AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_mjan_reg_300.orf -o00630_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: MJ0267 21 pyruvate ferredoxin oxidoreductase, subunit alpha (porA) MJ0266 27 pyruvate ferredoxin oxidoreductase, subunit beta (porB) MJ1425 25 malate dehydrogenase MJ0264 41 carbon monoxide dehydrogenase, iron sulfur subunit CooF-1 (cooF1) Input sequences: #1 MJ0005 87 formate dehydrogenase, beta subunit #2 MJ0006 300 formate dehydrogenase, alpha subunit #3 MJ0150 65 M. jannaschii predicted coding region MJ0150 #4 MJ0152 256 carbon monoxide dehydrogenase, subunit alpha #5 MJ0153 239 acetyl-CoA decarbonylase/synthase, subunit alpha (cdhA) #6 MJ0154 43 acetyl-CoA decarbonylase/synthase, subunit epsilon (cdhB) #7 MJ0210 86 succinyl-CoA synthetase, beta subunit #8 MJ0210.1 43 M. jannaschii predicted coding region MJ0210.1 #9 MJ0212 126 conserved hypothetical protein #10 MJ0213 114 M. jannaschii predicted coding region MJ0213 #11 MJ0214 89 hydrogenase expression/formation protein (hypA) #12 MJ0265 42 carbon monoxide dehydrogenase, iron sulfur subunit CooF-1 (cooF2) #13 MJ0269 283 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #14 MJ0270 300 M. jannaschii predicted coding region MJ0270 #15 MJ0516 113 carbon monoxide dehydrogenase, hydrogenase subunit CooL (cooL) #16 MJ0519 181 M. jannaschii predicted coding region MJ0519 #17 MJ0520 192 NADH-ubiquinone oxidoreductase, subunit 1 #18 MJ0522 108 NADH dehydrogenase I #19 MJ0524 123 conserved hypothetical protein #20 MJ0525 122 conserved hypothetical protein #21 MJ0528 74 conserved hypothetical protein #22 MJ0529 132 repressor protein, putative #23 MJ0713 146 hydrogenase expression regulatory protein (hypF) #24 MJ1027 125 formate hydrogenlyase, subunit 5 #25 MJ1235 284 ribulose bisphosphate carboxylase, large subunit (rbcL) #26 MJ1236 239 putative mRNA 3'-end processing factor 2 #27 MJ1237 120 proteasome, subunit beta (psmB) #28 MJ1238 90 prolyl-tRNA synthetase (proS) #29 MJ1363 300 formate hydrogenlyase, subunit 7 #30 MJ1424 202 tRNA intron endonuclease (endA) Motif number 1 CAACTAAACCATTAAAAATTTTGAAGATAAGA 2 11 0 ATTAAAATTT 0.889411 -290 CAACTATCATATATAAAATTTACTACTTAATT 2 113 0 ATATAAATTA 0.898983 -188 TTTGATACCTTTTTTAATATTTATTATGTCAA 2 174 0 TTTTTAATTT 0.86237 -127 TACATTTGTTATATAAATCTTTGACTGT 3 48 1 ATATAAATTT 0.949446 -18 AATAGGGCTTTTTTAAATGTTTCTATTTGATT 4 58 0 TTTTAAATTT 0.891679 -199 TTTGCAAGTCATAGAAATTTTTAATTAATGCT 4 96 1 ATAGAAATTT 0.854452 -161 TACCATGGATATTAAAATCTTTAATAAGTTAT 4 145 1 ATTAAAATTT 0.889411 -112 CAGTAGTCTAATTTTAAGTTTATGCATTACTA 4 215 0 ATTTTAATTA 0.875646 -42 TTGGCATAAAATATAAAGTTTATGATAGGGCA 5 12 0 ATATAAATTA 0.898983 -228 AAATTACGCATTTTAAAAATTGTTTTGTAGGG 5 89 0 TTTTAAATTG 0.635267 -151 CAAACTTTATATATTAAAGTTTTAAAAACTAA 5 179 1 ATATTAATTT 0.934622 -61 AAATTATCATATAAAAAATTTGGTGATAAATT 7 21 0 ATAAAAATTG 0.620779 -66 TTATATGATAATTTTAAAATTTTGCATTAAAA 7 39 1 ATTTTAATTT 0.93695 -48 ATTAAAAAATTATGGGAAATAA 8 32 0 ATTAAAATTA 0.792138 -12 TCATCGGATTTTAAAAAAGTTTCATTAAAAGT 9 36 0 TTAAAAATTT 0.765379 -91 TTCATCATCTATTTAAACCTTTCATCGGATTT 9 57 0 ATTTAAATTT 0.951274 -70 AAATGAAGACATTTTAATGTTGAGAAAATATA 10 53 0 ATTTTAATTG 0.758701 -62 AATTATTAAGATTTTTATAGTTTT 11 3 1 TTATTAATTT 0.857706 -87 ATCCAACTTTTTAAAAAGGTTTAATCAAAACT 11 29 0 TTAAAAATTT 0.765379 -61 ACCAAAAACTATTTTAATTTTAGTAAAAAAAG 12 20 0 ATTTTAATTA 0.875646 -23 TAAAAGTAATATATAAAGTTTTGGAGATTTAA 13 221 0 ATATAAATTT 0.949446 -63 ACATTTTTGTATATAAAATTTTTCATAAAAAT 14 138 1 ATATAAATTT 0.949446 -163 AATTCTAAGTATTTAAATATTTTTATGAAAAA 14 156 0 ATTTAAATTT 0.951274 -145 GAGGTGTAAATTAGTAAGATTTGGGGAGTATC 16 110 1 TTAGTAATTT 0.653276 -72 CCAGATTTTTATTTTAATATTT 17 1 0 ATTTTAATTT 0.93695 -192 TGTCCATTATTTAATAAAATTAGGTGAGATAA 18 86 1 TTAATAATTA 0.540569 -23 TCAATCTAATATATAAACTTTTCGTCTTATTT 22 35 1 ATATAAATTT 0.949446 -98 TCTGGGAAATATATAAAAGTTACCCACAAAAA 22 65 0 ATATAAATTA 0.898983 -68 AATTTGTTTTATATAAACTTTATCATAAAATT 23 36 1 ATATAAATTA 0.898983 -111 TTTAATATACATATTAAATTTTATGATAAAGT 23 52 0 ATATTAATTT 0.934622 -95 AATTGATATTATTAAAATTTTTAATATACATA 23 71 0 ATTAAAATTT 0.889411 -76 AAAACTACATATTAAAAAATTAAATAATAATC 23 111 1 ATTAAAATTA 0.792138 -36 TTAATTTTAAATTTGATTATTATTT 23 132 0 ATTTTAATTG 0.758701 -15 TAGTTTTGTTTTAATAAAGTTATCGAG 24 6 0 TTAATAATTA 0.540569 -120 AATTGATTTGATTTTAATATTTTGAAAAAATT 25 54 0 ATTTTAATTT 0.93695 -231 AATTAATGAATTAATAAATTTTCATTCCGAAT 25 83 0 TTAATAATTT 0.712899 -202 ATAAATAGTGTTAGAAAGCTTTACCTTTAGTT 25 195 0 TTAGAAATTT 0.712256 -90 GTATTAAGTATTATTAATTTTTTGTATGGTCG 25 235 0 TTATTAATTT 0.857706 -50 TTTTAATCTTATATTAAACTTATTAGCCTTTA 26 44 0 ATATTAATTA 0.871365 -196 TTAATATAAGATTAAAAATTTTAAGAAAAATA 26 59 1 ATTAAAATTT 0.889411 -181 TATATTTTTAATTTTAACATTTTTTCATAAAC 26 144 1 ATTTTAATTT 0.93695 -96 CGTGTTTTAAATTGAAAATTTTGATAATATTT 26 183 0 ATTGAAATTT 0.859205 -57 CGGCAGAGATTTTTAAAAGTTAAGGAGGAGGA 26 213 1 TTTTAAATTA 0.795945 -27 ATTTCAATAAATAAAAATTTTATTTTGTTCAT 27 39 0 ATAAAAATTA 0.785686 -82 ATTTTTATTTATTGAAATATTATTAGAAAGCT 27 53 1 ATTGAAATTA 0.74304 -68 ACAGTTGGTTATTTAAAGTTTTTCATGGTGGG 28 14 0 ATTTAAATTT 0.951274 -77 AAATTAATAAATATTAATTTTTATTTAAAATG 28 46 0 ATATTAATTT 0.934622 -45 TAATTTTTCAATTTTAAAGTTTTATTTTTAAG 29 65 0 ATTTTAATTT 0.93695 -236 ATCTTTCGGATTTTTAAGATTATAAGTAGGTT 29 136 0 TTTTTAATTA 0.748051 -165 CGAACAGGTTTTAGAAATCTTTCGGATTTTTA 29 152 0 TTAGAAATTT 0.712256 -149 TCCACAATAAATTTTAAGATTTTATAAATAAT 30 177 1 ATTTTAATTT 0.93695 -26 ******* *** Masking position 6 Map Score: 68.2679 Number of sites scoring better than the average of aligned sites = 1730 Number in coding regions = 1031 Number in noncoding regions = 699 Number of orfs with sites within 600 bp upstream = 479 Fraction of orfs with sites within 600 bp upstream = 0.0769354 Motif number 2 ATAAGATAGAATTTTAAATAAGTATTACTACTAT 2 61 0 ATTTTAAAAA 0.824471 -240 CTTAATTTAAATTATTATTACTTAAATAAGATAG 2 86 0 ATTATTATAA 0.646471 -215 ATCATATATAAAATTTACTACTTAATTTAAATTA 2 106 0 AAATTTACAA 0.744587 -195 TATCATTGACATAATAAATATTAAAAAAGGTATC 2 169 1 ATAATAAAAA 0.687696 -132 GCTAGAAATCAAAATTAAAACTTAGACAAAAATA 2 233 1 AAAATTAAAA 0.877237 -68 AACTTAGACAAAAATAAACACAGAGAATTTTTAT 2 251 1 AAAATAAAAA 0.827316 -50 AACACAGAGAATTTTTATGACAAATAGAACATTT 2 267 1 ATTTTTATAA 0.767852 -34 AATTTTATTACTAAATAATAAACA 4 1 1 AATTTTATAA 0.877994 -256 TTATTACTAAATAATAAACAAAAAAATCAGATAT 4 15 1 ATAATAAAAA 0.687696 -242 GGTTTGTGCTATTTTTACCATGGATATTAAAATC 4 130 1 ATTTTTACAA 0.612424 -127 GCATTGCGAAAAATTTAATACAAATAACTTATTA 4 166 0 AAATTTAAAA 0.928188 -91 AGTATCTATTAATTTAAAAAAATAAATTAGTGTT 5 42 0 AATTTAAAAA 0.910867 -198 TTTTGTAGGGATTTTTAAAAATGAGTATCTATTA 5 65 0 ATTTTTAAAA 0.875091 -175 CTAACCTTAAATTATAATGATTAATCATGACAAT 5 207 1 ATTATAATAA 0.550759 -33 TAAACCTATAAATTTATCACCAAATTTTTTATA 7 10 1 AAATTTATAA 0.8592 -77 GCAAAATTTTAAAATTATCATATAAAAAATTTGG 7 30 0 AAAATTATAA 0.771359 -57 CATTAAAAAGAAATTTATCATTTAAGGTGATAGG 7 63 1 AAATTTATAA 0.859198 -24 ATATAGAAATAATTTCATCATCTATTTAAACCTT 9 68 0 AATTTCATAA 0.578322 -59 AATATAATGTATTATCAAAACTTACCTTATAAAA 10 25 0 ATTATCAAAA 0.424679 -90 ATCATTAACAATTATTAAAAGTAATATATAAAGT 13 234 0 ATTATTAAAA 0.794797 -50 GTATTTAAATATTTTTATGAAAAATTTTATATAC 14 146 0 ATTTTTATAA 0.767832 -155 TTGAATTTGGAATTTAAATACTCAAAGAGTGTTA 14 244 0 AATTTAAAAA 0.910869 -57 TTTAAATTCCAAATTCAATATATAAACTGTGGAA 14 260 1 AAATTCAAAA 0.711256 -41 CCTCCCAATAAATTTTAAGAGGCATTGCTTCTTT 15 83 0 AATTTTAAAA 0.938433 -31 AAATATTAAAATAAAAATCTGGGTG 17 2 1 AATATTAAAA 0.893921 -191 TCGGAAGTGTAAATTTACAACTGATAAAATCTGG 17 169 1 AAATTTACAA 0.744587 -24 TATCTCACCTAATTTTATTAAATAATGGACATTA 18 83 0 AATTTTATAA 0.87782 -26 CCATGGCGATAATATAATGATTGATTATGAAAA 22 110 1 AATATAATAA 0.727329 -23 CTTTATCATAAAATTTAATATGTATATTAAAAAT 23 53 1 AAATTTAAAA 0.928188 -94 ACATATTAAAAAATTAAATAATAATCAAATTTAA 23 117 1 AAATTAAAAA 0.896541 -30 AATAATAATCAAATTTAAAATTAA 23 133 1 AAATTTAAAA 0.928187 -14 ATAATTTATCATAATTAATAATGATAATTAGCTT 24 49 0 ATAATTAAAA 0.766593 -77 TATTTTGAAAAAATTTAACAAATAGAATTAAACA 25 35 0 AAATTTAAAA 0.928188 -250 ATTTTTTCAAAATATTAAAATCAAATCAATTCGG 25 55 1 AATATTAAAA 0.893922 -230 GATGAATGTAAAATTAATGAATTAATAAATTTTC 25 92 0 AAATTAATAA 0.803547 -193 ATTTTAACCAAATATAAAAAAGGATGAATGTAAA 25 114 0 AATATAAAAA 0.849621 -171 TTCAATAATTAATTTAAATATATAAACTAAAGGT 25 171 1 AATTTAAAAA 0.910868 -114 TAAGATTAAAAATTTTAAGAAAAATATAGATAAA 26 65 1 AATTTTAAAA 0.938433 -175 AAAATCTCTTAATTTAACTAAATATCTCTATTTT 26 106 1 AATTTAACAA 0.697423 -134 AAAAATGTTAAAATTAAAAATATAGCATAAAATA 26 134 0 AAATTAAAAA 0.89654 -106 CACGGCAGAGATTTTTAAAAGTTAAGGAGGAGGA 26 211 1 ATTTTTAAAA 0.875091 -29 TATTTATTGAAATATTATTAGAAAGCTATTAAAA 27 58 1 AATATTATAA 0.799138 -63 ACCAACTGTCATTTTAAATAAAAATTAATATTTA 28 37 1 ATTTTAAAAA 0.82447 -54 TAAAACATACAAAATAAAAACAAACTCATAAATT 29 29 1 AAAATAAAAA 0.827316 -272 TTGGTATTGGAAAATTAATAAAAAGTATTACTAA 29 94 0 AAAATTAAAA 0.877237 -207 CTTTATTGAGAATTTTAATATGCATAATAGATTT 29 217 0 AATTTTAAAA 0.938433 -84 CGCAGTTTTTATATTAAAAAGGTATTTAGATGCC 30 76 0 ATATTAAAAA 0.799316 -127 TTATTTAACAAAATTAATGAATGAATTAATATAG 30 115 0 AAATTAATAA 0.803585 -88 ******** * * Masking position 7 Map Score: 60.2059 Number of sites scoring better than the average of aligned sites = 1490 Number in coding regions = 986 Number in noncoding regions = 504 Number of orfs with sites within 600 bp upstream = 363 Fraction of orfs with sites within 600 bp upstream = 0.0583039 Motif number 3 TATTCAGAAACCATAGGGCTTCGCCCTATT 15 26 1 CCATAGGGCT 0.893953 -88 CTGGGTATCCCAATAGGGCGAAGCCCTATG 15 37 0 CAATAGGGCG 0.984633 -77 TACATTGTATCCATAGGGGAAACCCCCTAT 16 21 1 CCATAGGGGA 0.974466 -161 AGGTTCATCCCAATAGGGGGTTTCCCCTAT 16 33 0 CAATAGGGGG 0.993958 -149 GGGAGTATCCCAATAGAGGGGCGAAGCCCC 16 133 1 CAATAGAGGG 0.983722 -49 TGTATAAGACCCATAGAGGGGCTTCGCCCC 16 150 0 CCATAGAGGG 0.987732 -32 GGTGGTATAGCAATAGGAGGTCTCCTCCTA 18 22 0 CAATAGGAGG 0.934949 -87 AACTTGGAAACCATAGAGGGAAACCCTCTA 19 29 1 CCATAGAGGG 0.987732 -95 GGGTGTATCCCAATAGAGGGTTTCCCTCTA 19 42 0 CAATAGAGGG 0.983722 -82 CTGGGTATCCCAATAGGGCGAAGCCCT 21 58 1 CAATAGGGCG 0.984633 -17 TTAAAAGTTCCCATAGGTGATAAA 22 5 0 CCATAGGTGA 0.769278 -128 ********** Masking position 5 Map Score: 20.0642 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 22 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 CCAAAACCTAACACCTCCTCGCTTACGCTCGG 16 79 1 ACACCTCCGC 0.998409 -103 TTACTAATTTACACCTCCGAGCGTAAGCGAGG 16 95 0 ACACCTCCGC 0.998409 -87 TCAAAAACTAACACCTCCTCGCTTCGCTCGGA 17 142 1 ACACCTCCGC 0.998409 -51 TTGTAAATTTACACTTCCGAGCGAAGCGAGGA 17 157 0 ACACTTCCGC 0.989804 -36 ATACACCCTAACACCTCCTCGCTTACGCTCGG 19 64 1 ACACCTCCGC 0.998409 -60 AAATTAATTTACACCTCCGAGCGTAAGCGAGG 19 80 0 ACACCTCCGC 0.998409 -44 ******** ** Masking position 6 Map Score: 18.13 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 0 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 5 TTGATATTAGAAAATCTAATAATAGTAGTA 2 40 1 AAAATCTAAT 0.852489 -261 AAAGGTATCAAAAATCTAAGATTAGTAAGA 2 194 1 AAAATCTAAG 0.590673 -107 AATAAACAAAAAAATCAGATATTACTAAAA 4 27 1 AAAATCAGAT 0.713798 -230 TATTACTAAAAAAATCAAATAGAAACATTT 4 46 1 AAAATCAAAT 0.92651 -211 TATGACTTGCAAAATAAAAAATAGGGCTTT 4 79 0 AAAATAAAAA 0.901083 -178 GTGTTGGCATAAAATATAAAGTTTATGATA 5 17 0 AAAATATAAA 0.806791 -223 TTAATTTAAAAAAATAAATTAGTGTTGGCA 5 38 0 AAAATAAATT 0.734165 -202 GAAATAATATAAAATAAAAATTATTTTG 8 9 0 AAAATAAAAA 0.901083 -35 TAATGTTGAGAAAATATAATGTATTATCAA 10 41 0 AAAATATAAT 0.852834 -74 AAGCTGTTTAAAAATCAAATCGGCTATTAT 13 55 1 AAAATCAAAT 0.92651 -229 GTCATTCTCAAAAATAAATACAACATCATT 13 117 1 AAAATAAATA 0.665526 -167 GGCATAAGAAAAAATAAAATTAATTTACAT 13 170 0 AAAATAAAAT 0.926706 -114 GTGTTATTATATAATAAAATATTTCCTCAT 14 220 0 ATAATAAAAT 0.614 -81 AAATATTAAAATAAAAATCTGGGTGAG 17 8 1 AAAATAAAAA 0.901083 -185 TTACCCACAAAAAATAAGACGAAAAGTTTA 22 48 0 AAAATAAGAC 0.476365 -85 TTCCATGGCGATAATATAATGATTGATTAT 22 108 1 ATAATATAAT 0.421645 -25 TGTAGTTTTGAAAATCTAATTGATATTATT 23 90 0 AAAATCTAAT 0.852489 -57 AAATTAAATAATAATCAAATTTAAAATTAA 23 127 1 ATAATCAAAT 0.613318 -20 TCAAAATATTAAAATCAAATCAATTCGGAA 25 61 1 AAAATCAAAT 0.92651 -224 AATATAGATAAAAATCTATAAAATCTCTTA 26 87 1 AAAATCTATA 0.476297 -153 TCTTAACCTAAAAATAAGAAAAGAT 27 6 0 AAAATAAGAA 0.643121 -115 ATTTATGAACAAAATAAAATTTTTATTTAT 27 35 1 AAAATAAAAT 0.926706 -86 AATTTGCTATAAAATAAAAGGTGATATC 28 73 1 AAAATAAAAG 0.759447 -18 TAAAACATACAAAATAAAAACAAACTCATA 29 29 1 AAAATAAAAA 0.901083 -272 AATTCTCTTAAAAATAAAACTTTAAAATTG 29 59 1 AAAATAAAAC 0.821387 -242 TTCCAATACCAAAATCAAACAACCTACTTA 29 116 1 AAAATCAAAC 0.820964 -185 ATTAAATTAAAAAATCTATTATGCATATTA 29 206 1 AAAATCTATT 0.557977 -95 AGTGATGTATAAAATATAAATAGATTATGC 29 250 0 AAAATATAAA 0.806791 -51 TGTGGATAATAAAATAAATAACATATGGTT 30 153 0 AAAATAAATA 0.665526 -50 ********** Masking position 5 Map Score: 32.1131 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 638 Number in noncoding regions = 339 Number of orfs with sites within 600 bp upstream = 260 Fraction of orfs with sites within 600 bp upstream = 0.0417604 Motif number 6 TATCCCAATAGGGCGAAGCCCTATGGTTTCT 15 31 0 GGGGAAGCCC 0.882051 -83 GCAATGCATCCTGGGTATCCCAATAGGGCGA 15 46 0 CTGGTATCCC 0.930128 -68 CATCCCAATAGGGGGTTTCCCCTATGGATAC 16 27 0 GGGGTTTCCC 0.977183 -155 GTAAGATTTGGGGAGTATCCCAATAGAGGGG 16 123 1 GGGGTATCCC 0.918391 -59 CCCAATAGAGGGGCGAAGCCCCTCTATGGGT 16 141 1 GGGGAAGCCC 0.882051 -41 TATCCCAATAGAGGGTTTCCCTCTATGGTTT 19 36 0 GAGGTTTCCC 0.923873 -88 GGAGGTGTTAGGGTGTATCCCAATAGAGGGT 19 51 0 GGGGTATCCC 0.990396 -73 GGGCTGAACGTAGTGAAGCCCCGCTCTGGGT 21 33 1 TAGGAAGCCC 0.783158 -42 AAGCCCCGCTCTGGGTATCCCAATAGGGCGA 21 48 1 CTGGTATCCC 0.930128 -27 TATCCCAATAGGGCGAAGCCCT 21 63 1 GGGGAAGCCC 0.882051 -12 *** ******* Masking position 9 Map Score: 15.8102 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 10 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 ATCTTAGATTTTTGATACCTTTTTTAATATTTAT 2 182 0 TTTATATTTT 0.825927 -119 TTGTCTAAGTTTTAATTTTGATTTCTAGCTTTCC 2 228 0 TTTATTATTT 0.443771 -73 CCTACATTTGTTATATAAATCTTTGACTGT 3 46 1 TTAATACTTT 0.520014 -20 TATTAAAATCTTTAATAAGTTATTTGTATTAAAT 4 154 1 TTTATATATT 0.784868 -103 TAAATTTCTTTTTAATGCAAAATTTTAAAATTAT 7 46 0 TTTATGAATT 0.692193 -41 ATAATTTTTATTTTATATTATTTCCCATAATTTT 8 15 1 TTTATATTTC 0.533964 -29 CCTATTAACTTTTAATGAAACTTTTTTAAAATCC 9 29 1 TTTATGCTTT 0.718517 -98 ATGAAATTATTTCTATATATCTTTAATCTAACAA 9 84 1 TTCATACTTT 0.767747 -43 ATTTTATAATTCTTTTTTATAAGGT 10 2 1 TTTATACTTT 0.88412 -113 TAAGGTAAGTTTTGATAATACATTATATTTTCTC 10 30 1 TTTATACATT 0.854366 -85 ATTTTAGCCCTTTAATAACAATTTCCTTAATCCA 11 56 0 TTTATAATTT 0.897346 -34 CTCCAAAACTTTATATATTACTTTTAATAATTGT 13 227 1 TTAATACTTT 0.520014 -57 ATTTAAATATTTTTATGAAAAATTTTATATACAA 14 144 0 TTTATGAATT 0.692193 -157 TTTCCACAGTTTATATATTGAATTTGGAATTTAA 14 261 0 TTAATAAATT 0.488346 -40 AGTGGTTTTATAGGATTTTCCACAGTTTA 14 282 0 TTTATATTTT 0.825927 -19 ATTCAACGAGTTCCATAAATATTCACCATACTTT 20 14 0 TTCATAATTC 0.477693 -109 TTTTCATAATCAATCATTATATTAT 22 118 0 TTTATAAATC 0.618773 -15 TTTGAATTTGTTTTATATAAACTTTATCATAAAA 23 32 1 TTTATAACTT 0.495074 -115 TATTTAATTTTTTAATATGTAGTTTTGAAAATCT 23 103 0 TTTATAAGTT 0.495074 -44 TAATTTTAAATTTGATTATTATTTAATTTTTTAA 23 122 0 TTTATTATTT 0.443771 -25 TAGCTTAACCTTTTATATAGTTTTGTTTTAATAA 24 21 0 TTTATATTTT 0.825927 -105 TTAATTTTATGTGCCTTTCAAAACTGTT 25 5 1 TTTATGCTTT 0.718517 -280 TATTTTACTGTTCAATAATTAATTTAAATATATA 25 161 1 TTCATAAATT 0.74439 -124 ATTCTAACAATTCCATATCTAATTTATT 26 5 0 TTCATAAATT 0.74439 -235 GGCTAATAAGTTTAATATAAGATTAAAAATTTTA 26 48 1 TTTATAGATT 0.460161 -192 AATTAAGAGATTTTATAGATTTTTATCTATATTT 26 86 0 TTTATATTTT 0.825927 -154 AATATCTCTATTTTATGCTATATTTTTAATTTTA 26 126 1 TTTATGTATT 0.549672 -114 TTTAACATTTTTTCATAAACAATTACAAAATATT 26 156 1 TTTATAAATT 0.870491 -84 AATTGAAAATTTTGATAATATTTTGTAATTGTTT 26 172 0 TTTATATTTT 0.825927 -68 TCACCTTTTATTTTATAGCAAATTAATAAATATT 28 63 0 TTTATAAATT 0.870491 -28 GGCATCATTATTCAATAAATCATTTATTCCTGCG 30 38 0 TTCATACATT 0.717657 -165 AACTGCGAAGTTCTATATTAATTCATTCATTAAT 30 103 1 TTCATAATTC 0.477693 -100 *** *** **** Masking position 6 Map Score: 23.7969 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 609 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 8 TTTAAGTAATAATAATTTAAATTAAGTAGTAAA 2 94 1 AATAATAATT 0.869932 -207 AACAAGCTTTATTAATGAATAATCCTACATTTG 3 23 1 ATTAATTAAT 0.749662 -43 AATTTTATTACTAAATAATAAACAAAAAA 4 7 1 ATTACTTAAT 0.682282 -250 AAACCTAAGCATTAATTAAAAATTTCTATGACT 4 102 0 ATTAATAAAT 0.852632 -155 AAGTTTATGCATTACTATATAATAGTGGTTACG 4 199 0 ATTACTTAAT 0.733219 -58 TAAATGATAAATTTCTTTTTAATGCAAAATTTT 7 54 0 ATTTCTTAAT 0.377684 -33 AATTATGGGAAATAATATAAAATAAAAATTATT 8 14 0 AATAATAAAT 0.898416 -30 AATCTCGCTAAATAATCATAAATCTCAAAAGGT 10 86 1 AATAATAAAT 0.63288 -29 ATTTATCCCAATTTTAGCCCTTT 11 77 0 ATTTATAATT 0.557637 -13 TATTACTTTTAATAATTGTTAATGATTGATAAT 13 242 1 AATAATTAAT 0.81152 -42 AAAATATTTAAATACTTAGAATTATAAATAATT 14 165 1 AATACTAATT 0.593997 -136 TAGAATTATAAATAATTGGAAATAAAATAGGAC 14 181 1 AATAATAAAT 0.891935 -120 TTCCAAACAAATTAATCAAAATTAATTTACACC 19 97 0 ATTAATAATT 0.813303 -27 TAAAAATTTTAATAATATCAATTAGATTTTCAA 23 80 1 AATAATAATT 0.869932 -67 TATCATAATTAATAATGATAATTAGCTTAACCT 24 44 0 AATAATAATT 0.590274 -82 TATCATTATTAATTATGATAAATTATCTATTCA 24 57 1 AATTATAAAT 0.476129 -69 ACAAAAAATTAATAATACTTAATACCAAAGAAT 25 242 1 AATAATTAAT 0.81152 -43 CCTTTAGCTTAATTCTAACAATTCCATATCTAA 26 17 0 AATTCTAATT 0.50794 -223 TTTATAGCAAATTAATAAATATTAATTTTTATT 28 53 0 ATTAATTATT 0.692325 -38 AAAAATTAGTAATACTTTTTATTAATTTTCCAA 29 89 1 AATACTTATT 0.695043 -212 TATCATTATCATTAATGACAAATAGTGATGTAT 29 270 0 ATTAATAAAT 0.852632 -31 ****** **** Masking position 6 Map Score: 16.5257 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 419 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 9 GATATCACCTTAGTTATTTCTTTT 1 74 0 TCACCTTAGT 0.899004 -14 AATATCACCTAAATGTTCTATTTG 2 287 0 TCACCTAAAT 0.891843 -14 TTTTAAAAACTAACCTTAAATTATAATGAT 5 198 1 TAACCTTAAA 0.809929 -42 CCTATCACCTTAAATGATAAATTT 7 73 0 TCACCTTAAA 0.95583 -14 TTATCAAAACTTACCTTATAAAAAAGAATT 10 18 0 TTACCTTATA 0.573844 -97 ACACTCACCTTAAACTGTCATTAT 13 270 0 TCACCTTAAA 0.95583 -14 TTTATCTCACCTAATTTTATTAAATA 18 93 0 TCACCTAATT 0.722662 -16 TATCTATTCATTACCTTAGTGAGTCATATA 24 80 1 TTACCTTAGT 0.636733 -46 TCATAAATCTTAACCTAAAAATAAGAAAAG 27 13 0 TAACCTAAAA 0.658643 -108 TCTTTCACCTTAAATAATTACCTA 27 107 0 TCACCTTAAA 0.95583 -14 AGATTCACCTCAATATTATAGAAC 30 5 1 TCACCTCAAT 0.828674 -198 ********** Masking position 3 Map Score: 7.04001 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 52 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 10 ACAGTCAAAGATTTATATAACAAA 3 52 0 AATAAGATTT 0.760025 -14 TTAATTTAAAAAAATAAATTAGTGTTGGCATAAA 5 34 0 AATAATAGTG 0.606388 -206 ATTAATCATGACAATTAAGAAGTG 5 226 1 AATAAAAGTG 0.466284 -14 TCAGAAATTTAAAGTAAAAGAATTAGGAG 6 6 0 AATAAGAATT 0.87923 -38 TTTTTTACTAAAATTAAAATAGTTTTTGGTG 12 22 1 AATAATAGTT 0.775287 -21 CAGTAATTCAACAATAAAGCTGTTTAAAAATCAA 13 39 1 AATAACTGTT 0.475027 -245 ATCGGCTATTATATTGAAGGAGTTAAAAAAGGAA 13 73 1 AATAAGAGTT 0.964625 -211 TTTGAGAATGACACTATAGCAGTTCCTTTTTTAA 13 95 0 AATTACAGTT 0.834591 -189 AAAGTTTTGGAGATTTAAGCAATTAACGAAAATA 13 205 0 AATAACAATT 0.771513 -79 AGAGTTTTTAATAATAGATGAATTAAAAGCAGAG 14 24 0 AATGAGAATT 0.515032 -277 TGGAATTTAAATACTCAAAGAGTGTTATTATATA 14 237 0 AATAAGAGTG 0.924105 -64 CCAGCTATGAAAACTCTAAGAGTTTTCGTTCAAC 17 87 0 AATTAGAGTT 0.915815 -106 CCAGATTTTATCAGTTGTAAATTTAC 17 177 0 AATTACAGTT 0.834591 -16 TATAGAGAATATATTCAACGAGTTCCATAAATAT 20 26 0 AATAAGAGTT 0.964625 -97 TTTAACAAATAGAATTAAACAGTTTTGAAAGGCA 25 22 0 AATAACAGTT 0.926725 -263 GGATGAATGTAAAATTAATGAATTAATAAATTTT 25 93 0 AATAAGAATT 0.87923 -192 TATTTTTAAGAGAATTTATGAGTTTGTTTTTATT 29 41 0 AATTAGAGTT 0.915816 -260 GTTATTTAACAAAATTAATGAATGAATTAATATA 30 116 0 AATAAGAATG 0.76475 -87 TATCCACAATAAATTTTAAGATTTTATAAATAAT 30 175 1 AATTAGATTT 0.557398 -28 * * * ** ***** Masking position 5 Map Score: 15.0079 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 261 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 TGATAGTTGAAAATAGTATTAATATATTAG 2 136 1 AAATAGTATT 0.70713 -165 TAAAAAAATAAATTAGTGTTGGCATAAAAT 5 32 0 AATTAGTGTT 0.733561 -208 CGCATTTTAAAAATTGTTTTGTAGGGATTT 5 85 0 AAATTGTTTT 0.796369 -155 CAAAATAATTTTTATTTTATAT 8 3 1 AAATAATTTT 0.80571 -41 ACTAAAATTAAAATAGTTTTTGGTG 12 28 1 AAATAGTTTT 0.954206 -15 AATCCATGTAAATTAATTTTATTTTTTCTT 13 165 1 AATTAATTTT 0.634355 -119 CAATTAACGAAAATAGTTTAGGCATAAGAA 13 190 0 AAATAGTTTA 0.672318 -94 CTAAGTATTTAAATATTTTTATGAAAAATT 14 154 0 AAATATTTTT 0.621064 -147 CGGAGGTGTAAATTAATTTTGATTAATTTG 19 93 1 AATTAATTTT 0.634355 -31 ATTATGTTTGAATTTGTTTTATATAAACTT 23 26 1 AATTTGTTTT 0.620535 -121 TTAACCTTTTATATAGTTTTGTTTTAATAA 24 21 0 ATATAGTTTT 0.672318 -105 AAATAGAATTAAACAGTTTTGAAAGGCACA 25 20 0 AAACAGTTTT 0.752517 -265 TTTCTAATATAAATAGTGTTAGAAAGCTTT 25 205 0 AAATAGTGTT 0.868177 -80 TTAGGGTTCGAAATAGTTTTT 29 2 0 AAATAGTTTT 0.954206 -299 ********** Masking position 1 Map Score: 6.76464 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 119 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 12 CCATTAAAAATTTTGAAGATAAGA 2 4 0 TTTTGAAATA 0.645899 -297 TTTTTAATGGTTTAGTTGATATTAGAAAATC 2 25 1 TTTAGTTATA 0.779408 -276 TATCTGATTTTTTTGTTTATTATTTAGTAAT 4 17 0 TTTTGTTATT 0.754405 -240 TGCGTAATTTTTTTGTTAAAAGAAAAATTCA 5 111 1 TTTTGTTAAA 0.922243 -129 ATAAGGTAAGTTTTGATAATACATTATATTT 10 29 1 TTTTGATATA 0.866268 -86 ATTTTTATAGTTTTGATTAAACCTTTTTAAA 11 21 1 TTTTGATAAA 0.876996 -69 CTATTTTAATTTTAGTAAAAAAAGAAATTTT 12 13 0 TTTAGTAAAA 0.523403 -30 TGTTTAACATTTTTGTATATAAAATTTTTCA 14 132 1 TTTTGTAATA 0.754399 -169 TTTCTAAAAGTTTCGTTTATAGTCCCTATCA 17 54 0 TTTCGTTATA 0.614147 -139 AGGTGTTAGTTTTTGATGAAATGGAGAGCTA 17 127 0 TTTTGATAAA 0.877373 -66 TGTAAATTAATTTTGATTAATTTGTTTGGAA 19 99 1 TTTTGATAAT 0.668866 -25 TTTTATATAGTTTTGTTTTAATAAAGTTATC 24 14 0 TTTTGTTTAA 0.463665 -112 GATTTTAATATTTTGAAAAAATTTAACAAAT 25 46 0 TTTTGAAAAA 0.667264 -239 CTTTTTTATATTTGGTTAAAATAAGCCTTTA 25 126 1 TTTGGTTAAA 0.637115 -159 AAGCTTTACCTTTAGTTTATATATTTAAATT 25 181 0 TTTAGTTATA 0.779405 -104 AATAGAGATATTTAGTTAAATTAAGAGATTT 26 107 0 TTTAGTTAAT 0.524142 -133 AAATTGAAAATTTTGATAATATTTTGTAATT 26 176 0 TTTTGATATA 0.866268 -64 AAAAATTTTATTTTGTTCATAAATCTTAACC 27 28 0 TTTTGTTATA 0.916044 -93 CATTCATTAATTTTGTTAAATAACATAAACC 30 126 1 TTTTGTTAAT 0.772796 -77 ******* *** Masking position 3 Map Score: 13.369 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 256 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 13 ACCTTGAGGATATATAAACTGTGAAAGTCC 1 39 1 TATATAAACT 0.823224 -49 TCAACTATCATATATAAAATTTACTACTTA 2 116 0 TATATAAAAT 0.665986 -185 TTAAAAAAGGTATCAAAAATCTAAGATTAG 2 189 1 TATCAAAAAT 0.516964 -112 TGACTTGCAAAATAAAAAATAGGGCTTTTT 4 77 0 AATAAAAAAT 0.569314 -180 GTTGGCATAAAATATAAAGTTTATGATAGG 5 15 0 AATATAAAGT 0.363751 -225 AATTACGCATTTTAAAAATTGTTTTGTAGG 5 90 0 TTTAAAAATT 0.228558 -150 AAAACTTTAATATATAAAGTTTGTTATGAC 5 172 0 TATATAAAGT 0.598852 -68 ATATTAAAGTTTTAAAAACTAACCTTAAAT 5 189 1 TTTAAAAACT 0.856613 -51 AAAATTATCATATAAAAAATTTGGTGATAA 7 24 0 TATAAAAAAT 0.775364 -63 ATTAAAAAATTATGGGAAAT 8 34 0 ATTAAAAAAT 0.494845 -10 ATAAAAAAGAATTATAAAAT 10 1 0 ATTATAAAAT 0.36121 -114 TATAATGTATTATCAAAACTTACCTTATAA 10 27 0 TATCAAAACT 0.714254 -88 AAAAAGGTTTAATCAAAACTATAAAAATCT 11 19 0 AATCAAAACT 0.489086 -71 ATTAAACCTTTTTAAAAAGTTGGATTAAGG 11 36 1 TTTAAAAAGT 0.656961 -54 TTAAAAGTAATATATAAAGTTTTGGAGATT 13 224 0 TATATAAAGT 0.598852 -60 AGCAGAGATATTTAAAAAAT 14 1 0 TTTAAAAAAT 0.718935 -300 TTCATCTATTATTAAAAACTCTGTTAAAAA 14 36 1 ATTAAAAACT 0.695856 -265 AACATTTTTGTATATAAAATTTTTCATAAA 14 137 1 TATATAAAAT 0.665986 -164 CATAAAAATATTTAAATACTTAGAATTATA 14 161 1 TTTAAATACT 0.305923 -140 GAATTTGGAATTTAAATACTCAAAGAGTGT 14 246 0 TTTAAATACT 0.305923 -55 CCAAATTCAATATATAAACTGTGGAAAATC 14 268 1 TATATAAACT 0.823224 -33 GCTTTCCAGCTATGAAAACTCTAAGAGTTT 17 96 0 TATGAAAACT 0.364324 -97 ATCAATCTAATATATAAACTTTTCGTCTTA 22 34 1 TATATAAACT 0.823224 -99 GAATTTGTTTTATATAAACTTTATCATAAA 23 35 1 TATATAAACT 0.823224 -112 TCAATTAGATTTTCAAAACTACATATTAAA 23 97 1 TTTCAAAACT 0.649416 -50 AAAACTACATATTAAAAAATTAAATAATAA 23 111 1 ATTAAAAAAT 0.494845 -36 TTTATGTGCCTTTCAAAACTGTTTAATTCT 25 16 1 TTTCAAAACT 0.649416 -269 TTAATTTAAATATATAAACTAAAGGTAAAG 25 179 1 TATATAAACT 0.823224 -106 GATAAAAATCTATAAAATCTCTTAATTTAA 26 93 1 TATAAAATCT 0.246337 -147 TTGGAAAATTAATAAAAAGTATTACTAATT 29 92 0 AATAAAAAGT 0.497412 -209 AAGAAATTAAATTAAAAAATCTATTATGCA 29 201 1 ATTAAAAAAT 0.494845 -100 ACCTTTTTAATATAAAAACTGCGAAGTTCT 30 87 1 TATAAAAACT 0.889644 -116 AGTTATTATTTATAAAATCTTAAAATTT 30 185 0 TTTATAAAAT 0.596382 -18 ********** Masking position 6 Map Score: 30.8839 Number of sites scoring better than the average of aligned sites = 1169 Number in coding regions = 869 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 288 Fraction of orfs with sites within 600 bp upstream = 0.0462576 Motif number 14 TTAGTAAGATAAAGGAAAGCTAGAAATCAAAA 2 215 1 AAAGAAGCTA 0.946937 -86 TATTTTTTTAAATTAATAGATACTCATTTTTA 5 52 1 AATTAAGATA 0.737984 -188 AGATGAATTAAAAGCAGAGATATTTAAAAAAT 14 11 0 AAAGAAGATA 0.947934 -290 AATGAAAAGCTACATTGTATCC 16 1 1 AATGAAGCTA 0.946937 -181 TTTTTGATGAAATGGAGAGCTATGCTTTCCAG 17 117 0 AATGAAGCTA 0.946937 -76 TCACTAAGGTAATGAATAGATAATTTATCATA 24 70 0 AATGAAGATA 0.947933 -56 AATTTTAAGAAAAATATAGATAAAAATCTATA 26 75 1 AAAAAAGATA 0.8324 -165 AATATAGCATAAAATAGAGATATTTAGTTAAA 26 118 0 AAAAAAGATA 0.832401 -122 **** * ***** Masking position 6 Map Score: 1.94357 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 102 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 AAACTTGGCTTTAGTCATAACAAACTTTATATAT 5 159 1 TTACTAAAAA 0.914075 -81 TGTCTTCATTTTAATCTCGCTAAATAATCATAAA 10 74 1 TTACCGCAAA 0.820318 -41 CGAAAATAGTTTAGGCATAAGAAAAAATAAAATT 13 179 0 TTACTAAAAA 0.914005 -105 TACAAAAATGTTAAACATACTTAACATAATGTAA 14 115 0 TTACTACTAA 0.714764 -186 AATAAAATATTTCCTCATGCGAAAGTCCTATTTT 14 204 0 TTCCTGCAAA 0.756156 -97 GGCTATTCCTCCCAATAAATTTTAAGAGG 15 95 0 TTCCCAAAAA 0.798606 -19 TATATAAAAGTTACCCACAAAAAATAAGACGAAA 22 54 0 TTACCAAAAA 0.887053 -79 TCAAACATAATTAAACGTAAAAAATT 23 3 0 TTACTAAAAA 0.914454 -144 TCTTTCACCTTAAATAATTACCTATTT 27 104 0 TTCCTAATAA 0.524483 -17 TTTCGAACCCTAAAACATACAAAATAAAAACAAA 29 19 1 TAACTACAAA 0.568725 -282 AAAAAATCTATTATGCATATTAAAATTCTCAATA 29 214 1 TTACTATAAA 0.656824 -87 AATAAATCATTTATTCCTGCGAAAGTTCTATAAT 30 25 0 TTACTGCAAA 0.861228 -178 ATTTATTTTATTATCCACAATAAATTTTAAGATT 30 164 1 TTACCAAAAA 0.887053 -39 *** * *** *** Masking position 13 Map Score: 3.41863 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 95 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459