AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_mjan_reg_100.orf -o00190_mjan_100.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 MJ0033 254 succinate dehydrogenase, flavoprotein subunit (sdhA) #2 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #3 MJ0090 80 collagenase (prtC) #4 MJ0091 95 Na+/Ca+ exchanger protein, putative #5 MJ0216 46 H+-transporting ATP synthase, subunit B (atpB) #6 MJ0217 39 H+-transporting ATP synthase, subunit A (atpA) #7 MJ0219 103 H+-transporting ATP synthase, subunit C (atpC) #8 MJ0220 56 H+-transporting ATP synthase, subunit E (atpE) #9 MJ0221 103 H+-transporting ATP synthase, subunit K (atpK) #10 MJ0223 88 M. jannaschii predicted coding region MJ0223 #11 MJ0224 300 conserved hypothetical protein #12 MJ0520 192 NADH-ubiquinone oxidoreductase, subunit 1 #13 MJ0615 71 H+-transporting ATP synthase, subunit D (atpD) #14 MJ0616 108 phosphoribosylaminoimidazole carboxylase, (purE) #15 MJ1225 80 conserved hypothetical protein #16 MJ1275 122 NA(+)/H(+) antiporter (napA) #17 MJ1309 37 carbon monoxide dehydrogenase, hydrogenase anchor subunit CooM (cooM) #18 MJ1310 83 conserved hypothetical protein #19 MJ1362 68 NADH ubiquinone oxidoreductase, subunit 1 isolog #20 MJ1363 300 formate hydrogenlyase, subunit 7 Motif number 1 TTTCTTGTTCTTTTTTTATTTATACTATGCCAA 1 139 1 TTTTTTTATT 0.850875 -116 CCTCATCAGATATTTAAAACTTATAAATCAAAA 1 208 0 TATTTAAATA 0.859252 -47 CTTTTTTCTATTTTTTATATAATTTTTATGAA 2 10 1 ATTTTTTATA 0.863268 -125 TTTAATATCTAATATATATTTTTCGGTAGTTTA 2 73 0 AATATATATT 0.678561 -62 ATGAACAAAAATTTTTAATATCTAATATATATT 2 86 0 ATTTTTAATT 0.892117 -49 GGTTATTGCTATTTTATACTTCAAATATAATTT 3 37 1 ATTTTATATA 0.844355 -44 AATTTTTTTAAATTTTAAATTATATTTGAAGTA 3 53 0 AATTTTAATT 0.896751 -28 ACTTAAGCAAAATTTTCAGTTCATCCATATTGT 4 13 0 AATTTTCATA 0.679399 -83 TCTGCAATAATATTTAAACTTAAGCAAAATTTT 4 30 0 TATTTAAATA 0.859252 -66 TTTTATAAAAATTTTTAAATTCAAAGAAGGAGC 8 19 0 ATTTTTAATA 0.887159 -38 TTTAAAAATTTTTATAAAAATTTAATTTTAACA 8 33 1 TTTATAAATT 0.68228 -24 CTTTCAAGATTATTTAAATCTTTCCAATACTCA 9 14 1 TATTTAAATT 0.865249 -90 GTATTTTTTGTTTTTATATTTTATTGTTATATT 9 46 0 TTTTTATATA 0.823359 -58 TGTATATAAAATTTTTTATCTCTGACTCTATCA 10 24 0 ATTTTTTATT 0.869122 -65 GATAAAAAATTTTATATACATAACCCTATTTTA 10 37 1 TTTATATATA 0.621155 -52 TACATAACCCTATTTTAAAATATTACCAATAAC 10 53 1 TATTTTAATT 0.881634 -36 AAAAATTTCGTTTTTAAAATTGTAATCTTTATT 11 13 1 TTTTTAAATT 0.859252 -288 GGTAATAATATTTATTAATTTAAATTAATAAAG 11 39 0 TTTATTAATA 0.703812 -262 GATGAACTCATATATATACTTTTCGGTTTCGTG 11 193 1 TATATATATT 0.644611 -108 CTTATTAATATATATTTATCTTTTGCACGAAAC 11 218 0 TATATTTATT 0.678561 -83 TTTAAATAGGTTTTTATAATTATGGGAAAACTT 11 248 0 TTTTTATATT 0.830581 -53 CCCAGATTTTTATTTTAATATTT 12 1 0 TATTTTAATT 0.881977 -192 CGGAAGTGTAAATTTACAACTGATAAAATCTGG 12 170 1 AATTTACATA 0.645492 -23 ATAACCATTAAATTTTTATGTTATAACGTTGCT 13 13 1 AATTTTTATA 0.869122 -59 CGTTGCTAATAATTTTTACTTATAAAAGTGGAG 13 39 1 AATTTTTATT 0.874758 -33 CCCTCCTGATATTTTATAGCTTACTCTATAATC 14 16 1 ATTTTATATA 0.844355 -93 TATGTAAGAGATTTTAAAACTAATTATAAATAA 14 60 0 ATTTTAAATA 0.871057 -49 AAAAGGTCTAAATTTTTATGTAAGAGATTTTAA 14 76 0 AATTTTTATA 0.869122 -33 TCTTACACATAATATTAATATTTCATTTAACGT 15 16 0 AATATTAATT 0.753658 -65 TAAGAATTCAAATTTAAATTTAAACTATTGAAA 15 44 1 AATTTAAATA 0.876622 -37 TATATCACCAATTTTTCATGTCTTTCAAAACTT 16 12 1 ATTTTTCATT 0.679399 -111 GTTAGAGGGCTATTTTAATATATAACCCTTTTG 16 70 0 TATTTTAATT 0.881977 -53 ATTAATATTTATGTTTTTAATAGCTT 18 4 1 AATATTTATT 0.710722 -80 GGTTTAACAGTATATAAACATTACGTTAGCAAC 18 48 0 TATATAAATA 0.682282 -36 GGTTTTTATAAAATTTTATGAGTGAGA 19 5 1 TTTATAAATT 0.682282 -64 CTAATTTTTCAATTTTAAAGTTTTATTTTTAAG 20 65 0 AATTTTAATT 0.896877 -236 AATCTTTCGGATTTTTAAGATTATAAGTAGGTT 20 136 0 ATTTTTAATA 0.887158 -165 GCATAATAGATTTTTTAATTTAATTTCTTGCTT 20 197 0 TTTTTTAATA 0.871056 -104 ATCTATTTATATTTTATACATCACTATTTGTCA 20 255 1 ATTTTATATA 0.844355 -46 ******** * * Masking position 8 Map Score: 44.5007 Number of sites scoring better than the average of aligned sites = 4377 Number in coding regions = 2884 Number in noncoding regions = 1493 Number of orfs with sites within 600 bp upstream = 686 Fraction of orfs with sites within 600 bp upstream = 0.110183 Motif number 2 AGAAAATAGTAATATTTTTAATAAGGCACTGGT 1 111 0 AATATTAATA 0.845537 -144 AATTATATAAAAAATAGAAAAAAG 2 2 0 AAAATAAAAA 0.922944 -133 AAAATACATCAATATTCATAAAAATTATATAAA 2 24 0 AATATTAAAA 0.893368 -111 TATTTTTGATAAACTACCGAAAAATATATATTA 2 64 1 AAACTAAAAA 0.887393 -71 GATATGAACAAAAATTTTTAATATCTAATATAT 2 89 0 AAAATTAATA 0.900019 -46 TTTGAAGTATAAAATAGCAATAACCAATATGAC 3 29 0 AAAATAATAA 0.772088 -52 AATATAATTTAAAATTTAAAAAAATTTCTAA 3 60 1 AAAATTAAAA 0.932329 -21 ATTATTGCAGAATATATTCAAAAACAAACTTTA 4 52 1 AATATAAAAA 0.879279 -44 GATTACGATAAAACCAATAAAAACGTTAA 6 21 1 AAACCAAAAA 0.689065 -19 TTTGAATTTAAAAATTTTTATAAAAATTTAATT 8 27 1 AAAATTATAA 0.795781 -30 AGATTATTTAAATCTTTCCAATACTCAATATAA 9 20 1 AATCTTAATA 0.782682 -84 TCCAATACTCAATATAACAATAAAATATAAAAA 9 36 1 AATATAATAA 0.673207 -68 ATAAAATATAAAAACAAAAAATACAACTTAAAA 9 55 1 AAAACAAATA 0.687575 -49 GACTCTATCAAATATTTTTAATA 10 1 0 AATATTAATA 0.845537 -88 CCTATTTTAAAATATTACCAATAACTGCAGGTG 10 61 1 AATATTAATA 0.845537 -28 AATTATGGGAAAACTTATTAATATATATTTATC 11 231 0 AAACTTAATA 0.855546 -70 AAATATTAAAATAAAAATCTGGGT 12 2 1 AATATTATAA 0.703227 -191 ATTATAGAGTAAGCTATAAAATATCAGGAGGGA 14 15 0 AAGCTAAATA 0.696891 -94 AGAGATTTTAAAACTAATTATAAATAAATTATG 14 54 0 AAACTAATAA 0.690293 -55 CGTTAAATGAAATATTAATATTATGTGTAAGAA 15 17 1 AATATTATTA 0.607572 -64 ATTTAAATTTAAACTATTGAAAATTTCCTGTGA 15 55 1 AAACTAAAAA 0.887393 -26 AAAGTTTTGAAAGACATGAAAAATTGGTGATAT 16 13 0 AAGACAAAAA 0.600643 -110 AAAAAGCTAAAAGCTATTAAAAACATAAATATT 18 14 0 AAGCTAAAAA 0.778704 -70 TTCGAACCCTAAAACATACAAAATAAAAACAAA 20 20 1 AAAACAAAAA 0.771077 -281 TTAAAATTGAAAAATTAGTAATACTTTTTATTA 20 80 1 AAAATTAATA 0.900019 -221 TTGGTATTGGAAAATTAATAAAAAGTATTACTA 20 95 0 AAAATTAAAA 0.932329 -206 AAAAATCCGAAAGATTTCTAAAACCTGTTCGCT 20 153 1 AAGATTAAAA 0.860179 -148 TATGCATATTAAAATTCTCAATAAAGCATAATC 20 225 1 AAAATTAATA 0.900019 -76 ****** **** Masking position 10 Map Score: 35.2223 Number of sites scoring better than the average of aligned sites = 1904 Number in coding regions = 1380 Number in noncoding regions = 524 Number of orfs with sites within 600 bp upstream = 377 Fraction of orfs with sites within 600 bp upstream = 0.0605525 Motif number 3 TAAACTACCGAAAAATATATATTAGATATT 2 73 1 AAAAATATAT 0.536195 -62 ATTAGATATTAAAAATTTTTGTTCATATCA 2 93 1 AAAAATTTTT 0.491128 -42 TTTAAAATTTAAAAAAATTTCTAA 3 67 1 AAAAAAATTT 0.771743 -14 TATATTCTGCAATAATATTTAAACTTAAGC 4 38 0 AATAATATTT 0.863114 -58 CTTTGAATTTAAAAATTTTTATAAAAATTT 8 26 1 AAAAATTTTT 0.491128 -31 TCAATATAACAATAAAATATAAAAACAAAA 9 44 1 AATAAAATAT 0.638043 -60 TATTAAAAATATTTGATAGAGTCA 10 5 1 AAAAATATTT 0.731399 -84 AGTCAGAGATAAAAAATTTTATATACATAA 10 30 1 AAAAAATTTT 0.757108 -59 TATTTTAGGTAATAATATTTATTAATTTAA 11 49 0 AATAATATTT 0.863114 -252 CACGAAACCGAAAAGTATATATATGAGTTC 11 196 0 AAAAGTATAT 0.537721 -105 AATATATATTAATAAGTTTTCCCATAATTA 11 235 1 AATAAGTTTT 0.781435 -66 TTCCTATTTAAATAGGTTTTTATAATTATG 11 257 0 AATAGGTTTT 0.790266 -44 TAACGTTGCTAATAATTTTTACTTATAAAA 13 36 1 AATAATTTTT 0.846694 -36 ACTAATTATAAATAAATTATGGTTTTGATT 14 45 0 AATAAATTAT 0.752178 -64 ATTTTTATGTAAGAGATTTTAAAACTAATT 14 68 0 AAGAGATTTT 0.807386 -41 TTATGTTTTTAATAGCTTTTAGCTTTTTGG 18 19 1 AATAGCTTTT 0.6634 -65 TCCCTCACTAAAGAAATTTTACAAACATAA 19 43 0 AAGAAATTTT 0.805401 -26 TAGGGTTCGAAATAGTTTTT 20 1 0 AATAGTTTTT 0.901606 -300 TTTTATTTTTAAGAGAATTTATGAGTTTGT 20 48 0 AAGAGAATTT 0.709232 -253 AAAAATTAGTAATACTTTTTATTAATTTTC 20 89 1 AATACTTTTT 0.597355 -212 TAATATGCATAATAGATTTTTTAATTTAAT 20 206 0 AATAGATTTT 0.908187 -95 ATAAAATATAAATAGATTATGCTTTATTGA 20 242 0 AATAGATTAT 0.75293 -59 ********** Masking position 8 Map Score: 19.3208 Number of sites scoring better than the average of aligned sites = 1417 Number in coding regions = 1033 Number in noncoding regions = 384 Number of orfs with sites within 600 bp upstream = 335 Fraction of orfs with sites within 600 bp upstream = 0.0538066 Motif number 4 TAGTAAAAGGTTCATCAAAACGGATGCACT 1 36 0 TTCATCAAAA 0.976346 -219 GATTATTTTTTTCATCAAAGCTATTTTGAT 1 185 1 TTCATCAAAG 0.866858 -70 TTAAAACTTATAAATCAAAATAGCTTTGAT 1 198 0 TAAATCAAAA 0.628493 -57 TTTTTATCACCAAAAATAGGATACC 1 240 0 ATCACCAAAA 0.835698 -15 TACATCAATATTCATAAAAATTATATAAAA 2 23 0 TTCATAAAAA 0.839297 -112 TTTTCGGTAGTTTATCAAAAATAATCGTTA 2 57 0 TTTATCAAAA 0.80177 -78 ATATTTAAACTTAAGCAAAATTTTCAGTTC 4 24 0 TTAAGCAAAA 0.836318 -72 AGCTCTCCATTTCATCAAAAACTAACACCT 12 128 1 TTCATCAAAA 0.976346 -65 AGCTTACTCTATAATCAAAACCATAATTTA 14 33 1 ATAATCAAAA 0.81041 -76 CTTTTCACCAAAAAGGTCTAAAT 14 96 0 TTCACCAAAA 0.940628 -13 TAAGAATGGTTCCAGCAAAAGGGTTATATA 16 55 1 TCCAGCAAAA 0.845934 -68 TACCCCACCATCAAAATTTTAATTGT 16 107 0 ACCATCAAAA 0.821206 -16 TATTGGAAAATTAATAAAAAGTATTACTAA 20 94 0 TTAATAAAAA 0.6275 -207 ********** Masking position 4 Map Score: 12.5608 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 384 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 TATTTTCTTGTTCTTTTTTTATTTATACTA 1 136 1 TTCTTTTTTT 0.619791 -119 TCATTTAGGATTATTTTTTTCATCAAAGCT 1 177 1 TTATTTTTTT 0.689439 -78 CTTTTTTCTATTTTTTATATAATTT 2 6 1 TTCTATTTTT 0.747992 -129 TTTTTAACGATTATTTTTGATAAACTACCG 2 53 1 TTATTTTTGA 0.607449 -82 AAATTTTAAATTATATTTGAAGTATAAAAT 3 47 0 TTATATTTGA 0.738039 -34 AGAAATTTTTTTAAATTTTAAATTATATTT 3 59 0 TTAAATTTTA 0.827273 -22 TTAATTAAAGTTTGTTTTTGAATATATTCT 4 60 0 TTTGTTTTTG 0.583899 -36 TTTATAAAAATTTAATTTTAACAG 8 43 1 TTTAATTTTA 0.791192 -14 TTTTTTGTTTTTATATTTTATTGTTATATT 9 46 0 TTATATTTTA 0.903557 -58 TTAAAAATTTCGTTTTTAAAATTGTAAT 11 9 1 TTCGTTTTTA 0.756327 -292 CCTGCACCATTTTTATTTTAGGTAATAATA 11 62 0 TTTTATTTTA 0.880349 -239 TCACCCAGATTTTTATTTTAATATTT 12 7 0 TTTTATTTTA 0.880349 -186 CGAGGAGGTGTTAGTTTTTGATGAAATGGA 12 133 0 TTAGTTTTTG 0.641216 -60 CTATAACCATTAAATTTTTATGTTATAAC 13 10 1 TTAAATTTTT 0.675504 -62 TAGTTTAAATTTAAATTTGAATTCTTACAC 15 41 0 TTAAATTTGA 0.59125 -40 AATTTATGAGTTTGTTTTTATTTTGTATGT 20 33 0 TTTGTTTTTA 0.768461 -268 AATTTTAAAGTTTTATTTTTAAGAGAATTT 20 58 0 TTTTATTTTT 0.76041 -243 TTACTAATTTTTCAATTTTAAAGTTTTATT 20 71 0 TTCAATTTTA 0.779909 -230 AAGTAGGTTGTTTGATTTTGGTATTGGAAA 20 115 0 TTTGATTTTG 0.71871 -186 CATAATCTATTTATATTTTATACATCACTA 20 251 1 TTATATTTTA 0.903557 -50 ********** Masking position 6 Map Score: 14.7006 Number of sites scoring better than the average of aligned sites = 1909 Number in coding regions = 1263 Number in noncoding regions = 646 Number of orfs with sites within 600 bp upstream = 446 Fraction of orfs with sites within 600 bp upstream = 0.0716351 Motif number 6 ACGGATGCACTGCCTCGCTACGCTCGGCAG 1 17 0 TGCCTCGCTA 0.822075 -238 AGATACTAATTGCCTCTCTAATGAATTCGG 7 18 1 TGCCTCTCTA 0.937602 -86 TCTGTAATTCTCGCCCTCCATAGGAAAACC 7 59 0 TCGCCCTCCA 0.978112 -45 CTGGAAAGCATAGCTCTCCATTTCATCAAA 12 117 1 TAGCTCTCCA 0.943784 -76 GTAAATCCCTCTCCACTTTTATAAG 13 57 0 TCCCTCTCCA 0.982604 -15 TATATTAAAATAGCCCTCTAACCTAAACAA 16 81 1 TAGCCCTCTA 0.916711 -42 TACCCCACCATCAAAATTTT 16 113 0 TACCCCACCA 0.928003 -10 ATTCTCCCTCCAATCTTTTAGA 17 26 0 TCTCCCTCCA 0.918368 -12 AACCTATCCCTCACTAAAGAAATTTT 19 53 0 TCCCTCACTA 0.913231 -16 ********** Masking position 1 Map Score: 8.19814 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 111 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 TGAACCTTTTACTAAAAGGTTCATGTGAAGG 1 52 1 ACTAAAAGTT 0.936103 -203 TTCAACTTTTTCTAAAAGTTTCGTTTATAGT 12 62 0 TCTAAAAGTT 0.983439 -131 CTATGAAAACTCTAAGAGTTTTCGTTCAACT 12 86 0 TCTAAGAGTT 0.980092 -107 TAAATTTTTATGTAAGAGATTTTAAAACTAA 14 70 0 TGTAAGAGTT 0.91862 -39 TCTTAGTCATTCTAAAAGTTTTGAAAGACAT 16 29 0 TCTAAAAGTT 0.983439 -94 TTTAACTTTCTCTAAAAGATTGGAGGGAGAA 17 16 1 TCTAAAAGTT 0.983439 -22 ******** ** Masking position 5 Map Score: 6.34645 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 46 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 CTATTTCCTTCACATGAACCTTTTAGTAAA 1 59 0 CACATGAACC 0.882103 -196 CAAATCCCCTCCCCTGCACCATTTTTATTT 11 74 0 CCCCTGCACC 0.994064 -227 GGGATTTGAACCCCCGAACCCCTACGGGAC 11 96 1 CCCCCGAACC 0.994064 -205 GGCTTGGCGACCCCTGCACCGCAAGCGAAT 11 154 1 CCCCTGCACC 0.994064 -147 ATTAAAATAGCCCTCTAACCTAAACAATTA 16 84 1 CCCTCTAACC 0.889829 -39 ********** Masking position 8 Map Score: 2.62207 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 1 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 AGGCACTGCCGAGCGTAGCGAGGCAGTGCAT 1 12 1 GAGCTAGCGA 0.995197 -243 GAAGGAAATAGAGCATAGGAAAGAATTAGGA 1 78 1 GAGCTAGGAA 0.951917 -177 TTACACTTCCGAGCGAAGCGAGGAGGTGTTA 12 150 0 GAGCAAGCGA 0.98795 -43 TGCTTCTTGTGAGCATAGCGAACAGGTTTTA 20 171 0 GAGCTAGCGA 0.995197 -130 **** ****** Masking position 7 Map Score: 1.65385 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 5 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 AAAGAACAAGAAAATAGTAATATTTTTAATAAG 1 119 0 AAAAGTATAT 0.827022 -136 CATATAGCCTAAAATGGTGACAAT 2 121 1 AAAGGTACAA 0.812908 -14 TTTTTTATATAATGAGGTCATATTGGTTATTGC 3 13 1 AATGGTATAT 0.963885 -68 CTTAGACAAAAATGAGGTGATATTAT 9 88 1 AATGGTATAT 0.963885 -16 AATATTTTAAAATAGGGTTATGTATATAAAATT 10 44 0 AATGGTATGT 0.876374 -45 AAACCTATTTAAATAGGAAACATATTTCCTCCT 11 268 1 AAAGGAACAT 0.812908 -33 AAGACATGAAAAATTGGTGATATAA 16 3 0 AAAGGTATAT 0.97717 -120 TGGTTCCAGCAAAAGGGTTATATATTAAAATAG 16 61 1 AAAGGTATAT 0.977177 -62 *** *** **** Masking position 10 Map Score: 2.84033 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 18 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 Motif number 11 AAATAGGATACCCTCATCAGATATTTAAAACT 1 220 0 CCCTCTAGAT 0.878703 -35 AACCAATATGACCTCATTATATAAAAAAGA 3 9 0 ACCTCTATAT 0.924969 -72 TCTTATCCCTACTAAATTAATTAAAGTT 4 78 0 CCCTATAATT 0.884137 -18 AAACTTTACAAACTCTTTATTTGAGGTGATGA 5 24 1 AACTCTATTT 0.644262 -23 CTAATTGCCTCTCTAATGAATTCGGTATTTCA 7 23 1 CTCTATAATT 0.600091 -81 CATAGGAAAACCCTATTGAAATACCGAATTCA 7 39 0 CCCTATAAAT 0.936358 -65 AATTATAAAAACCTATTTAAATAGGAAACATA 11 260 1 ACCTATAAAT 0.90188 -41 AATATCCCTCCTGATATTTTATAGCTT 14 6 1 CCCTCTATAT 0.951961 -103 AAATCATTCTCACTCATAAAATTTTATAAAAA 19 13 0 CACTCTAAAT 0.869181 -56 AATAAAAACAAACTCATAAATTCTCTTAAAAA 20 41 1 AACTCTAATT 0.682636 -260 AAATCAAACAACCTACTTATAATCTTAAAAAT 20 127 1 ACCTATATAA 0.47257 -174 ATAAAGCATAATCTATTTATATTTTATACATC 20 245 1 ATCTATATAT 0.603552 -56 ***** * **** Masking position 9 Map Score: 3.04997 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 263 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 12 GAGGCAGTGCATCCGTTTTGATGAACCTTT 1 31 1 ATCCGTTTTG 0.818615 -224 TTTTCAGTTCATCCATATTGTAT 4 4 0 ATCCATATTG 0.874871 -92 TCTTATCCCTACTAAATTAATTAA 4 82 0 ATCCCTACTA 0.795351 -14 TCCATAGGAAAACCCTATTGAAATACCGAA 7 43 0 AACCCTATTG 0.962448 -61 TTATATACATAACCCTATTTTAAAATATTA 10 48 1 AACCCTATTT 0.874871 -41 AATATCCCTCCTGATATTTTATA 14 4 1 ATCCCTCCTG 0.918811 -105 CTTTTGCTGGAACCATTCTTAGTCATTCTA 16 46 0 AACCATTCTT 0.589445 -77 TTTAATATATAACCCTTTTGCTGGAACCAT 16 60 0 AACCCTTTTG 0.951652 -63 ********** Masking position 1 Map Score: 0.320138 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 77 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 ********** No masking Map Score: -2.655e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: -2.655e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: -2.655e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0