AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -irpoN_mjan_opreg_100.orf -g0.314 -x5 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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0443 43 conserved hypothetical protein #2 MJ0444 265 conserved hypothetical protein #3 MJ0516 113 carbon monoxide dehydrogenase, hydrogenase subunit CooL (cooL) #4 MJ0520 192 NADH-ubiquinone oxidoreductase, subunit 1 #5 MJ0676 108 hydrogenase expression/formation protein (hypE) #6 MJ0792 300 M. jannaschii predicted coding region MJ0792 #7 MJ0792.1 68 M. jannaschii predicted coding region MJ0792.1 #8 MJ0793 60 M. jannaschii predicted coding region MJ0793 #9 MJ0794 48 M. jannaschii predicted coding region MJ0794 #10 MJ0795 79 M. jannaschii predicted coding region MJ0795 #11 MJ0995 57 VAR1 protein isolog #12 MJ1027 125 formate hydrogenlyase, subunit 5 #13 MJ1089 40 cobalt transport protein (cbiQ) #14 MJ1091 281 cobalamin biosynthesis protein (cbiM) #15 MJ1309 37 carbon monoxide dehydrogenase, hydrogenase anchor subunit CooM (cooM) #16 MJ1310 83 conserved hypothetical protein #17 MJ1345 300 O-linked GlnNAc transferase #18 MJ1346 87 glutamine synthetase (glnA) #19 MJ1363 300 formate hydrogenlyase, subunit 7 Motif number 1 TAAAAACCATATAAAATAAAAATTAGAAATAA 1 21 0 ATAAATAAAA 0.916567 -23 TTCCTCCCAATAAATTTTAAGAGGCATTGCTT 3 87 0 TAAATTTAAA 0.805593 -27 AAATATTAAAATAAAAATCTGGGTGAG 4 6 1 TTAAATAAAA 0.754326 -187 TCCAGCTATGAAAACTCTAAGAGTTTTCGTTC 4 90 0 AAAATCTAAA 0.736246 -103 ATTTTAAAACAAAATTAAAAAAATGAAGTAAA 5 19 0 AAAATAAAAA 0.825904 -90 ATCTTTCAATAAAATTTTAAAACAAAATTAAA 5 32 0 AAAATTTAAA 0.936813 -77 AAAGATTGTAAAAAATATATCAAAATATTTAA 5 58 1 AAAATATATA 0.471788 -51 ACTTTTATTGAATACTTAAATATTTTGATATA 5 73 0 AATATTAAAA 0.633726 -36 AGTATTCAATAAAAGTTAAAGAGTGAGATT 5 89 1 AAAATTAAAA 0.970095 -20 AAAATGAAATATAACATAATCAATA 6 4 0 ATAAATAATA 0.819022 -297 ATTTTTTGATATAAAATTATAAAATAGTTAAA 6 31 1 ATAAATTATA 0.674093 -270 AAAATTATAAAATAGTTAAAAATAATTTACTT 6 43 1 AATATTAAAA 0.633726 -258 TAAAACAATTATAACTTTAAAAAAGTAAATTA 6 65 0 ATAATTTAAA 0.908594 -236 AAAAATTCTAATAAGTTAAAAATTTTAACATA 6 102 1 ATAATTAAAA 0.956042 -199 TATTATGATTTAAAGTTAAATAGTAAATTATA 6 134 0 TAAATTAAAA 0.900662 -167 GCACCATACAAAAAATTAAAGAATAGTTGGCG 6 219 1 AAAATTAAAA 0.970095 -82 AAAAAATTATTAAAATTAAAAAAGAAAAACAT 7 13 0 TAAATTAAAA 0.900662 -56 AATAATGATGATAAAATAAATAATAACTTTAA 8 26 1 ATAAATAAAA 0.916567 -35 AAAATAAATAATAACTTTAACAATTGTGAAAC 8 38 1 ATAATTTAAA 0.908594 -23 ACAATCATTGAAAAATCTAATAG 9 36 1 AAAATCTAAA 0.736246 -13 TCATTTTATAGTAACTTTAATACACTGTATAG 10 49 0 GTAATTTAAA 0.60833 -31 CTCGATAACTTTATTAAAACAAAACT 12 5 1 ATAATTTATA 0.803723 -121 TTATTAAAACAAAACTATATAAAAGGTTAAGC 12 21 1 AAAATATATA 0.471788 -105 TAAAAAAGTAAAAAATTAAAGAA 13 2 0 AAAATTAAAA 0.970095 -39 TTTAAATTTTAAAATTTAAAAAAGTAAAAAAT 13 18 0 AAAATTAAAA 0.970095 -23 TAAGTATTACTAAAAATAAAGATATATAAAAA 14 20 0 TAAAATAAAA 0.820779 -262 ACTAAAAAAGAAAAATTAATCATTATTAAAAA 14 90 1 AAAATTAATA 0.930378 -192 AAAAATGTCTTTAATTTAAATAAGTAATAAAA 14 117 1 TTAATTAAAA 0.858731 -165 AAATATGAAAAAAACAAAATAACTCATTAATA 14 148 1 AAAAAAAATA 0.49676 -134 TTAAATTTATATAAGATAAAGAGTACTATAAA 14 221 1 ATAAATAAAA 0.916567 -61 ACCCCTGAATATAATTCAAAAAAACTTAACAC 14 254 0 ATAATCAAAA 0.803722 -28 ATCTTTTAGAGAAAGTTAAATAGAA 15 4 0 GAAATTAAAA 0.83522 -34 AAAGCTATTAAAAACATAAATATTAAT 16 6 0 AAAAATAAAA 0.942481 -78 TATAAATATAAAAATTTAATTATAAAAGTCCA 17 54 0 AAAATTAATA 0.930378 -247 ATTATACGCTATAATATAATTATAAATATAAA 17 74 0 ATAAATAATA 0.819021 -227 GTATAATGTCATAAAACAATTAATACCCCAAT 17 99 1 ATAAACAATA 0.460058 -202 TTAGTTTATTTAAAGTTAATAAGATTGGGGTA 17 122 0 TAAATTAATA 0.788806 -179 TTACACTAAAATAATTTTAATAAATAATATCA 17 216 1 ATAATTTAAA 0.908594 -85 AATTTAAATTAAAATATAAAAAT 18 2 0 AAAAATAAAA 0.942481 -86 TAAAACATACAAAATAAAAACAAACTCATAAA 19 29 1 AAAAAAAAAA 0.705556 -272 TCTTAAAAATAAAACTTTAAAATTGAAAAATT 19 64 1 AAAATTTAAA 0.936813 -237 TTTGGTATTGGAAAATTAATAAAAAGTATTAC 19 97 0 GAAATTAATA 0.676169 -204 TTTCGGATTTTTAAGATTATAAGTAGGTTGTT 19 133 0 TTAAATTATA 0.366325 -168 AAGCAAGAAATTAAATTAAAAAATCTATTATG 19 197 1 TTAATTAAAA 0.858732 -104 AGTGATGTATAAAATATAAATAGATTATGCTT 19 248 0 AAAAATAAAA 0.942481 -53 **** ***** * Masking position 4 Map Score: 63.2366 Number of sites scoring better than the average of aligned sites = 3005 Number in coding regions = 2113 Number in noncoding regions = 892 Number of orfs with sites within 600 bp upstream = 542 Fraction of orfs with sites within 600 bp upstream = 0.0870543 Motif number 2 AGAATTCTTATTTCTAATTTTTATTTTATATGG 1 14 1 TTTCATTTTA 0.764089 -30 TCACCCAGATTTTTATTTTAATATTT 4 4 0 TTTTTTTAAA 0.698702 -189 TGAATTTTACTTCATTTTTTTAATTTTGTTTTA 5 14 1 TTCATTTTTA 0.676849 -95 ATTTTTTTAATTTTGTTTTAAAATTTTATTGAA 5 27 1 TTTTTTTAAA 0.698702 -82 TATTGAATACTTAAATATTTTGATATATTTTTT 5 67 0 TTAAATTTTA 0.821389 -42 TTATGTTATATTTCATTTTTTGATATAAAATTA 6 17 1 TTTCTTTTTA 0.793161 -284 TTTAACTATTTTATAATTTTATATCAAAAAATG 6 30 0 TTATTTTTAA 0.532481 -271 TTAAAAATAATTTACTTTTTTAAAGTTATAATT 6 58 1 TTTATTTTTA 0.928746 -243 TTATAATTGTTTTATTATTAAAAATTCTAATAA 6 83 1 TTTAATTAAA 0.845879 -218 TTCTAATAAGTTAAAAATTTTAACATATATAAT 6 107 1 TTAAATTTTA 0.47937 -194 TATATAGAGGTTTTGTATTATTACATTTGTGAA 6 166 1 TTTTATTATA 0.744786 -135 GTTTTTCTTTTTTAATTTTAATAATTTTTTGAT 7 15 1 TTTATTTAAA 0.866634 -54 TAATAATTTTTTGATATTTTTTAGGTGATATAA 7 33 1 TTGATTTTTA 0.676849 -36 AATAATAACTTTAACAATTGTGAAACC 8 44 1 TTAAATTGTA 0.460268 -17 ATAAAATATTTTAACTATTATTATAAG 11 41 1 TTAAATTATA 0.773551 -17 TTTTATATAGTTTTGTTTTAATAAAGTTATCGA 12 12 0 TTTTTTTAAA 0.698806 -114 GATAATTAGCTTAACCTTTTATATAGTTTTGTT 12 28 0 TTAATTTTAA 0.785621 -98 CTAATTATCATTATTAATTATGATAAATTATCT 12 52 1 TTATATTATA 0.549043 -74 CTTTAAATTTTAAAATTTAAAAAAGTAAAAA 13 20 0 TTTAATTTAA 0.489327 -21 TAATGATTAATTTTTCTTTTTTAGTAATAAACT 14 82 0 TTTTTTTTTA 0.823392 -200 AAAAGAAAAATTAATCATTATTAAAAATGTCTT 14 95 1 TTAAATTATA 0.773551 -187 ATATTTTTTATTACTTATTTAAATTAAAGACAT 14 121 0 TTACATTTAA 0.475752 -161 TTTTGTTTTTTTCATATTTTTTATTACTTATTT 14 134 0 TTCATTTTTA 0.676849 -148 TAAAATAAACTTTAATTTTGTTACTATTAATGA 14 171 0 TTTATTTGTA 0.707551 -111 TTAACGGTATTTTATTATTAATAAAATAAACTT 14 192 0 TTTAATTAAA 0.846081 -90 ATTAATATTTATGTTTTTAATAGCTTTTAG 16 8 1 TTTATTTTTA 0.928746 -76 TAATTAAATTTTTATATTTATAATTATATTATA 17 64 1 TTTATTTATA 0.897863 -237 GATAGAAAAATTTATATTTTACACTAAAATAAT 17 198 1 TTTATTTTAA 0.89726 -103 ATTTTTATATTTTAATTTAAATTGA 18 3 1 TTTTATTTTA 0.779442 -85 ATTTTAAAGTTTTATTTTTAAGAGAATTTATGA 19 54 0 TTTATTTAAA 0.866809 -247 ATTACTAATTTTTCAATTTTAAAGTTTTATTTT 19 69 0 TTTCTTTTAA 0.489216 -232 CTTTCGGATTTTTAAGATTATAAGTAGGTTGTT 19 133 0 TTTAATTATA 0.88116 -168 TTATGCTTTATTGAGAATTTTAATATGCATAAT 19 223 0 TTGAATTTTA 0.638434 -78 GCATAATCTATTTATATTTTATACATCACTATT 19 250 1 TTTATTTTAA 0.89726 -51 CAGTAATTTATCATTATCATTAATGACAA 19 282 0 TTTAATTATA 0.891138 -19 **** ***** * Masking position 8 Map Score: 39.365 Number of sites scoring better than the average of aligned sites = 2026 Number in coding regions = 1346 Number in noncoding regions = 680 Number of orfs with sites within 600 bp upstream = 448 Fraction of orfs with sites within 600 bp upstream = 0.0719563 Motif number 3 ACCATATAAAATAAAAATTAGAAATAAGAA 1 18 0 ATAAAAATTA 0.662078 -26 ATGAAAACTCTTAAAGAGTTTTCATAGCCC 2 28 1 TTAAAGAGTT 0.558425 -238 TATTGAATACTTAAATATTTTGATATATTT 5 70 0 TTAAATATTT 0.432928 -39 TATTAGAATTTTTAATAATAAAACAATTAT 6 85 0 TTTAATAATA 0.447972 -216 TGATTTAAAGTTAAATAGTAAATTATATAT 6 131 0 TTAAATAGTA 0.928513 -170 ATACAAAAAATTAAAGAATAGTTGGCGATG 6 224 1 TTAAAGAATA 0.637074 -77 TGATGATAAAATAAATAATAACTTTAACAA 8 31 1 ATAAATAATA 0.8779 -30 GATTTAAATAGTTGAAGTAACAA 9 4 1 TTAAATAGTT 0.763817 -45 AAAATATTTTATAAAAAGTATTTTAATGTC 11 23 0 ATAAAAAGTA 0.892468 -35 ATAAAGATATATAAAAAGTAGTTATT 14 7 0 ATAAAAAGTA 0.892468 -275 AATAAACTATTTAAATAGTAAGGCAACTTA 14 60 0 TTAAATAGTA 0.928513 -222 TAAATAAGTAATAAAAAATATGAAAAAAAC 14 133 1 ATAAAAAATA 0.741497 -149 AAAATAACTCATTAATAGTAACAAAATTAA 14 163 1 ATTAATAGTA 0.78995 -119 AGTTTATTTTATTAATAATAAAATACCGTT 14 193 1 ATTAATAATA 0.565175 -89 TTTATATAAGATAAAGAGTACTATAAATGT 14 226 1 ATAAAGAGTA 0.890531 -56 TTAGAGAAAGTTAAATAGAA 15 1 0 TTAAATAGAA 0.701314 -37 TATTAAAAACATAAATATTAAT 16 3 0 ATAAATATTA 0.830826 -81 TAATATAATTATAAATATAAAAATTTAATT 17 65 0 ATAAATATAA 0.47027 -236 AATAATTTTAATAAATAATATCATAGTAAT 17 225 1 ATAAATAATA 0.8779 -76 TGGAAAATTAATAAAAAGTATTACTAATTT 19 91 0 ATAAAAAGTA 0.892468 -210 TGTATAAAATATAAATAGATTATGCTTTAT 19 245 0 ATAAATAGAT 0.483575 -56 ********** Masking position 2 Map Score: 19.4989 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 287 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 4 CATATAAAATAAAAATTAGAAATAAGAATT 1 16 0 AAAAATTAGA 0.788052 -28 CCATGATGAAAGAATTATTCAGAAACCAT 3 10 1 AAGAATTATT 0.616075 -104 GAAAGATTGTAAAAAATATATCAAAATATT 5 57 1 AAAAAATATA 0.622672 -52 TATAACTTTAAAAAAGTAAATTATTTTTAA 6 58 0 AAAAAGTAAA 0.830221 -243 TTAATAATAAAACAATTATAACTTTAAAAA 6 74 0 AACAATTATA 0.820569 -227 GCACCATACAAAAAATTAAAGAATAGTTGG 6 219 1 AAAAATTAAA 0.818437 -82 AAAAATATCAAAAAATTATTAAAATTAAAA 7 24 0 AAAAATTATT 0.907466 -45 AATATTTTATAAAAAGTATTTTAATGTCTT 11 21 0 AAAAAGTATT 0.917714 -37 CCAACAATTATAAACATGATAA 12 114 0 AACAATTATA 0.820569 -12 TTAAAATTTAAAAAAGTAAAAAATTAAAGA 13 12 0 AAAAAGTAAA 0.830221 -29 AAAGATATATAAAAAGTAGTTATT 14 5 0 AAAAAGTAGT 0.861888 -277 ACTAAAAAAGAAAAATTAATCATTATTAAA 14 90 1 AAAAATTAAT 0.874533 -192 ATGCAAAATAAACAAATATTGGGATAAACA 17 15 1 AACAAATATT 0.637151 -286 TATTGGGATAAACAAGTAATTTATGGACTT 17 31 1 AACAAGTAAT 0.838823 -270 AATGTCATAAAACAATTAATACCCCAATCT 17 103 1 AACAATTAAT 0.827453 -198 AAAAACTATTTCGAACCCTA 19 1 1 AAAAACTATT 0.682086 -300 TTTAAAATTGAAAAATTAGTAATACTTTTT 19 79 1 AAAAATTAGT 0.851849 -222 GAAAATTAATAAAAAGTATTACTAATTTTT 19 89 0 AAAAAGTATT 0.917714 -212 ********** Masking position 7 Map Score: 18.6257 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 374 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 5 ATAGCCCGAAGCTACGCTTCGGTTTCATCA 2 51 1 GCTACGCTTC 0.974484 -215 ACACCTCCTTGCTACGCTCGGAGGTGTAAA 2 87 1 GCTACGCTCG 0.975137 -179 TCCATAGGGGGCTTCGCCCCCTATTGGCAC 2 229 0 GCTTCGCCCC 0.97835 -37 AAACCATAGGGCTTCGCCCTATTGGGATAC 3 33 1 GCTTCGCCCT 0.938536 -81 TACCCAGGATGCATTGCTTCTGCAAAGAAG 3 60 1 GCATTGCTTC 0.883291 -54 ATTTTAAGAGGCATTGCTTCTTTGCAGAAG 3 76 0 GCATTGCTTC 0.883291 -38 GAAATGGAGAGCTATGCTTTCCAGCTATGA 4 111 0 GCTATGCTTT 0.867877 -82 ACACCTCCTCGCTTCGCTCGGAAGTGTAAA 4 152 1 GCTTCGCTCG 0.979725 -41 AAACCTGTTCGCTATGCTCACAAGAAGCAA 19 173 1 GCTATGCTCA 0.87979 -128 ********** Masking position 7 Map Score: 7.5443 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 38 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 ACTCTTAAAGAGTTTTCATAGCCCGAAGCTA 2 34 1 ATTTTCATAG 0.888363 -232 AATTTGGGGGTATATCCACAGAACTTTCACA 2 120 1 TTATCCACAG 0.849949 -146 ATATCCACAGAACTTTCACAGCTTTATAATA 2 131 1 ACTTTCACAG 0.847331 -135 ATTGGCACAGAACTTTCACAGGAAAGTATCC 2 206 0 ACTTTCACAG 0.847331 -60 AATAACCTTTTCTTTCCATAGGGGGCTTCGC 2 242 0 TTTTCCATAG 0.92738 -24 CTATCAGTGAAGTATCCATATCCTCACCCAG 4 29 0 ATATCCATAT 0.718688 -164 AAACTCTTAGAGTTTTCATAGCTGGAAAGCA 4 96 1 ATTTTCATAG 0.888363 -97 TGCCCCTATTATTTTCCACATTTTTCACAAA 6 191 0 ATTTCCACAT 0.916626 -110 GTTATTTTGTTTTTTTCATATTTTTTATTAC 14 140 0 TTTTTCATAT 0.786997 -142 ATTTCCATATTATTTCCACATTAGTTTATTT 17 143 0 TTTTCCACAT 0.904673 -158 TATTTTCTTTTATTTCCATATTATTTCCACA 17 154 0 TTTTCCATAT 0.872919 -147 GAAAATATCCAGTATTCACAGATAGAAAAAT 17 178 1 ATATTCACAG 0.779233 -123 GTAAGTTTCCTACTTCCATATATATATAATT 18 46 0 TCTTCCATAT 0.776168 -42 * ********* Masking position 8 Map Score: 11.2623 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 188 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 TATTTCTAATTTTTATTTTATATGGTTTTTAT 1 22 1 TTTATTATAT 0.477568 -22 GCTCGGAGGTGTAAATTAAATTTGGGGGTATAT 2 102 1 GAAATAATTT 0.660794 -164 CCTATGGAAAGAAAAGGTTATTTAG 2 251 1 GAAAGTATTT 0.651961 -15 TTGAAAGATTGTAAAAAATATATCAAAATATTT 5 55 1 GAAAATATAT 0.523732 -54 TATTGATTATGTTATATTTCATTTTTT 6 5 1 GTTAGTATAT 0.36102 -296 TTAACTATTTTATAATTTTATATCAAAAAATGA 6 29 0 TTAATTATAT 0.547243 -272 CTTTAAAAAAGTAAATTATTTTTAACTATTTTA 6 50 0 GAAATTTTTT 0.382385 -251 AAGTTAAATAGTAAATTATATATGTTAAAATTT 6 121 0 GAAATTATAT 0.938921 -180 TAACTTTAAATCATAATATATATAGAGGTTTTG 6 148 1 TATATTATAT 0.785927 -153 ATTGTTAAAGTTATTATTTATTTTATCATCATT 8 29 0 TATTTTATTT 0.292962 -32 TTATTTTTAGTAATACTTAATATTACCTAAGTT 14 33 1 TATATAATAT 0.426951 -249 AGTAACAAAATTAAAGTTTATTTTATTAATAAT 14 179 1 TAAATTATTT 0.751903 -103 ATAAAATACCGTTAAATTTATATAAGATAAAGA 14 210 1 GTAATTATAT 0.792881 -72 GGTTGCTAACGTAATGTTTATATACTGTTAAAC 16 47 1 GAATTTATAT 0.735405 -37 CTTTTATAATTAAATTTTTATATTTATAATTAT 17 58 1 TAATTTATAT 0.467392 -243 TTCTATCTGTGAATACTGGATATTTTCTTTTAT 17 172 0 GATATGATAT 0.718103 -129 TTCACAGATAGAAAAATTTATATTTTACACTAA 17 192 1 GAAATTATAT 0.938924 -109 ATAATTTACGGTATATTCAATTTAAATTAAAAT 18 19 0 GATATAATTT 0.595668 -69 TGAATATACCGTAAATTATATATATATGGAAGT 18 33 1 GAAATTATAT 0.938921 -55 ATTTTAATATGCATAATAGATTTTTTAATTTAA 19 207 0 GATATGATTT 0.613967 -94 TCTCAATAAAGCATAATCTATTTATATTTTATA 19 240 1 GATATTATTT 0.878928 -61 * *** * ***** Masking position 11 Map Score: 8.02075 Number of sites scoring better than the average of aligned sites = 816 Number in coding regions = 591 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 8 AGCGTAGCAAGGAGGTGTTAGCTTTGATGA 2 75 0 GGAGGTGTTA 0.991871 -191 TGCTACGCTCGGAGGTGTAAATTAAATTTG 2 96 1 GGAGGTGTAA 0.991871 -170 AGCGAAGCGAGGAGGTGTTAGTTTTTGATG 4 140 0 GGAGGTGTTA 0.991871 -53 CGCTTCGCTCGGAAGTGTAAATTTACAACT 4 161 1 GGAAGTGTAA 0.968465 -32 ********** Masking position 6 Map Score: 4.37242 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 1 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 TACCCCCAAATTTAATTTACACCTCCGAGC 2 102 0 TTTAATTTAC 0.823127 -164 CTAAATAACCTTTTCTTTCCATAGGGGGCT 2 246 0 TTTTCTTTCC 0.655645 -20 AATGGAGAGCTATGCTTTCCAGCTATGAAA 4 109 0 TATGCTTTCC 0.547452 -84 TATTTTGATATATTTTTTACAATCTTTCAA 5 55 0 TATTTTTTAC 0.742901 -54 AATAGTTAAAAATAATTTACTTTTTTAAAG 6 53 1 AATAATTTAC 0.522826 -248 TTTTAACATATATAATTTACTATTTAACTT 6 124 1 TATAATTTAC 0.917576 -177 ATGGTGCCCCTATTATTTTCCACATTTTTC 6 196 0 TATTATTTTC 0.670298 -105 TTGTTAAAGTTATTATTTATTTTATCATCA 8 31 0 TATTATTTAT 0.70043 -30 TTTATTTCCATATTATTTCCACATTAGTTT 17 147 0 TATTATTTCC 0.929287 -154 GGATATTTTCTTTTATTTCCATATTATTTC 17 158 0 TTTTATTTCC 0.846006 -143 TAGAAAAATTTATATTTTACACTAAAATAA 17 200 1 TATATTTTAC 0.713816 -101 ATTACTATGATATTATTTATTAAAATTATT 17 225 0 TATTATTTAT 0.70043 -76 TCCATATATATATAATTTACGGTATATTCA 18 33 0 TATAATTTAC 0.917576 -55 GATTTTTTAATTTAATTTCTTGCTTCTTGT 19 192 0 TTTAATTTCT 0.462293 -109 ********** Masking position 6 Map Score: 6.3363 Number of sites scoring better than the average of aligned sites = 538 Number in coding regions = 429 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 10 CGTCCATATCAATAAGGATACTTTCCTGTG 2 191 1 AATAAGGATA 0.88655 -75 TATACTATACAATAATGATGATAAAATAAA 8 16 1 AATAATGATG 0.944507 -45 TATCATAATTAATAATGATAATTAGCTTAA 12 47 0 AATAATGATA 0.961898 -79 TATCATTATTAATTATGATAAATTATCTAT 12 57 1 AATTATGATA 0.819683 -69 TATTACTAAAAATAAAGATATATAAAAAGT 14 18 0 AATAAAGATA 0.840577 -264 AGACATTTTTAATAATGATTAATTTTTCTT 14 97 0 AATAATGATT 0.857125 -185 ATTAATGACAAATAGTGATGTATAAAATAT 19 263 0 AATAGTGATG 0.819468 -38 ACTATTTGTCATTAATGATAATGATAAATT 19 277 1 ATTAATGATA 0.819865 -24 ********** Masking position 8 Map Score: 3.92624 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 65 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 ********** No masking Map Score: 7.05869e-13 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 12 ********** No masking Map Score: 7.05869e-13 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: 7.05869e-13 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