AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00020_mjan_reg_100.orf -o00020_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) MJ1425 25 malate dehydrogenase 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 MJ0210 86 succinyl-CoA synthetase, beta subunit #6 MJ0617 108 tartrate dehydratse, subunit beta (ttdB) #7 MJ0636 239 dihydrolipoamide dehydrogenase #8 MJ0720 194 3-isopropylmalate dehydrogenase 1 (leuB1) #9 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) #10 MJ1296 38 biotin synthetase (bioB) #11 MJ1424 202 tRNA intron endonuclease (endA) #12 MJ1596 226 3-isopropylmalate dehydrogenase 2 (leuB2) Motif number 1 GAAAATAGTAATATTTTTAATAAGGCACTGGTA 1 110 0 ATATTTTTTA 0.863785 -145 TTTTCTTGTTCTTTTTTTATTTATACTATGCCA 1 138 1 CTTTTTTTTA 0.882235 -117 TACTATGCCAATTTTTTCATTTAGGATTATTTT 1 161 1 ATTTTTTCTA 0.864865 -94 ATTTAGGATTATTTTTTTCATCAAAGCTATTTT 1 179 1 ATTTTTTTTA 0.952958 -76 AGATATTTAAAACTTATAAATCAAAATAGCTTT 1 201 0 AACTTATATA 0.624093 -54 TGAGGGTATCCTATTTTTGGTGATAAAAA 1 236 1 CTATTTTTTA 0.701432 -19 CTTTTTTCTATTTTTTATATAATTTTTATGAA 2 10 1 ATTTTTTATA 0.973246 -125 TAGATATTAAAAATTTTTGTTCATATCATATAG 2 95 1 AAATTTTTTA 0.737522 -40 TCTTTTTTATATAATGAGGTCATA 3 2 1 CTTTTTTATA 0.930809 -79 GGTTATTGCTATTTTATACTTCAAATATAATTT 3 37 1 ATTTTATATA 0.943855 -44 AAATTTTTTTAAATTTTAAATTATATTTGAAGT 3 54 0 AAATTTTATA 0.834399 -27 TTCTGCAATAATATTTAAACTTAAGCAAAATTT 4 31 0 ATATTTAATA 0.834591 -65 TTATCACCAAATTTTTTATATGATAATTTTAAA 5 24 1 ATTTTTTATA 0.973246 -63 TTTAATGCAAAATTTTAAAATTATCATATAAAA 5 37 0 AATTTTAATA 0.876791 -50 ATTAAAAAGAAATTTATCATTTAAGGTGATAGG 5 64 1 AATTTATCTA 0.566751 -23 AAAAGGTCTAAATTTTTATGTAAGAGATTTTAA 6 21 1 AATTTTTATA 0.941486 -88 TATGTAAGAGATTTTAAAACTAATTATAAATAA 6 37 1 ATTTTAAATA 0.881454 -72 TCAAAACCATAATTTATTTATAATTAGTTTTAA 6 50 0 AATTTATTTA 0.805471 -59 CCCTCCTGATATTTTATAGCTTACTCTATAATC 6 81 0 ATTTTATATA 0.943855 -28 TTAAAATTTTTTAAATAATATCTATTTT 7 6 1 ATTTTTTATA 0.973241 -234 TTTTCTTTTTATTTTCTTTTTAAGAGAAAGTTA 7 35 1 ATTTTCTTTA 0.638071 -205 TGTTGTTCTTATTTTTTATTTGATTAAAAAATT 7 156 1 ATTTTTTATA 0.973246 -84 TTGATTAAAAAATTTAATTGTAATTGTTATTAA 7 175 1 AATTTAATTA 0.646817 -65 ATTAACCATTAACTTTATATTCAATAACATTAA 7 203 1 AACTTTATTA 0.469459 -37 TAAAAGTTTTATTTTTAATTTTAAAATCATTTT 8 20 0 ATTTTTAATA 0.941486 -175 ACCAACAAAACATTTTTATGTGAAAGTATTTTT 8 135 1 CATTTTTATA 0.856119 -60 GCTATAATTAATCTTTTTGGTGATAAGT 8 177 1 ATCTTTTTTA 0.818946 -18 CACCCCCACCATTTTTTAAATAACTTAAATCTT 9 24 0 ATTTTTTATA 0.973241 -277 TAAATTTTAAAAGTTAATGTTTATTT 10 4 1 ATTTTAAATA 0.881454 -35 ATCTAAATACCTTTTTAATATAAAAACTGCGAA 11 79 1 CTTTTTAATA 0.856119 -124 AAATTTTAAGATTTTATAAATAATAACT 11 185 1 ATTTTATATA 0.943853 -18 GTTTCTATTTCTATTAAACGTTAATAAGAGGGA 12 16 0 CTATTAAATA 0.463033 -211 AGGCATTTAAATATTTATTGTCAAATATTTATT 12 121 0 ATATTTATTA 0.737522 -106 ******** * * Masking position 5 Map Score: 43.6171 Number of sites scoring better than the average of aligned sites = 1615 Number in coding regions = 1184 Number in noncoding regions = 431 Number of orfs with sites within 600 bp upstream = 338 Fraction of orfs with sites within 600 bp upstream = 0.0542885 Motif number 2 ATTATTTTTTTCATCAAAGCTATTTTGATTTATAAG 1 186 1 TTAAAATTTT 0.750391 -69 CCCTCATCAGATATTTAAAACTTATAAATCAAAATA 1 206 0 ATTAATTATA 0.570939 -49 TTTTTTATATAATTTTTATGAATATTGATGTATTTT 2 21 1 ATTTAATATT 0.704324 -114 ATATTGATGTATTTTTAACGATTATTTTTGATAAAC 2 42 1 ATTAATTATT 0.873225 -93 AATTTTTAATATCTAATATATATTTTTCGGTAGTTT 2 74 0 ATATAATTTT 0.79498 -61 AATTTTTTTAAATTTTAAATTATATTTGAAGTATAA 3 50 0 ATTAAATATT 0.905295 -31 AATTTTGCTTAAGTTTAAATATTATTGCAGAATATA 4 32 1 ATTAATTATT 0.873225 -64 TTCAAAAACAAACTTTAATTAATTTAGTAGGGATAA 4 68 1 ATTAAATTTA 0.802733 -28 GTCTAAATTTTTATGTAAGAGATTTTAAAACTAATT 6 26 1 TTTAAATTTT 0.802741 -83 ACCATAATTTATTTATAATTAGTTTTAAAATCTCTT 6 42 0 ATTAAGTTTT 0.840242 -67 AAAATTTTTTAAATAATATCTATTTTCTTTTTATTT 7 13 1 ATATAATTTT 0.794961 -227 TAAAAAATTTAATTGTAATTGTTATTAACCATTAAC 7 180 1 ATTAATTATT 0.873225 -60 ATATTCAATAACATTAAACCAATTTTTAATT 7 219 1 ATAAAATTTT 0.939619 -21 TTTATTTTTAATTTTAAAATCATTTTGGTGATTAA 8 10 0 ATAAAATTTT 0.939619 -185 TTTTGTTGAGTATTTTAATCATTTTTGATATGGTTT 8 94 1 TTTAATTTTT 0.745671 -101 AAACATTTTTATGTGAAAGTATTTTTATTAATATTG 8 142 1 ATAAATTTTT 0.918111 -53 TAAATCAGAAAGATTTAAGTTATTTAAAAAATGGTG 9 15 1 ATTAAATTTA 0.802741 -286 CAATTTATATATTTATAAGGCACTTTGATGCCTAAA 9 211 0 ATTAAACTTT 0.617728 -90 CGCAGTTTTTATATTAAAAAGGTATTTAGATGCCTA 11 74 0 ATAAAGTATT 0.638139 -129 AACATAAACCATATGTTATTTATTTTATTATCCACA 11 147 1 ATTTAATTTT 0.839973 -56 TATCCACAATAAATTTTAAGATTTTATAAATAATAA 11 175 1 ATTTATTTTA 0.42216 -28 AAGACAGTATAGTTTAAAGATATTTTTAAGTATTAA 12 64 0 ATAAAATTTT 0.939619 -163 TTTATTAATAAACTTTAATTAATTTTGAAGACAGTA 12 91 0 ATTAAATTTT 0.95463 -136 TAAATATTTATTGTCAAATATTTATTAATAAACTTT 12 111 0 TTAAATTATT 0.495716 -116 GCTACTGGTTACTTCAAAATGTTTTTGAAAGACACT 12 175 1 ATAAATTTTT 0.918111 -52 GAAAGACACTATATAAAAAAGTTTTTGGTGCTGTCT 12 201 1 ATAAATTTTT 0.918111 -26 * * *** ***** Masking position 4 Map Score: 30.7825 Number of sites scoring better than the average of aligned sites = 1322 Number in coding regions = 963 Number in noncoding regions = 359 Number of orfs with sites within 600 bp upstream = 306 Fraction of orfs with sites within 600 bp upstream = 0.0491487 Motif number 3 TCAAAATAGCTTTGATGAAAAAAATAATCCTA 1 182 0 TTTGTGAAAA 0.978369 -73 GTATCCTATTTTTGGTGATAAAAA 1 241 1 TTTGTGAAAA 0.969825 -14 TTAAATTATATTTGAAGTATAAAATAGCAATA 3 40 0 TTTGAGTTAA 0.530272 -41 ATATAAAAAATTTGGTGATAAATTTATAGGTT 5 13 0 TTTGTGAAAA 0.969825 -74 TAAATTTCTTTTTAATGCAAAATTTTAAAATT 5 48 0 TTTATGCAAA 0.809788 -39 CCTATCACCTTAAATGATAAATTTCTTTTTA 5 66 0 TTAATGAAAA 0.620002 -21 TTTAGACCTTTTTGGTGAAAAG 6 1 0 TTTGTGAAAG 0.915868 -108 TTAAAATTTTTTAAATAATATCTATTTT 7 7 1 TTTTTAATAA 0.558106 -233 TTTATTTTCTTTTTAAGAGAAAGTTATTCTCA 7 42 1 TTTTAGAAAA 0.669192 -198 TATTCTCATTTTTGCAGAAAAATAGCTTATTG 7 66 1 TTTGAGAAAA 0.909785 -174 TTATTTTTTATTTGATTAAAAAATTTAATTGT 7 164 1 TTTGTTAAAA 0.709215 -76 TTAAAATCATTTTGGTGATTAA 8 1 0 TTTGTGATAA 0.978577 -194 TGTGTTGTTTTTTGTTGAGTATTTTAATCATT 8 85 1 TTTGTGATAT 0.770058 -110 AATTAATCTTTTTGGTGATAAGT 8 182 1 TTTGTGAAAG 0.915834 -13 ACCCCCACCATTTTTTAAATAACTTAAATCTT 9 24 0 TTTTTAATAA 0.558106 -277 TATAAGGCACTTTGATGCCTAAAGGGTATCGT 9 202 0 TTTGTGCTAA 0.934192 -99 GAATAAATGATTTATTGAATAATGATGCCTTT 11 43 1 TTTATGATAA 0.920162 -160 AAAAAGGTATTTAGATGCCTAAAGGCATCATT 11 63 0 TTAGTGCTAA 0.626497 -140 ATTCATTAATTTTGTTAAATAACATAAACCAT 11 127 1 TTTGTAATAA 0.751985 -76 AATTTTAAGATTTTATAAATAATAACT 11 186 1 TTTTTAATAA 0.643283 -17 TTGTCAAATATTTATTAATAAACTTTAATTAA 12 105 0 TTTATAAAAA 0.46752 -122 CATTTAAATATTTATTGTCAAATATTTATTAA 12 119 0 TTTATGTAAA 0.575047 -108 **** *** *** Masking position 2 Map Score: 24.7021 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 952 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 4 AAGAACAAGAAAATAGTAATATTTTTAATAAG 1 119 0 AAATAGAAAT 0.858846 -136 GGCATAGTATAAATAAAAAAAGAACAAGAAAA 1 138 0 AAATAAAAAG 0.833863 -117 AAATAATCCTAAATGAAAAAATTGGCATAGTA 1 161 0 AAATGAAAAT 0.814295 -94 ATTATATAAAAAATAGAAAAAAG 2 2 0 AAATAGAAAA 0.964487 -133 ATATAGCCTAAAATGGTGACAAT 2 122 1 AAATGGGAAA 0.773936 -13 TTGAAGTATAAAATAGCAATAACCAATATGAC 3 29 0 AAATAGAAAA 0.964487 -52 CTTAAAAAGAAAATAAAAAGAAAATAGATATT 7 27 0 AAATAAAAAA 0.963837 -213 TTTTCTGCAAAAATGAGAATAACTTTCTCTTA 7 55 0 AAATGAAAAA 0.951387 -185 ATCAAATAAAAAATAAGAACAACAACAATAAC 7 148 0 AAATAAAAAA 0.963837 -92 ATGATTTTAAAATTAAAAATAAAACTTTTAAG 8 23 1 AATTAAAAAA 0.73933 -172 ACCATATCAAAAATGATTAAAATACTCAACAA 8 96 0 AAATGATAAA 0.69389 -99 TAATTTTGTTAAATAACATAAACCATATGTTA 11 133 1 AAATAAATAA 0.73933 -70 CGTTTAATAGAAATAGAAACAATAAATATACC 12 29 1 AAATAGAAAA 0.964487 -198 ****** ** ** Masking position 2 Map Score: 12.9636 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 244 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 5 AATTATATAAAAAATAGAAAAAAG 2 4 0 AAAATAAAAA 0.858482 -131 ATATTCATAAAAATTATATAAAAAATAGAAA 2 15 0 AAATTAATAA 0.482749 -120 AAAATACATCAATATTCATAAAAATTATATA 2 26 0 AATATTATAA 0.639749 -109 AAACTACCGAAAAATATATATTAGATATTAA 2 74 1 AAAATAATAT 0.91886 -61 AATATAATTTAAAATTTAAAAAAATTTCTAA 3 60 1 AAAATTAAAA 0.803733 -21 AAATAAAAAGAAAATAGATATTATTTAAAAA 7 18 0 AAAATAATAT 0.91886 -222 AACAACAATAACAATTGAAATAAAACCATGC 7 129 0 ACAATTAAAT 0.748177 -111 AAATGATTTTAAAATTAAAAATAAAACTTTT 8 21 1 AAAATTAAAA 0.803733 -174 AAAACAACACAAAATATAAATACTTATAATG 8 65 0 AAAATAAAAT 0.833154 -130 TAATTATAGCAATATTAATAAAAATACTTTC 8 156 0 AATATTATAA 0.639749 -39 AAAATAAATCAGAAAGATTTA 9 1 1 AAAATAATCA 0.606776 -300 TAGAACTTTCACAATTTATATATTTATAAGG 9 227 0 ACAATTATAT 0.870765 -74 ATTAAACCGTAAAATTTATATATCCCCTTTT 9 278 0 AAAATTATAT 0.884322 -23 CCTATATACAATAAATAAACATTAACTT 10 21 0 ACAATAATAA 0.923811 -18 TGTGGATAATAAAATAAATAACATATGGTTT 11 152 0 AAAATAATAA 0.932236 -51 TTTATTATCCACAATAAATTTTAAGATTTTA 11 170 1 ACAATAATTT 0.571096 -33 AGAAATAGAAACAATAAATATACCGTATTAA 12 37 1 ACAATAATAT 0.908931 -190 TACTGTCTTCAAAATTAATTAAAGTTTATTA 12 91 1 AAAATTATTA 0.553426 -136 TAAATATTTGACAATAAATATTTAAATGCCT 12 123 1 ACAATAATAT 0.908931 -104 TTTGAAAGACACTATATAAAAAAGTTTTTGG 12 198 1 ACTATAAAAA 0.505532 -29 ****** **** Masking position 5 Map Score: 21.0543 Number of sites scoring better than the average of aligned sites = 1032 Number in coding regions = 645 Number in noncoding regions = 387 Number of orfs with sites within 600 bp upstream = 328 Fraction of orfs with sites within 600 bp upstream = 0.0526823 Motif number 6 CTGGTAATCCTAATTCTTTCCTATGCTCTA 1 86 0 TAATTCTTTC 0.325041 -169 ATCAGATATTTAAAACTTATAAATCAAAAT 1 207 0 TAAAACTTAT 0.829094 -48 TCAATATTCATAAAAATTATATAAAAAATA 2 19 0 TAAAAATTAT 0.619277 -116 TATTAGATATTAAAAATTTTTGTTCATATC 2 92 1 TAAAAATTTT 0.878913 -43 TTAAAATTTAAAAAAATTTCTAA 3 68 1 AAAAAATTTC 0.830684 -13 AATTATCATATAAAAAATTTGGTGATAAAT 5 22 0 TAAAAAATTT 0.555338 -65 CATAAAAATTTAGACCTTTTTGGTGAAAAG 6 11 0 TAGACCTTTT 0.384517 -98 GATATTATTTAAAAAATTTTAA 7 3 0 AAAAAATTTT 0.830174 -237 CAAAAATGAGAATAACTTTCTCTTAAAAAG 7 50 0 AATAACTTTC 0.737521 -190 AAAACTTATCTAAAACTTTCGATACCATTG 7 98 0 TAAAACTTTC 0.949923 -142 AAAACCATGCAAAAACTTATCTAAAACTTT 7 109 0 AAAAACTTAT 0.789783 -131 TTTATTTGATTAAAAAATTTAATTGTAATT 7 170 1 TAAAAAATTT 0.555338 -70 AAATTAAAAATAAAACTTTTAAGGGAAGTA 8 32 1 TAAAACTTTT 0.955952 -163 CACAAAATATAAATACTTATAATGCATTAC 8 59 0 AAATACTTAT 0.456144 -136 ATATTAATAAAAATACTTTCACATAAAAAT 8 146 0 AAATACTTTC 0.766331 -49 TTAAATAACTTAAATCTTTCTGATTTATTT 9 12 0 TAAATCTTTC 0.683268 -289 TGTGTCGTTGTAGAACTTTCACAATTTATA 9 238 0 TAGAACTTTC 0.850833 -63 AAAGGGGATATATAAATTTTACGGTTTAAT 9 279 1 TATAAATTTT 0.582205 -22 CTCAATATTATAGAACTTTCGCAGGAATAA 11 19 1 TAGAACTTTC 0.850833 -184 TTAGGCATCTAAATACCTTTTTAATATAAA 11 73 1 AAATACCTTT 0.274221 -130 TATTATCCACAATAAATTTTAAGATTTTAT 11 172 1 AATAAATTTT 0.518937 -31 AGTGTCTTTCAAAAACATTTTGAAGTAACC 12 181 0 AAAAACATTT 0.742127 -46 AGACAGCACCAAAAACTTTTTTATATAGTG 12 207 0 AAAAACTTTT 0.940919 -20 ********** Masking position 8 Map Score: 16.3999 Number of sites scoring better than the average of aligned sites = 2056 Number in coding regions = 1590 Number in noncoding regions = 466 Number of orfs with sites within 600 bp upstream = 405 Fraction of orfs with sites within 600 bp upstream = 0.0650498 Motif number 7 TAGGATTATTTTTTTCATCAAAGCTATTTT 1 182 1 TTTTTCATCA 0.76894 -73 TTTTTATCACCAAAAATAGGAT 1 243 0 TTTATCACCA 0.977877 -12 ATTGTCACCATTTTAGGCTA 2 125 0 ATTGTCACCA 0.883826 -10 AACCTATAAATTTATCACCAAATTTTTTAT 5 13 1 TTTATCACCA 0.977877 -74 CTTTTCACCAAAAAGGTCTA 6 1 1 CTTTTCACCA 0.95055 -108 ATTGTAATTGTTATTAACCATTAACTTTAT 7 191 1 TTATTAACCA 0.635785 -49 TTAATCACCAAAATGATTTT 8 1 1 TTAATCACCA 0.958655 -194 TGATATGGTTTAAGTCACCAACAAAACATT 8 119 1 TAAGTCACCA 0.751878 -76 ACTTATCACCAAAAAGATTAA 8 184 0 CTTATCACCA 0.961583 -11 ********** Masking position 5 Map Score: 8.1953 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 68 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 GGACTCCAGTTGCCTATAGGGCGCTGGACC 9 96 0 TGCCTATAGG 0.991157 -205 GGCACTTTGATGCCTAAAGGGTATCGTCAT 9 199 0 TGCCTAAAGG 0.991157 -102 GTTTATTTATTGTATATAGG 10 29 1 TGTATATAGG 0.876509 -10 GGTATTTAGATGCCTAAAGGCATCATTATT 11 60 0 TGCCTAAAGG 0.991157 -143 ********** Masking position 5 Map Score: 2.62639 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 2 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 TAGTAAAAGGTTCATCAAAACGGATGCACT 1 36 0 TTCATCAAAA 0.949173 -219 TACCAGTGCCTTATTAAAAATATTACTATT 1 110 1 TTATTAAAAA 0.397333 -145 GATTATTTTTTTCATCAAAGCTATTTTGAT 1 185 1 TTCATCAAAG 0.579695 -70 TTAAAACTTATAAATCAAAATAGCTTTGAT 1 198 0 TAAATCAAAA 0.765769 -57 TTTTTATCACCAAAAATAGGATACC 1 240 0 ATCACCAAAA 0.662075 -15 TACATCAATATTCATAAAAATTATATAAAA 2 23 0 TTCATAAAAA 0.620438 -112 TCGTTAAAAATACATCAATATTCATAAAAA 2 33 0 TACATCAATA 0.599208 -102 TTTTCGGTAGTTTATCAAAAATAATCGTTA 2 57 0 TTTATCAAAA 0.666967 -78 AAATTTTCAGTTCATCCATATTGTAT 4 7 0 TTCATCCATA 0.273154 -89 ATATTTAAACTTAAGCAAAATTTTCAGTTC 4 24 0 TTAAGCAAAA 0.835166 -72 TTTGAATATATTCTGCAATAATATTTAAAC 4 44 0 TTCTGCAATA 0.595564 -52 ATTGCAGAATATATTCAAAAACAAACTTTA 4 55 1 ATATTCAAAA 0.69099 -41 AATTTCTTTTTAATGCAAAATTTTAAAATT 5 48 0 TAATGCAAAA 0.482779 -39 CTTTTCACCAAAAAGGTCTAAAT 6 4 1 TTCACCAAAA 0.868706 -105 AGCTTACTCTATAATCAAAACCATAATTTA 6 67 0 ATAATCAAAA 0.773895 -42 AAAATAGATATTATTTAAAAAATTTTAA 7 9 0 TTATTTAAAA 0.315578 -231 TAAGCTATTTTTCTGCAAAAATGAGAATAA 7 65 0 TTCTGCAAAA 0.811034 -175 ATTAAATTTTTTAATCAAATAAAAAATAAG 7 163 0 TTAATCAAAT 0.365297 -77 CATTAACTTTATATTCAATAACATTAAACC 7 209 1 ATATTCAATA 0.387444 -31 TTAATCACCAAAATGATTTTAAA 8 4 1 ATCACCAAAA 0.662075 -191 TATAGCAATATTAATAAAAATACTTTCACA 8 153 0 TTAATAAAAA 0.502782 -42 AAAGATTAATTATAGCAATATTAATAAAAA 8 163 0 TATAGCAATA 0.0657133 -32 ACTTATCACCAAAAAGATTAATTA 8 181 0 ATCACCAAAA 0.662075 -14 AAAATAAATCAGAAAGATTTAAGT 9 5 1 TAAATCAGAA 0.188591 -296 AAGATTTAAGTTATTTAAAAAATGGTGGGG 9 24 1 TTATTTAAAA 0.315578 -277 AAAGGCATCATTATTCAATAAATCATTTAT 11 45 0 TTATTCAATA 0.681023 -158 AAACTATACTGTCTTCAAAATTAATTAAAG 12 85 1 GTCTTCAAAA 0.526628 -142 AGCTACTGGTTACTTCAAAATGTTTTTGAA 12 174 1 TACTTCAAAA 0.77469 -53 ********** Masking position 7 Map Score: 14.8035 Number of sites scoring better than the average of aligned sites = 2056 Number in coding regions = 1777 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 10 GAGGCACTGCCGAGCGTAGC 1 1 1 GAGGCACTGC 0.974686 -254 CGAGCGTAGCGAGGCAGTGCATCCGTTTTG 1 21 1 GAGGCAGTGC 0.881053 -234 TATTTTTAATAAGGCACTGGTAATCCTAAT 1 102 0 AAGGCACTGG 0.986948 -153 AAAAATGGTGGGGGTGCTGGGATTTGAACC 9 41 1 GGGGTGCTGG 0.961642 -260 AGTTGCCTATAGGGCGCTGGACCACGGCAG 9 89 0 AGGGCGCTGG 0.983986 -212 AGCGCCCTATAGGCAACTGGAGTCCCCGAT 9 101 1 AGGCAACTGG 0.88072 -200 AGGTGTTCATAAGCTACTGGTTACTTCAAA 12 163 1 AAGCTACTGG 0.915123 -64 ********** Masking position 8 Map Score: 2.03416 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 53 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 TCTTATCCCTACTAAATTAATT 4 84 0 TTATCCCTAC 0.956376 -12 AATATCCCTCCTGATATTTTA 6 98 0 ATATCCCTCC 0.94785 -11 AATAGTAGATTTATTCCTGTGAAGATTCTA 9 166 0 TTATTCCTGT 0.921748 -135 AATAAATCATTTATTCCTGCGAAAGTTCTA 11 29 0 TTATTCCTGC 0.96369 -174 TTTTATCCCTCTTATTAACGTT 12 3 1 TTATCCCTCT 0.96369 -224 ********** Masking position 4 Map Score: 0.292199 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 94 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 ********** No masking Map Score: 1.77879e-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 13 ********** No masking Map Score: 1.77879e-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: 1.77879e-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