenase, delta subunit (frcD) #2 MJ0033 254 succinate dehydrogenase, flavoprotein subunit (sdhA) #3 MJ0081 300 methyl coenzyme M reductase II, subunit beta (mrtB) #4 MJ0084 261 CODH nickel-insertion accessory protein (cooC) #5 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #6 MJ0090 80 collagenase (prtC) #7 MJ0091 95 Na+/Ca+ exchanger protein, putative #8 MJ0216 46 H+-transporting ATP synthase, subunit B (atpB) #9 MJ0217 39 H+-transporting ATP synthase, subunit A (atpA) #10 MJ0219 103 H+-transporting ATP synthase, subunit C (atpC) #11 MJ0220 56 H+-transporting ATP synthase, subunit E (atpE) #12 MJ0221 103 H+-transporting ATP synthase, subunit K (atpK) #13 MJ0223 88 M. jannaschii predicted coding region MJ0223 #14 MJ0224 300 conserved hypothetical protein #15 MJ0520 192 NADH-ubiquinone oxidoreductase, subunit 1 #16 MJ0522 108 NADH dehydrogenase I #17 MJ0524 123 conserved hypothetical protein #18 MJ0525 122 conserved hypothetical protein #19 MJ0528 74 conserved hypothetical protein #20 MJ0529 132 repressor protein, putative #21 MJ0615 71 H+-transporting ATP synthase, subunit D (atpD) #22 MJ0616 108 phosphoribosylaminoimidazole carboxylase, (purE) #23 MJ1225 80 conserved hypothetical protein #24 MJ1275 122 NA(+)/H(+) antiporter (napA) #25 MJ1309 37 carbon monoxide dehydrogenase, hydrogenase anchor subunit CooM (cooM) #26 MJ1310 83 conserved hypothetical protein #27 MJ1362 68 NADH ubiquinone oxidoreductase, subunit 1 isolog #28 MJ1363 300 formate hydrogenlyase, subunit 7 Motif number 1 TTATAGAAGTTAGAAAAATGTTATAAGCCTCGA 1 116 1 TAAAAAATTA 0.854571 -185 AATTAAACCCTTAAAAAACTTAAA 1 287 1 TTAAAAATAA 0.476144 -14 CCAGTGCCTTATTAAAAATATTACTATTTTCTT 2 112 1 ATAAAAATTA 0.667538 -143 AATAGCTTTGATGAAAAAAATAATCCTAAATGA 2 177 0 ATAAAAATAA 0.417346 -78 CCTCATCAGATATTTAAAACTTATAAATCAAAA 2 208 0 TATTAAATTA 0.879605 -47 ATTCAAAATTTTTTTAAAGATTTTAAAGATTTT 3 142 1 TTTTAAATTT 0.745352 -159 ATGATAAAATTAAAAAAATCTTTAAAATCTTTA 3 156 0 TAAAAAATTT 0.844467 -145 TAGTAATAGGTATATAAAATTTTCTATTTTATC 3 228 0 TAATAAATTT 0.895465 -73 TAAAGTCCAAAAAATAAAACTTAAAATAAGATA 4 18 0 AAATAAATTA 0.879605 -244 TAAAATTTTAAAATTAAAAATAAAGTCCAAAAA 4 38 0 AATTAAATAA 0.672556 -224 TATGCCCTCCAATTAAAATTTTAAAATTAAAAA 4 51 0 AATAAAATTA 0.784916 -211 ATATTATTTTATCTAAAACTTTTGATAAAATGT 4 97 0 ATTAAAATTT 0.593832 -165 CTCCACTTGTTAGAAAAAGATTTATACTAAATA 4 194 1 TAAAAAATTT 0.844467 -68 TATTAGGTTTTAATTAAATTTAAATCAGACTGA 4 230 1 TATTAAATAA 0.722711 -32 TACATCAATATTCATAAAAATTATATAAAAAAT 5 20 0 TTATAAATTA 0.800787 -115 ATATATTAGATATTAAAAATTTTTGTTCATATC 5 89 1 TATAAAATTT 0.810562 -46 CTTCAAATATAATTTAAAATTTAAAAAAATTTC 6 55 1 AATTAAATTA 0.852018 -26 AATATGGATGAACTGAAAATTTTGCTTAAGTTT 7 15 1 AATGAAATTT 0.662999 -81 TCTGCAATAATATTTAAACTTAAGCAAAATTTT 7 30 0 TATTAAATAA 0.722712 -66 CGATAAAACCAATAAAAACGTTAA 9 26 1 AAAAAAATTA 0.822405 -14 TCCTTCTTTGAATTTAAAAATTTTTATAAAAAT 11 21 1 AATTAAATTT 0.84177 -36 CTGTTAAAATTAAATTTTTATAAAAATTT 11 38 0 AATTAAATTT 0.841769 -19 CTTTCAAGATTATTTAAATCTTTCCAATACTCA 12 14 1 TATTAAATTT 0.870978 -90 CAAAAAATACAACTTAAAACTTAGACAAAAATG 12 69 1 AATTAAATTA 0.852018 -35 TATTAAAAATATTTGATAGAGTCA 13 2 1 ATAAAAATTT 0.649765 -87 TAGGGTTATGTATATAAAATTTTTTATCTCTGA 13 32 0 TAATAAATTT 0.895465 -57 CATAACCCTATTTTAAAATATTACCAATAACTG 13 55 1 TTTAAAATTA 0.667538 -34 TTAATTTAAATTAATAAAGATTACAATTTTAAA 14 25 0 TTATAAATTA 0.800787 -276 TTAATTTAAATTAATAAATATTATTACCTAAAA 14 44 1 TTATAAATTA 0.800786 -257 TTTCGTGCAAAAGATAAATATATATTAATAAGT 14 219 1 AAATAAATAT 0.706592 -82 TTCCCATAATTATAAAAACCTATTTAAATAGGA 14 253 1 TAAAAAATAT 0.659508 -48 ATCAATCTAATATATAAACTTTTCGTCTTATTT 20 34 1 TAATAAATTT 0.895465 -99 CTCTGGGAAATATATAAAAGTTACCCACAAAAA 20 65 0 TAATAAATTA 0.902637 -68 GCAACGTTATAACATAAAAATTTAATGGTTATA 21 12 0 AAATAAATTT 0.870978 -60 CCACTTTTATAAGTAAAAATTATTAGCAACGTT 21 37 0 AATAAAATAT 0.546055 -35 TATGTAAGAGATTTTAAAACTAATTATAAATAA 22 60 0 ATTTAAATAA 0.47106 -49 TAAAATCTCTTACATAAAAATTTAGACCTTTTT 22 77 1 TAATAAATTT 0.895465 -32 TTTATACGTTAAATGAAATATTAATATTATGTG 23 11 1 AATGAAATTA 0.680429 -70 TAAGAATTCAAATTTAAATTTAAACTATTGAAA 23 44 1 AATTAAATAA 0.672557 -37 TTCTTAGTCATTCTAAAAGTTTTGAAAGACATG 24 28 0 TTTAAAATTT 0.649765 -95 TCCAATCTTTTAGAGAAAGTTAAATAGAA 25 7 0 TAAGAAATAA 0.550171 -31 AGCTATTAAAAACATAAATATTAAT 26 3 0 AAATAAATTA 0.879605 -81 GGTTTAACAGTATATAAACATTACGTTAGCAAC 26 48 0 TAATAAATTA 0.902637 -36 GGTTTTTATAAAATTTTATGAGTGAGA 27 5 1 TTATAAATTT 0.787874 -64 TATCCCTCACTAAAGAAATTTTACAAACATAAA 27 42 0 TAAGAAATTA 0.774186 -27 AATTCTCTTAAAAATAAAACTTTAAAATTGAAA 28 59 1 AAATAAATTT 0.870978 -242 AAAACTTTAAAATTGAAAAATTAGTAATACTTT 28 74 1 AATGAAATTA 0.68043 -227 ATTGGAAAATTAATAAAAAGTATTACTAATTTT 28 90 0 TATAAAATAT 0.604182 -211 GCGAACAGGTTTTAGAAATCTTTCGGATTTTTA 28 152 0 TTAGAAATTT 0.578687 -149 AGAAATTAAATTAAAAAATCTATTATGCATATT 28 202 1 TTAAAAATAT 0.456471 -99 ** ***** *** Masking position 7 Map Score: 50.4143 Number of sites scoring better than the average of aligned sites = 2485 Number in coding regions = 1513 Number in noncoding regions = 972 Number of orfs with sites within 600 bp upstream = 579 Fraction of orfs with sites within 600 bp upstream = 0.0929971 Motif number 2 TGGCATAGTATAAATAAAAAAAGAACAAGA 2 141 0 TAAATAAAAA 0.783217 -114 TTAAAATGATAAAATTAAAAAAATCTTTAA 3 164 0 AAAATTAAAA 0.877589 -137 TTAAAATAATAATATTAAAATGATAAAATT 3 178 0 AATATTAAAA 0.929618 -123 TTAAAATTTTAAAATTAAAAATAAAGTCCA 4 42 0 AAAATTAAAA 0.877589 -220 TCATAAAAATTATATAAAAAATAGAAAAAA 5 12 0 TATATAAAAA 0.869223 -123 ATGACCTCATTATATAAAAAAGA 6 4 0 TATATAAAAA 0.869223 -77 TATAATTTAAAATTTAAAAAAATTTCTAA 6 62 1 AATTTAAAAA 0.788413 -19 TCCTTCTTTGAATTTAAAAATTTTTATAAA 11 21 1 AATTTAAAAA 0.788413 -36 ATAACAATAAAATATAAAAACAAAAAATAC 12 49 1 AATATAAAAA 0.91096 -55 TACATAACCCTATTTTAAAATATTACCAAT 13 53 1 TATTTTAAAA 0.757869 -36 TAAAGATTACAATTTTAAAAACGAAATTTT 14 14 0 AATTTTAAAA 0.828023 -287 TTTATTAATTTAAATTAATAAAGATTACAA 14 32 0 TAAATTAATA 0.676424 -269 ATTATTACCTAAAATAAAAATGGTGCAGGG 14 63 1 AAAATAAAAA 0.847406 -238 AAGATAAATATATATTAATAAGTTTTCCCA 14 229 1 TATATTAATA 0.793722 -72 TATAAAAACCTATTTAAATAGGAAACATAT 14 263 1 TATTTAAATA 0.38526 -38 AAATATTAAAATAAAAATCTG 15 2 1 AATATTAAAA 0.929618 -191 TCTTACACATAATATTAATATTTCATTTAA 23 19 0 AATATTAATA 0.855486 -62 AAAAGGGTTATATATTAAAATAGCCCTCTA 24 71 1 TATATTAAAA 0.895758 -52 TAAAACATACAAAATAAAAACAAACTCATA 28 29 1 AAAATAAAAA 0.847406 -272 TTGGTATTGGAAAATTAATAAAAAGTATTA 28 98 0 AAAATTAATA 0.76265 -203 AGCAAGAAATTAAATTAAAAAATCTATTAT 28 198 1 TAAATTAAAA 0.823454 -103 CTTTATTGAGAATTTTAATATGCATAATAG 28 221 0 AATTTTAATA 0.683208 -80 TGATGTATAAAATATAAATAGATTATGCTT 28 248 0 AATATAAATA 0.820808 -53 ********** Masking position 5 Map Score: 26.8771 Number of sites scoring better than the average of aligned sites = 1353 Number in coding regions = 854 Number in noncoding regions = 499 Number of orfs with sites within 600 bp upstream = 391 Fraction of orfs with sites within 600 bp upstream = 0.0628012 Motif number 3 GAGGCACTGCCGAGCGTAGCGAGGC 2 5 1 CACTCCGAGC 0.992928 -250 AAAACGGATGCACTGCCTCGCTACGCTCGGC 2 19 0 CACTCCTCGC 0.992928 -236 CAAAAACTAACACCTCCTCGCTTCGCTCGGA 15 143 1 CACCCCTCGC 0.995491 -50 TGTAAATTTACACTTCCGAGCGAAGCGAGGA 15 157 0 CACTCCGAGC 0.992928 -36 TACACCCTAACACCTCCTCGCTTACGCTCGG 17 65 1 CACCCCTCGC 0.995491 -59 AATTAATTTACACCTCCGAGCGTAAGCGAGG 17 80 0 CACCCCGAGC 0.995491 -44 **** ****** Masking position 2 Map Score: 11.3827 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 0 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 TAGTAAAAGGTTCATCAAAACGGATGCACT 2 36 0 TTCATCAAAA 0.975256 -219 GATTATTTTTTTCATCAAAGCTATTTTGAT 2 185 1 TTCATCAAAG 0.851847 -70 TTTTTATCACCAAAAATAGGATACC 2 240 0 ATCACCAAAA 0.850983 -15 GCCTAAAAGTATCATCAATAGCAAATAGAG 3 52 0 ATCATCAATA 0.618576 -249 ATTCAAACATTTTATCAAAAGTTTTAGATA 4 91 1 TTTATCAAAA 0.858554 -171 TACATCAATATTCATAAAAATTATATAAAA 5 23 0 TTCATAAAAA 0.705823 -112 TTTTCGGTAGTTTATCAAAAATAATCGTTA 5 57 0 TTTATCAAAA 0.858554 -78 ATATTTAAACTTAAGCAAAATTTTCAGTTC 7 24 0 TTAAGCAAAA 0.750954 -72 AGCTCTCCATTTCATCAAAAACTAACACCT 15 128 1 TTCATCAAAA 0.975256 -65 TCCAAACAAATTAATCAAAATTAATTTACA 17 99 0 TTAATCAAAA 0.896919 -25 AGCTTACTCTATAATCAAAACCATAATTTA 22 33 1 ATAATCAAAA 0.784364 -76 CTTTTCACCAAAAAGGTCTAAAT 22 96 0 TTCACCAAAA 0.931789 -13 TAAGAATGGTTCCAGCAAAAGGGTTATATA 24 55 1 TCCAGCAAAA 0.798596 -68 TACCCCACCATCAAAATTTTAATTGT 24 107 0 ACCATCAAAA 0.827075 -16 ********** Masking position 4 Map Score: 11.5488 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 303 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 TATTAAAAATATTACTATTTTCTTGTTCTTT 2 121 1 ATTCTATTTT 0.91656 -134 CTGATGAGGGTATCCTATTTTTGGTGATAAA 2 232 1 TATCTATTTT 0.633695 -23 TTTTAAAGATTTTTTTAATTTTATCATTTTA 3 162 1 TTTTTAATTT 0.820278 -139 TCATTTTAATATTATTATTTTAACATTTTTT 3 185 1 ATTTTATTTT 0.921651 -116 GTATATAAAATTTTCTATTTTATCCTAAAAA 3 221 0 TTTCTATTTT 0.909848 -80 TCTTTATTATCTTATTTTAAGTTTTATT 4 8 1 TATTTATTTT 0.649444 -254 TCTTATTTTAAGTTTTATTTTTTGGACTTTA 4 20 1 AGTTTATTTT 0.685211 -242 TTTGGACTTTATTTTTAATTTTAAAATTTTA 4 40 1 ATTTTAATTT 0.832431 -222 CTCTTCCATTAATATTATTTTATCTAAAACT 4 110 0 AATTTATTTT 0.668468 -152 CTTTTTTCTATTTTTTATATAATT 5 4 1 TTTCTATTTT 0.909848 -131 CATATTGGTTATTGCTATTTTATACTTCAAA 6 31 1 ATTCTATTTT 0.91656 -50 TATTTTTTGTTTTTATATTTTATTGTTATAT 12 47 0 TTTATATTTT 0.635656 -57 ATTAATAAAGATTACAATTTTAAAAACGAAA 14 18 0 ATTCAATTTT 0.381696 -283 AATTGTAATCTTTATTAATTTAAATTAATAA 14 30 1 TTTTTAATTT 0.820278 -271 GGTAATAATATTTATTAATTTAAATTAATAA 14 41 0 TTTTTAATTT 0.820278 -260 CCCCTGCACCATTTTTATTTTAGGTAATAAT 14 63 0 ATTTTATTTT 0.921651 -238 AGGAAATATGTTTCCTATTTAAATAGGTTTT 14 267 0 TTTCTATTTA 0.361911 -34 CCTCACCCAGATTTTTATTTTAATATTT 15 8 0 ATTTTATTTT 0.921651 -185 TTATGAGTTTGTTTTTATTTTGTATGTTTTA 28 29 0 GTTTTATTTT 0.649783 -272 TCAATTTTAAAGTTTTATTTTTAAGAGAATT 28 59 0 AGTTTATTTT 0.685211 -242 AATAAAAAGTATTACTAATTTTTCAATTTTA 28 81 0 ATTCTAATTT 0.822658 -220 AGTAATACTTTTTATTAATTTTCCAATACCA 28 96 1 TTTTTAATTT 0.820278 -205 GCATAATAGATTTTTTAATTTAATTTCTTGC 28 199 0 TTTTTAATTT 0.820278 -102 AGCATAATCTATTTATATTTTATACATCACT 28 249 1 ATTATATTTT 0.655044 -52 *** ******* Masking position 3 Map Score: 27.2472 Number of sites scoring better than the average of aligned sites = 734 Number in coding regions = 407 Number in noncoding regions = 327 Number of orfs with sites within 600 bp upstream = 260 Fraction of orfs with sites within 600 bp upstream = 0.0417604 Motif number 6 AAATAATCCTAAATGAAAAAATTGGCATAG 2 163 0 AAATGAAAAA 0.691404 -92 AGATATTTAAAACTTATAAATCAAAATAGC 2 204 0 AACTTATAAA 0.772223 -51 AATAATATTAAAATGATAAAATTAAAAAAA 3 171 0 AAATGATAAA 0.900093 -130 AATTACTAAAAAATGTTAAAATAATAATAT 3 193 0 AAATGTTAAA 0.795343 -108 ACTTTATTTTTAATTTTAAAATTTTAATTG 4 45 1 TAATTTTAAA 0.704298 -217 AAATTTTTTTAAATTTTAAATTATATTTGA 6 57 0 AAATTTTAAA 0.680097 -24 AGTTTTCCCATAATTATAAAAACCTATTTA 14 249 1 TAATTATAAA 0.846663 -52 GTAAATTTACAACTGATAAAATCTGG 15 177 1 AACTGATAAA 0.861061 -16 AGGGGGAAATAATGAAAAAACTTGGAAAC 17 10 1 TAATGAAAAA 0.715107 -114 TAATAATTTTTACTTATAAAAGTGGAGAGG 21 45 1 TACTTATAAA 0.79159 -27 ATTTTAAAACTAATTATAAATAAATTATGG 22 53 0 TAATTATAAA 0.846663 -56 AATGTTTATATACTGTTAAACCTAATCTGT 26 59 1 TACTGTTAAA 0.749686 -25 AATAAAAACAAACTCATAAATTCTCTTAAA 28 41 1 AACTCATAAA 0.62366 -260 AACCTACTTATAATCTTAAAAATCCGAAAG 28 136 1 TAATCTTAAA 0.53794 -165 GCAAGAAATTAAATTAAAAAATCTATTATG 28 199 1 AAATTAAAAA 0.550693 -102 TCATTATCATTAATGACAAATAGTGATGTA 28 271 0 TAATGACAAA 0.59553 -30 TCATTAATGATAATGATAAATTACTG 28 285 1 TAATGATAAA 0.909857 -16 ********** Masking position 4 Map Score: 10.9789 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 344 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 7 TCCAAAGATGTCAAAGTTCCAAAGTGCATA 1 221 1 TCAAAGTTCC 0.848779 -80 AACCTTTTAGTAAAAGGTTCATCAAAACGG 2 43 0 TAAAAGGTTC 0.909416 -212 AACCTTTTACTAAAAGGTTCATGTGAAGGA 2 54 1 TAAAAGGTTC 0.909416 -201 AAAGAAAGCCTAAAAGTATCATCAATAGCA 3 59 0 TAAAAGTATC 0.800253 -242 TATTTTATCCTAAAAATTACTAAAAAATGT 3 207 0 TAAAAATTAC 0.543884 -94 AATAGGTATATAAAATTTTCTATTTTATCC 3 227 0 TAAAATTTTC 0.826522 -74 ATTCTCTATCTCAAAGTCTCTTCCATTAAT 4 128 0 TCAAAGTCTC 0.760303 -134 TTAAAAATTTCGTTTTTAAAA 14 2 1 TAAAAATTTC 0.827733 -299 CAACTTTTTCTAAAAGTTTCGTTTATAGTC 15 61 0 TAAAAGTTTC 0.97187 -132 TTCGGCCCTATAACAGTTCCAAGAGTTCCA 18 82 0 TAACAGTTCC 0.738272 -41 TTAGATTGATTAAAAGTTCCCATAGGTGAT 20 14 0 TAAAAGTTCC 0.950828 -119 GGGAAATATATAAAAGTTACCCACAAAAAA 20 64 0 TAAAAGTTAC 0.89564 -69 TTAGTCATTCTAAAAGTTTTGAAAGACATG 24 28 0 TAAAAGTTTT 0.67797 -95 TTATGCATATTAAAATTCTCAATAAAGCAT 28 224 1 TAAAATTCTC 0.602888 -77 ********** Masking position 5 Map Score: 9.7424 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 151 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 TGCCTCGCTACGCTCGGCAGTGCCTC 2 7 0 CGCTCGGCAG 0.971532 -248 TGCCGAGCGTAGCGAGGCAGTGCATCCGTT 2 18 1 AGCGAGGCAG 0.955954 -237 TTCCGAGCGAAGCGAGGAGGTGTTAGTTTT 15 145 0 AGCGAGGAGG 0.976284 -48 CTCCTCGCTTCGCTCGGAAGTGTAAATTTA 15 156 1 CGCTCGGAAG 0.976283 -37 TCCGAGCGTAAGCGAGGAGGTGTTAGGGTG 17 67 0 AGCGAGGAGG 0.976284 -57 TCCTCGCTTACGCTCGGAGGTGTAAATTAA 17 79 1 CGCTCGGAGG 0.984785 -45 ********** Masking position 6 Map Score: 4.12175 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 1 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 CACAGCAGTATGCTGAAGTCATAATGAGAGC 1 23 1 TGCTAAGTCA 0.872382 -278 TATTTATTCCTGCGAAAGTCCTGTTATGCCT 1 172 0 TGCGAAGTCC 0.990617 -129 ATATATAAACTGCGAAAGTCCTGTTTCTTTG 1 248 1 TGCGAAGTCC 0.990617 -53 GTATAGCCTCTGCGTAAGTTCCATTGTGGGA 3 22 0 TGCGAAGTTC 0.985324 -279 TTCAAAAAAATGCGTAAGTTCTATTGAATAG 3 93 1 TGCGAAGTTC 0.985324 -208 CTGAAAATTTTGCTTAAGTTTAAATATTATT 7 27 1 TGCTAAGTTT 0.812991 -69 **** ****** Masking position 6 Map Score: 4.93523 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 8 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 CCCTTTCGGGTTCCCCTCGAGGCTTATAAC 1 135 0 TTCCCCTCGA 0.848939 -166 ATCTATTATTATGCCCTCCAATTAAAATTT 4 63 0 ATGCCCTCCA 0.862553 -199 TCTGTAATTCTCGCCCTCCATAGGAAAACC 10 59 0 TCGCCCTCCA 0.985941 -45 CTGGAAAGCATAGCTCTCCATTTCATCAAA 15 117 1 TAGCTCTCCA 0.909413 -76 CAATAGAGGGTTTCCCTCTATGGTTTCCAA 17 32 0 TTTCCCTCTA 0.809602 -92 GTAAATCCCTCTCCACTTTTATAAG 21 57 0 TCCCTCTCCA 0.902247 -15 AATATCCCTCCTGATATTTTAT 22 3 1 TATCCCTCCT 0.798243 -106 TATATTAAAATAGCCCTCTAACCTAAACAA 24 81 1 TAGCCCTCTA 0.919582 -42 TACCCCACCATCAAAATTTT 24 113 0 TACCCCACCA 0.86152 -10 ATTCTCCCTCCAATCTTTTAGA 25 26 0 TCTCCCTCCA 0.971392 -12 ********** Masking position 6 Map Score: 5.04096 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 108 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 TGGTCTGAAACTATGCCAACAGCTTGATTCTC 4 152 0 CTATCAACAG 0.919038 -110 AATGAATTCGGTATTTCAATAGGGTTTTCCTA 10 37 1 GTATCAATAG 0.869096 -67 TTATAAAAACCTATTTAAATAGGAAACATATT 14 262 1 CTATAAATAG 0.486001 -39 TGGACGGGTGGTATAGCAATAGGAGGTCTCCT 16 26 0 GTATCAATAG 0.940531 -83 GTGTTAGGGTGTATCCCAATAGAGGGTTTCCC 17 46 0 GTATCAATAG 0.98227 -78 CCCGCTCTGGGTATCCCAATAGGGCGAAGCCC 19 52 1 GTATCAATAG 0.98227 -23 **** ****** Masking position 8 Map Score: 3.16136 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 6 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 12 TGAAGAGACAAAAGAGATTATAGAAGTTAGAAA 1 99 1 AAAATTATAG 0.636432 -202 CATGTGAAGGAAATAGAGCATAGGAAAGAATTA 2 73 1 AAAAGCATAG 0.654487 -182 ATAAAAAAAGAACAAGAAAATAGTAATATTTTT 2 125 0 AAAAAAATAG 0.944354 -130 AATAATCCTAAATGAAAAAATTGGCATAGTATA 2 159 0 AAAAAAATTG 0.576821 -96 CATCAATAGCAAATAGAGTATAGCCTCTGCGTA 3 37 0 AAAAGTATAG 0.692656 -264 TAGTAATTTTTAGGATAAAATAGAAAATTTTAT 3 215 1 TAAAAAATAG 0.576821 -86 TAAAACTTAAAATAAGATAATAAAGA 4 4 0 AAAATAATAA 0.380262 -258 ATTTATACTAAATAAGATATTAGGTTTTAATTA 4 213 1 AAAATATTAG 0.778344 -49 CATAAAAATTATATAAAAAATAGAAAAAAG 5 8 0 ATAAAAATAG 0.719146 -127 AACTACCGAAAAATATATATTAGATATTAAAAA 5 75 1 AAAATATTAG 0.778344 -60 ATTATATTTGAAGTATAAAATAGCAATAACCAA 6 35 0 AAAAAAATAG 0.944354 -46 TACTCAATATAACAATAAAATATAAAAACAAAA 12 41 1 AAAAAAATAT 0.489859 -63 TAAAATATAAAAACAAAAAATACAACTTAAAAC 12 56 1 AAAAAAATAC 0.587322 -48 ACCGCAAGCGAATTATAGAATAGATGAACTCAT 14 171 1 AAAAGAATAG 0.93316 -130 ATCCTCTGGGAAATATATAAAAGTTACCCACAA 20 68 0 AAAATAAAAG 0.465522 -65 TAATGACAGATTAGGTTTAACAGT 26 70 0 AAAAGATTAG 0.818868 -14 AAACTTTAAAATTGAAAAATTAGTAATACTTTT 28 75 1 ATAAAATTAG 0.4533 -226 ** * ******* Masking position 7 Map Score: 2.47706 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 327 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 13 TGATATATGAGCTTCATGTGCAACACACGT 1 57 1 GCTTCATGTG 0.928863 -244 TTTACTAAAAGGTTCATGTGAAGGAAATAG 2 59 1 GGTTCATGTG 0.944906 -196 ATTACCAATAACTGCAGGTGGAAGT 13 74 1 ACTGCAGGTG 0.808583 -15 AAATAAAAATGGTGCAGGGGAGGGGATTTG 14 74 1 GGTGCAGGGG 0.981009 -227 GTCCCGTAGGGGTTCGGGGGTTCAAATCCC 14 96 0 GGTTCGGGGG 0.939906 -205 ATTCGCTTGCGGTGCAGGGGTCGCCAAGCC 14 154 0 GGTGCAGGGG 0.981009 -147 TTAATTTCTTGCTTCTTGTGAGCATAGCGA 28 181 0 GCTTCTTGTG 0.763107 -120 ********** Masking position 3 Map Score: 1.97522 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 6 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 ATTACTATCATTTTCTATAGCTGTAGTAATAT 3 254 1 TTTTCATGCT 0.922836 -47 CTTTTTTCTATTTTTTATATAATTT 5 4 1 TTTTCATTTT 0.602834 -131 TAATATATATTTTTCGGTAGTTTATCAAAAAT 5 65 0 TTTTCGTGTT 0.741775 -70 TGAACAAAAATTTTTAATATCTAATATATATT 5 86 0 TTTTTATTCT 0.863373 -49 TTAACGTTTTTATTGGTTTTATCGTAA 9 23 0 GTTTTATGGT 0.586831 -17 TTTGTTTTTATATTTTATTGTTATATTGAGTA 12 41 0 TATTTATGTT 0.577086 -63 TTAAGTTGTATTTTTTGTTTTTATATTTTATT 12 54 0 TTTTTGTTTT 0.602834 -50 GTATATAAAATTTTTTATCTCTGACTCTATCA 13 24 0 TTTTTATTCT 0.863373 -65 AACTCTTAGAGTTTTCATAGCTGGAAAGCATA 15 97 1 GTTTTATGCT 0.841562 -96 TTTCGTCTTATTTTTTGTGGGTAACTTTTATA 20 54 1 TTTTTGTGGT 0.761788 -79 TCCCTCCTGATATTTTATAGCTTACTCTATAA 22 15 1 TATTTATGCT 0.774464 -94 TCACAGGAAATTTTCAATAGTTTAAATTTAAA 23 56 0 TTTTCATGTT 0.82616 -25 ATATCACCAATTTTTCATGTCTTTCAAAACTT 24 13 1 TTTTTATTCT 0.863373 -110 AATATTTATGTTTTTAATAGCTTTTAGCTTTT 26 14 1 TTTTTATGCT 0.95189 -70 AGCTTTTAGCTTTTTGGTTGCTAACGTAATGT 26 32 1 TTTTTGTGCT 0.922836 -52 ***** ** *** Masking position 8 Map Score: 8.91023 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 479 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 15 CTTATTAAAAATATTACTATTTTCTTGTTCTTT 2 119 1 ATATACTTTT 0.741048 -136 GCAATAACCAATATGACCTCATTATATAAAAAA 6 13 0 ATATACCATT 0.966362 -68 ATAATATCACCTCATTTTTGTCTAAG 12 88 0 ATATACCATT 0.966362 -16 AATTTTATATACATAACCCTATTTTAAAATATT 13 44 1 ACATACCATT 0.898371 -45 TTTATCTCACCTAATTTTATTAAATA 16 93 0 ATCTACCATT 0.898371 -16 TTATATCACCAATTTTTCATGTCTT 24 3 1 ATATACCTTT 0.956634 -120 CTATTTTAATATATAACCCTTTTGCTGGAACCA 24 61 0 ATATACCTTT 0.95664 -62 **** *** *** Masking position 6 Map Score: 1.56069 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 14 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802