AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -icrp_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 MJ0020 300 asparaginase (ansA) #2 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #3 MJ0086 36 unspecified methyltransferase #4 MJ0087 23 hemin permease (hemU) #5 MJ0090 80 collagenase (prtC) #6 MJ0091 95 Na+/Ca+ exchanger protein, putative #7 MJ0210 86 succinyl-CoA synthetase, beta subunit #8 MJ0210.1 43 M. jannaschii predicted coding region MJ0210.1 #9 MJ0277 183 acetolactate synthase large subunit (ilvB) #10 MJ0667 91 thymidine phosphorylase (deoA) #11 MJ0703.1 125 M. jannaschii predicted coding region MJ0703.1 #12 MJ0704 95 M. jannaschii predicted coding region MJ0704 #13 MJ0792 300 M. jannaschii predicted coding region MJ0792 #14 MJ0792.1 68 M. jannaschii predicted coding region MJ0792.1 #15 MJ0793 60 M. jannaschii predicted coding region MJ0793 #16 MJ0794 48 M. jannaschii predicted coding region MJ0794 #17 MJ0795 79 M. jannaschii predicted coding region MJ0795 #18 MJ0956 145 M. jannaschii predicted coding region MJ0956 #19 MJ1022 80 alignment in /usr/local/projects/ARG/Intergenic/ARG_R428_orf1.nr #20 MJ1054 300 UDP-glucose dehydrogenase, putative #21 MJ1081 130 conserved hypothetical protein #22 MJ1083 69 iron-sulfur flavoprotein (isf) #23 MJ1084 88 shikimate 5-dehydrogenase (aroE) #24 MJ1085 25 M. jannaschii predicted coding region MJ1085 #25 MJ1243 91 conserved hypothetical protein #26 MJ1245 148 M. jannaschii predicted coding region MJ1245 #27 MJ1368 122 sulfate transport system permease protein (cysT) #28 MJ1411 300 glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent (gapN) #29 MJ1672 34 conserved hypothetical protein #30 MJ1674 113 M. jannaschii predicted coding region MJ1674 Motif number 1 AAGTTCCTTAATATATTTAAATTGCA 1 7 1 CTTAATATAT 0.646 -294 CTTAAAGCTACTTAATATATTTATGGCGGA 1 104 1 CTTAATATAT 0.646 -197 ACTGACGCCACTTTTTATTTTGCAAATATT 1 177 1 CTTTTTATTT 0.851758 -124 TCATATAAATTTTTATATTTAAATATATAA 1 210 0 TTTTATATTT 0.949625 -91 TAGCTATCTTTTTATAATTTTTATACCCTA 1 240 1 TTTATAATTT 0.914988 -61 CTTTTTTCTATTTTTTATATAATTTTTATG 2 11 1 TTTTTTATAT 0.876837 -124 TGAACAAAAATTTTTAATATCTAATATATA 2 88 0 TTTTTAATAT 0.753527 -47 TTTTTAATTTTTTATAATTT 3 1 1 TTTTTAATTT 0.904127 -36 TTTTTAATTTTTTATAATTTTTATTTTGGT 3 11 1 TTTATAATTT 0.914988 -26 TCTTTTTTATATAATGAGGTCA 5 3 1 TTTTTTATAT 0.876837 -78 TCAAATATAATTTAAAATTTAAAAAAATTT 5 57 1 TTTAAAATTT 0.902333 -24 TATCACCAAATTTTTTATATGATAATTTTA 7 25 1 TTTTTTATAT 0.876837 -62 ATATGATAATTTTAAAATTTTGCATTAAAA 7 41 1 TTTAAAATTT 0.902333 -46 TAAAAAGAAATTTATCATTTAAGGTGATAG 7 66 1 TTTATCATTT 0.90313 -21 ATAATTTTTATTTTATATTATTTCCCATAA 8 15 1 TTTTATATTA 0.72874 -29 TTTAATTCTATTTTTTATTTTTAGTCTTTA 9 19 1 TTTTTTATTT 0.956448 -165 AGTGTTGGTATTTAATATTTAATTACTAAT 9 51 0 TTTAATATTT 0.955585 -133 ATACCAACACTTTTTTATATCAAACTTTTT 9 70 1 TTTTTTATAT 0.876837 -114 GTATAAAAATTTTTATATATGATTTCAATT 9 126 1 TTTTATATAT 0.859374 -58 TGATTTCAATTTTATCATTACTTTACCCTT 9 145 1 TTTATCATTA 0.57057 -39 TTACTTTACCCTTAACATTTTTTGGTGATT 9 162 1 CTTAACATTT 0.676776 -22 ATATATTTTCTTTAATATTACTTCTCATTG 10 19 0 TTTAATATTA 0.754068 -73 ATTTTCTAAACTTTATATATTTTCTTTAAT 10 33 0 CTTTATATAT 0.615228 -59 TCTATTAAATTTTTATATTTTCTAAACTTT 10 49 0 TTTTATATTT 0.949625 -43 TAGTGTTTATTTTTTCATTAGATTGAATTC 11 30 0 TTTTTCATTA 0.537931 -96 TAACACCATCTTTTAAATATGTTTCTGTAA 11 64 0 TTTTAAATAT 0.724083 -62 ATAGAACTATTTTATTATTTTT 11 114 1 TTTATTATTT 0.961633 -12 TGTAGGAGATTTTAATAAATGGATATCTAT 12 48 1 TTTAATAAAT 0.693358 -48 TTTTAACTATTTTATAATTTTATATCAAAA 13 34 0 TTTATAATTT 0.914988 -267 TTATAATTGTTTTATTATTAAAAATTCTAA 13 83 1 TTTATTATTA 0.781275 -218 AGTTAAAAATTTTAACATATATAATTTACT 13 115 1 TTTAACATAT 0.721794 -186 ACATATATAATTTACTATTTAACTTTAAAT 13 129 1 TTTACTATTT 0.57951 -172 ATGTTTTTCTTTTTTAATTTTAATAATTTT 14 13 1 TTTTTAATTT 0.904127 -56 TTAATAATTTTTTGATATTTTTTAGGTGAT 14 32 1 TTTGATATTT 0.870552 -37 AAATAATAACTTTAACAATTGTGAAACC 15 43 1 TTTAACAATT 0.721794 -18 ATCTTTTTAATTTTTGTTTTATT 18 4 1 TTTTTAATTT 0.904127 -142 TAATTTTTGTTTTATTATTTTATTTTTATT 18 18 1 TTTATTATTT 0.961633 -128 TTATTTTATTTTTATTAATTTATCCATTTA 18 32 1 TTTATTAATT 0.890416 -114 ATGTAAGTCTTTTGATAATTAAAATTTACT 18 88 1 TTTGATAATT 0.685555 -58 TAATATAGATTTTTTTATATAGTGGGTTTT 18 125 1 TTTTTTATAT 0.876837 -21 TTCTTTTGAGTTTTAAAATTAAAGTTGTTG 19 51 1 TTTTAAAATT 0.724083 -30 TATAGCATTACTTATAATTTTCGTTATCAA 20 148 0 CTTATAATTT 0.737942 -153 CCTGAGTTTATTTATTAATAATTGTATAAT 20 273 0 TTTATTAATA 0.536605 -28 ATAGTTATAATTTAATAATTTAGAAC 21 7 0 TTTAATAATT 0.874606 -124 ACTATTCAAGTTTAATATTTAAAATTTAAT 21 45 1 TTTAATATTT 0.955585 -86 TTTTGTGTTATTTGATATTTATTTTTTACC 23 16 1 TTTGATATTT 0.870552 -73 TTACCTTCTCTTTGTAATTTACAATTTTTA 23 41 1 TTTGTAATTT 0.770868 -48 TTAAATTAGTTTTTATAATTAAAAATTGTA 23 60 0 TTTTATAATT 0.859374 -29 CTCTATTAAATTTATTAAATATTT 24 5 0 TTTATTAAAT 0.724834 -21 GTTTTTTGCGTTTTTTATTTGAGGAATTTT 25 48 0 TTTTTTATTT 0.956448 -44 TATCCTATTATTTAAAAATTTGAAAATTAT 26 11 1 TTTAAAAATT 0.749697 -138 AAAAAGAAATTTTAACAATTATCGTATTAT 26 39 0 TTTAACAATT 0.721794 -110 TAAAATTTCTTTTTTTAATAACATATTAAG 26 55 1 TTTTTTAATA 0.503347 -94 GAATATAAAGTTTTTCATTTAGTTTCCTTA 26 81 0 TTTTTCATTT 0.890935 -68 TTTAATAAATTTTTAATGAA 27 1 1 TTTAATAAAT 0.693358 -122 TTAACACAAATTTTATATAATTAGGTAATT 27 63 1 TTTTATATAA 0.464902 -60 TTTCTAAGGGTTTGTTAATTTGATTATTTA 28 48 0 TTTGTTAATT 0.717503 -253 GCATTTAGAATTTATTAATTAGTTCAAAGG 28 90 0 TTTATTAATT 0.890416 -211 GTTGAATATGTTTGAAATTTGAAAATAAGA 28 120 0 TTTGAAATTT 0.742792 -181 ATTTTTAGGATTTTTAATTTTGTTGTTTGG 28 165 0 TTTTTAATTT 0.904127 -136 TCCTAAAAATCTTAATAATTATAAGCACAC 28 185 1 CTTAATAATT 0.646 -116 TTGTAACTAATTTATAATTTGTGCCTCTTT 28 258 0 TTTATAATTT 0.914988 -43 TTACAACATTCTTTTTATTTGGTGGAATC 28 282 1 CTTTTTATTT 0.851758 -19 AATCCCCCAACTTTACATTTCTAAACCAAC 29 12 0 CTTTACATTT 0.647218 -23 ATATAAATAGTTTTTTATTTTGTAAATTTG 30 50 0 TTTTTTATTT 0.956448 -64 ATATGACTTTTTTATTATTTTTAAGGTTCC 30 76 1 TTTATTATTT 0.961633 -38 ********** Masking position 7 Map Score: 82.3531 Number of sites scoring better than the average of aligned sites = 3324 Number in coding regions = 2315 Number in noncoding regions = 1009 Number of orfs with sites within 600 bp upstream = 605 Fraction of orfs with sites within 600 bp upstream = 0.0971731 Motif number 2 TATAAAAATTATAAAAAGATAGCTATCATATAAAT 1 230 0 ATAAAAAATA 0.885895 -71 TATTTTATACTTCAAATATAATTTAAAATTTAAAA 5 46 1 TTAAATTATA 0.832771 -35 AATTTAAAATTTAAAAAAATTTCTAA 5 65 1 TTAAAAATTA 0.844035 -16 AATGCAAAATTTTAAAATTATCATATAAAAAATTT 7 32 0 TTAAAATTTA 0.915682 -55 AAATTTTGCATTAAAAAGAAATTTATCATTTAAGG 7 55 1 TTAAAAAATA 0.832771 -32 GGGAAATAATATAAAATAAAAATTATTTTG 8 6 0 ATAAATAATA 0.815945 -38 AGACTAAAAATAAAAAATAGAATTAAAGAAAGAAA 9 11 0 TAAAAAAATA 0.661181 -173 AAGATTAGTAATTAAATATTAAATACCAACACTTT 9 48 1 ATAAATTATA 0.885895 -136 TTGAAGAACTTTAAAAAGTTTGATATAAAAAAGTG 9 77 0 TTAAAATTTA 0.9154 -107 GAAATCATATATAAAAATTTTTATACTAAGGATTT 9 117 0 ATAAAATTTA 0.94394 -67 GTTTAGAAAATATAAAAATTTAATAGATAAAGAAA 10 52 1 TAAAAATTTA 0.782521 -40 AAAAATAATAAAATAGTTCTATACCTCAACT 11 105 0 AAAAAAATTA 0.791027 -21 TTAAAAAAATTATTATAACTACAAT 12 1 1 TTAAAAATTA 0.860981 -95 ATATCAAAAAATGAAATATAACATAATCAATA 13 8 0 ATAAATTATA 0.885895 -293 ATTATAACTTTAAAAAAGTAAATTATTTTTAACTA 13 55 0 TAAAAATATA 0.77363 -246 AATTTTTAATAATAAAACAATTATAACTTTAAAAA 13 74 0 AAAAAAATTA 0.791027 -227 TGTTTTATTATTAAAAATTCTAATAAGTTAAAAAT 13 90 1 TTAAAATTTA 0.915682 -211 CCTAAAAAATATCAAAAAATTATTAAAATTAAAAA 14 23 0 ATAAAAATTA 0.90626 -46 AATAATGATGATAAAATAAATAATAACTTTAACAA 15 26 1 ATAAATATTA 0.846635 -35 AATACAATCATTGAAAAATCTAATAG 16 33 1 TTAAAATTTA 0.915682 -16 TGGATAAATTAATAAAAATAAAATAATAAAACAAA 18 23 0 AAAAAATATA 0.841977 -123 TTAAAGAATAATAAAAACTTTTATATGTAAGTCTT 18 64 1 ATAAAATTTA 0.94394 -82 TCTTTTGATAATTAAAATTTACTTAAAAAATAATA 18 95 1 ATAAAATATA 0.931492 -51 CCACTATATAAAAAAATCTATATTATTTTTTAAGT 18 115 0 AAAAATTTTA 0.791166 -31 ACCCTCAGACATAAAATTACAGCTAAATAAACTCC 20 212 0 ATAAATAATA 0.815945 -89 GTTCTAAATTATTAAATTATAACTATAAATTATAA 21 11 1 ATAAATAATA 0.815945 -120 AAGTTTAATATTTAAAATTTAATTAAGGTCTTATC 21 52 1 TTAAAATATA 0.897131 -79 GCAATACCCAATTAAATTTTTGATATGTTTTTGAT 21 94 0 ATAAATTTTA 0.90626 -37 GAAGGTAAAAAATAAATATCAAATAACACAAAAGT 23 14 0 AAAAATTATA 0.752621 -75 ATTTTTAATTATAAAAACTAATTTAATGTGATAAT 23 64 1 ATAAAATATA 0.931492 -25 ATTTAAAAATTTGAAAATTATAATACGATAATTGT 26 20 1 TTAAAATTTA 0.915682 -129 TAATATTTTCATTAAAAATTTATTAAA 27 3 0 ATAAAATTTA 0.94423 -120 ACCTAATTATATAAAATTTGTGTTAAACAAAATTG 27 54 0 ATAAATTTTA 0.906261 -69 ATATATAAACATTAAATGTTTGTTAAAAACATTTA 28 218 1 ATAAATTTTA 0.90626 -83 TTTGAAAATATACAAATATGAATTAATTTTAAGGT 30 19 0 TAAAATTATA 0.661181 -95 CCTTAAAAATAATAAAAAAGTCATATAAATAGTTT 30 67 0 AAAAAAATTA 0.791166 -47 ** **** * * ** Masking position 6 Map Score: 57.6046 Number of sites scoring better than the average of aligned sites = 899 Number in coding regions = 600 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028 Motif number 3 CTTCGCAGGAATAAAATCTTTAAAGGAAAGTTT 1 48 0 AAATCTTTAA 0.866276 -253 GATAGCTATCATATAAATTTTTATATTTAAATA 1 215 0 AAAATTTTTA 0.814281 -86 AGATTAGGGTATAAAAATTATAAAAAGATAGCT 1 241 0 AAAATTATAA 0.379545 -60 TCTATTTTTTATATAATTTTTATGAATATTGAT 2 17 1 AAATTTTTAT 0.529968 -118 TATGATATGAACAAAAATTTTTAATATCTAATA 2 92 0 AAAATTTTTA 0.84264 -43 TATCACCAAAATAAAAATTATAAAAAATTAAAA 3 12 0 AAAATTATAA 0.379545 -25 TTAGAAATTTTTTTAAATTTTAAATTATATTTG 5 58 0 TTAATTTTAA 0.500968 -23 ATATATTCAAAAACAAACTTTAATTAATTTAGT 6 63 1 AAAACTTTAA 0.933229 -33 CAAAATAATTTTTATTTTATATTA 8 2 1 AAAATTTTTA 0.814327 -42 ATTTAGCATTTGAAGAACTTTAAAAAGTTTGAT 9 88 0 TAAACTTTAA 0.879866 -96 AATCCTTAGTATAAAAATTTTTATATATGATTT 9 118 1 AAAATTTTTA 0.602917 -66 TCCAACTATAACACCATCTTTTAAATATGTTTC 11 69 0 AAATCTTTTA 0.699417 -57 TATTGTAGTTATAATAATTTTTTTAA 12 4 0 AAAATTTTTT 0.422348 -92 TTAAAAAAGTAAATTATTTTTAACTATTTTATA 13 48 0 AAATTTTTAA 0.891746 -253 TAATAAAACAATTATAACTTTAAAAAAGTAAAT 13 67 0 ATAACTTTAA 0.611308 -234 TTTTAACTTATTAGAATTTTTAATAATAAAACA 13 90 0 TAATTTTTAA 0.770153 -211 TTCTAATAAGTTAAAAATTTTAACATATATAAT 13 107 1 TAAATTTTAA 0.513904 -194 TATAATTTACTATTTAACTTTAAATCATAATAT 13 134 1 TTAACTTTAA 0.451784 -167 AAAAAATATCAAAAAATTATTAAAATTAAAAAA 14 22 0 AAATTATTAA 0.470243 -47 GATAAAATAAATAATAACTTTAACAATTGTGAA 15 35 1 AAAACTTTAA 0.93231 -26 CCCTCATTTTATAGTAACTTTAATACACTGTAT 17 51 0 AAAACTTTAA 0.933236 -29 TTAAAGAATAATAAAAACTTTTATATGTAAGTC 18 64 1 AAAACTTTTA 0.816859 -82 AAAAAAATCTATATTATTTTTTAAGTAAATTTT 18 108 0 AAATTTTTTA 0.728873 -38 AATCTCCCAACATTAATTTTATTAATGGTGAT 19 10 1 AAAATTTTAT 0.748041 -71 TTTAAAACTCAAAAGAATATTAATAATCACCAT 19 35 0 AAAATATTAA 0.746505 -46 TTTATCACATCAACAACTTTAATTTTAAAACT 19 59 0 TAAACTTTAA 0.879879 -22 TAATAATATTATACAATTATTAATAAATAAACT 20 266 1 AAATTATTAA 0.59329 -35 ATAAGACCTTAATTAAATTTTAAATATTAAACT 21 53 0 ATAATTTTAA 0.657831 -78 TCTTTGTAATTTACAATTTTTAATTATAAAAAC 23 49 1 TAATTTTTAA 0.770153 -40 AAATGAACTTTCACATGTGGTGT 25 1 1 AAAACTTTCA 0.464352 -91 GTTATTAAAAAAAGAAATTTTAACAATTATCGT 26 44 0 AAAATTTTAA 0.942859 -105 GGAAACTAAATGAAAAACTTTATATTCTATATT 26 84 1 TAAACTTTAT 0.557872 -65 TTTAATAAATTTTTAATGAAAATAT 27 3 1 TAAATTTTTA 0.693623 -120 ATTTTGTTTAACACAAATTTTATATAATTAGGT 27 56 1 AAAATTTTAT 0.748066 -67 TAATCAATCTTAATCATTTTTAAGGTAATTAAA 27 91 0 TAATTTTTAA 0.81791 -32 TAATTAGTTCAAAGGATTTTTATTTAATTTCTA 28 72 0 AAATTTTTAT 0.600215 -229 ATTAAGATTTTTAGGATTTTTAATTTTGTTGTT 28 168 0 TAATTTTTAA 0.818607 -133 TTATGTGTGCTTATAATTATTAAGATTTTTAGG 28 186 0 TAATTATTAA 0.355972 -115 CACACATAATATATAAACATTAAATGTTTGTTA 28 210 1 AAAACATTAA 0.708171 -91 TAAATGTTTGTTAAAAACATTTAAAATGAAAGA 28 230 1 TAAACATTTA 0.286811 -71 ATACAAATATGAATTAATTTTAAGGTGGTAATT 30 12 0 GAAATTTTAA 0.548522 -102 TATGACTTTTTTATTATTTTTAAGGTTCCACAA 30 77 1 TAATTTTTAA 0.758106 -37 * * ******** Masking position 6 Map Score: 50.4557 Number of sites scoring better than the average of aligned sites = 1473 Number in coding regions = 1057 Number in noncoding regions = 416 Number of orfs with sites within 600 bp upstream = 354 Fraction of orfs with sites within 600 bp upstream = 0.0568583 Motif number 4 CGTTCCACCTTAAAAACTGATTC 1 288 0 TTCCACCTAA 0.797335 -13 TTTATCACCAAAATAAAAATTAT 3 24 0 TATCACCAAA 0.971798 -13 ACTATCACATTTTTTGAATTATT 4 11 0 TATCACATTT 0.52637 -13 CCTATAAATTTATCACCAAATTTTTTATATG 7 15 1 TATCACCAAT 0.923457 -72 CCTATCACCTTAAATGATAAATT 7 74 0 TATCACCTAA 0.977721 -13 CCAATCACCAAAAAATGTTAAGG 9 171 0 AATCACCAAA 0.923457 -13 TTAAATCACCACTAATTTCTTTAT 10 78 0 AATCACCATA 0.750018 -14 GTGCCTACACAACCACCTTAAGAGGTGGCAA 13 279 1 AACCACCTAA 0.895103 -22 TCACCCATTATATCACCTAAAAAATATCAAA 14 42 0 TATCACCTAA 0.977721 -27 GAATATTAATAATCACCATTAATAAAATTAA 19 23 0 AATCACCATA 0.750018 -58 TTTATCACATCAACAACTTTAAT 19 68 0 TATCACATAA 0.927346 -13 GAATTTATTATCACAAGATTAAAGAGGTT 20 9 1 TATCACAAAT 0.778216 -292 ATTAAGGTCTTATCACATCAAATCAAAAACA 21 73 1 TATCACATAA 0.927346 -58 ATTATCACATTAAATTAGTTTTT 23 76 0 TATCACATAA 0.927346 -13 GATTCCACCAAATAAAAAGAATG 28 288 0 TTCCACCAAT 0.51959 -13 AAATTACCACCTTAAAATTAATTCA 30 5 1 TACCACCTAA 0.960586 -109 ******** ** Masking position 5 Map Score: 18.0284 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 133 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 5 TGATAGCTATCTTTTTATAATTTTTATACCCTAAT 1 237 1 CTTTTATTTT 0.47631 -64 TTTTTCTATTTTTTATATAATTTTTATGAATATTG 2 13 1 TTTTTATTTT 0.944473 -122 TAATATATATTTTTCGGTAGTTTATCAAAAATAAT 2 62 0 TTTTTATTTT 0.944473 -73 TTTTTAATTTTTTATAATTTTTATTTTGGTGA 3 8 1 TTTTTATTTT 0.944473 -29 GTCATATTGGTTATTGCTATTTTATACTTCAAATA 5 29 1 TTATTATTTT 0.694093 -52 TTAGAAATTTTTTTAAATTTTAAATTATATTT 5 59 0 TTTTAATTTA 0.529923 -22 GAACTGAAAATTTTGCTTAAGTTTAAATATTATTG 6 24 1 TTTTTAGTTA 0.557842 -72 TAAAGTTTGTTTTTGAATATATTCTGCAATAATAT 6 50 0 TTTTTAATTT 0.650044 -46 CAAAATAATTTTTATTTTATATTATTTCCC 8 6 1 TAATTATTTT 0.598435 -38 TTTTATATTATTTCCCATAATTTTTTAAT 8 25 1 TTTCTATTTT 0.469538 -19 TCTTTAATTCTATTTTTTATTTTTAGTCTTTAAGA 9 17 1 TATTTATTTA 0.786047 -167 AAAGTGTTGGTATTTAATATTTAATTACTAATCTT 9 48 0 TATTTATTAT 0.28174 -136 AATTTTTATATTTTCTAAACTTTATATATTTTCTT 10 37 0 TTTTAATTTT 0.774161 -55 CTGTAAAAAGTAGTGTTTATTTTTTCATTAGATTG 11 35 0 TAGTTATTTT 0.552668 -91 TAACACCATCTTTTAAATATGTTTCTGTAAAAAGT 11 59 0 TTTTTAGTTC 0.208304 -67 GGTATAGAACTATTTTATTATTTTT 11 111 1 TATTTTTTTT 0.415455 -15 AATATTGTAGTTATAATAATTTTTTTAA 12 4 0 TTATAATTTT 0.313786 -92 TATTGATTATGTTATATTTCATTTT 13 1 1 TATTTAGTTT 0.715888 -300 AGTAAATTATTTTTAACTATTTTATAATTTTATAT 13 39 0 TTTTTATTTT 0.944473 -262 CATCGCCAACTATTCTTTAATTTTTTGTATGGTGC 13 219 0 TATTTATTTT 0.917842 -82 TTTTAATAATTTTTTGATATTTTTTAGGTGATATA 14 30 1 TTTTTATTTT 0.944473 -39 TTGTTAAAGTTATTATTTATTTTATCATCATTATT 15 26 0 TATTTATTTT 0.917842 -35 TATTATTTTATTTTTATTAATTTATCCATTTAAAT 18 30 1 TTTTTATTTT 0.944473 -116 AAGTTTTTATTATTCTTTAATTTAAATGGATAAAT 18 49 0 TATTTATTTA 0.786047 -97 CTATATTATTTTTTAAGTAAATTTTAATTATCAAA 18 98 0 TTTTTAATTT 0.650044 -48 AGGAGTAGTTTATTTTGGAGTTTATTTAGCTGTAA 20 196 1 TATTGATTTT 0.409254 -105 CCCAATTAAATTTTTGATATGTTTTTGATTTGATG 21 88 0 TTTTTAGTTT 0.793234 -43 TCAGAAATAGGTTTTAATAGTTTTTC 22 2 0 GTTTTATTTT 0.47631 -68 ATTTGATATTTATTTTTTACCTTCTCTTTGTAATT 23 25 1 TATTTACTTT 0.417124 -64 AAATATTTAATAAATTTAATAGAGG 24 4 1 TATTTAATTA 0.286331 -22 AATAGAAGTTTTTTGCGTTTTTTATTTGAGGAATT 25 50 0 TTTTTTTTTT 0.519719 -42 TATCCTATTATTTAAAAATTTGAAAATTATAAT 26 9 1 TATTAATTTA 0.425425 -140 AAAAACTTTATATTCTATATTTTTAACAGTTAAAT 26 96 1 TATTTATTTA 0.786047 -53 AATTACCTAATTATATAAAATTTGTGTTAAACAAA 27 58 0 TTATAATTTT 0.313786 -65 TTCAAAGGATTTTTATTTAATTTCTAAGGGTTTGT 28 63 0 TTTTTATTTT 0.944473 -238 TAAATGCTCTTATTTTCAAATTTCAAACATATTCA 28 113 1 TATTAATTTA 0.425425 -188 AAAAAGAATGTTGTAACTAATTTATAATTTGTGCC 28 263 0 TTGTTATTTT 0.652905 -38 TTATATGACTTTTTTATTATTTTTAAGGTTCCACA 30 74 1 TTTTTATTTA 0.848339 -40 **** ** *** * Masking position 12 Map Score: 41.5321 Number of sites scoring better than the average of aligned sites = 1616 Number in coding regions = 1190 Number in noncoding regions = 426 Number of orfs with sites within 600 bp upstream = 350 Fraction of orfs with sites within 600 bp upstream = 0.0562159 Motif number 6 ATTTAAATATATTAAGGAACTT 1 3 0 ATTAAGGAAC 0.368376 -298 ATTCATAAAAATTATATAAAAAATAGAAAA 2 14 0 ATTATATAAA 0.750485 -121 ATATGACCTCATTATATAAAAAAGA 5 6 0 ATTATATAAA 0.750485 -75 TCCCTACTAAATTAATTAAAGTTTGTTTTT 6 71 0 ATTAATTAAA 0.553007 -25 GGGAAATAATATAAAATAAAAATTATTTTG 8 11 0 ATAAAATAAA 0.674276 -33 ATTAAAAAATTATGGGAAAT 8 34 0 ATTAAAAAAT 0.454066 -10 AAAAAATAGAATTAAAGAAAGAAA 9 5 0 ATTAAAGAAA 0.948483 -179 GAGAAGTAATATTAAAGAAAATATATAAAG 10 23 1 ATTAAAGAAA 0.948483 -69 CATACAAAAAATTAAAGAATAGTTGGCGAT 13 223 1 ATTAAAGAAT 0.808988 -78 AATAATGATGATAAAATAAATAATAACTTT 15 26 1 ATAAAATAAA 0.674276 -35 ATCCATTTAAATTAAAGAATAATAAAAACT 18 53 1 ATTAAAGAAT 0.808988 -93 TACAATTATTAATAAATAAACTCAGGGGAT 20 277 1 AATAAATAAA 0.525198 -24 AAATATTTAATAAATTTAATAGAG 24 5 1 ATTTAATAAA 0.52507 -21 ATTTTAGCATATTAAAGAAACACCACATGT 25 23 0 ATTAAAGAAA 0.948483 -69 TTAATATGTTATTAAAAAAAGAAATTTTAA 26 54 0 ATTAAAAAAA 0.783802 -95 TTAATAACATATTAAGGAAACTAAATGAAA 26 69 1 ATTAAGGAAA 0.811266 -80 AAATTACCTAATTATATAAAATTTGTGTTA 27 64 0 ATTATATAAA 0.750485 -59 ACCCTTAGAAATTAAATAAAAATCCTTTGA 28 67 1 ATTAAATAAA 0.934978 -234 ********** Masking position 8 Map Score: 15.0728 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 437 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 7 AATTATATAAAAAATAGAAAAAAG 2 4 0 AAAAAGAAAA 0.853411 -131 AATAATTCAAAAAATGTGATAG 4 2 1 ATAATCAAAA 0.747747 -22 ATTATGGGAAATAATATAAAATAAAAATTAT 8 15 0 ATAAATAAAA 0.74079 -29 TTAAAGACTAAAAATAAAAAATAGAATTAAA 9 19 0 AAAAAAAAAA 0.843579 -165 TAAAGTTTAGAAAATATAAAAATTTAATAGA 10 48 1 AAAAATAAAA 0.79008 -44 CACAAATGTAATAATACAAAACCTCTATATA 13 166 0 ATAAACAAAA 0.93554 -135 TATTAAAATTAAAAAAGAAAAACATTT 14 7 0 AAAAAGAAAA 0.853411 -62 AAATAAAATAATAAAACAAAAATTAAAAAGA 18 12 0 ATAAACAAAA 0.93554 -134 CTTTAATTTTAAAACTCAAAAGAATATTAAT 19 44 0 AAAATCAAAA 0.796078 -37 TAAATATCAAATAACACAAAAGTGTT 23 6 0 ATAAACAAAA 0.93554 -83 CCTCAAATAAAAAACGCAAAAAACTTCTATT 25 54 1 AAAAGCAAAA 0.766421 -38 TCCATCAACCAAACAACAAAATTAAAAATCC 28 157 1 AAACACAAAA 0.73602 -144 TCAAATTTACAAAATAAAAAACTATTTATAT 30 49 1 AAAAAAAAAA 0.843579 -65 AACCTTAAAAATAATAAAAAAGTCATATAAA 30 73 0 ATAAAAAAAA 0.803731 -41 **** ****** Masking position 8 Map Score: 12.8372 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 99 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 8 AGCTATGATGATTGATGGGCGAACTGACGCCA 1 155 1 ATGATGGGGA 0.932 -146 TATCATATAAAAAATTTGGTGATAAATTTATA 7 17 0 AAATTTGGGA 0.752582 -70 AGATGGTGTTATAGTTGGATGAAGTTGAGGTA 11 83 1 AAGTTGGAGA 0.959101 -43 TAATAAAATTAATGTTGGGAGATT 19 3 0 ATGTTGGGGA 0.985079 -78 ATAATGTTCTACAATTGGGTGAAGTCGTTAAC 20 100 1 AAATTGGGGA 0.959101 -201 TTTACAATTAATTGTTGGAGGAGTAGTTTATT 20 178 1 ATGTTGGAGA 0.947395 -123 TTAGAAATGTAAAGTTGGGGGATTTAG 29 18 1 AAGTTGGGGA 0.988501 -17 * ******* ** Masking position 1 Map Score: 3.81517 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 21 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ATGGGCGAACTGACGCCACTTTTTATTTTGCAA 1 169 1 TCGCACTTTT 0.683002 -132 ATTGTCACCATTTTAGGCTATATGA 2 120 0 TCACATTTTA 0.911667 -15 ATAACCAATATGACCTCATTATATAAAAAAGA 5 10 0 TCCCATTATA 0.785909 -71 TATAAATTTATCACCAAATTTTTTATATGATAA 7 17 1 TCCAATTTTT 0.802103 -70 TTATATTATTTCCCATAATTTTTTAAT 8 27 1 TCAAATTTTT 0.769318 -17 AAATATTAAATACCAACACTTTTTTATATCAAA 9 61 1 TCACACTTTT 0.902169 -123 CATCCAACTATAACACCATCTTTTAAATATGTT 11 71 0 TCACATCTTT 0.731102 -55 CCCCTATTATTTTCCACATTTTTCACAAATGTA 13 187 0 TCCCATTTTT 0.960559 -114 TTATTTATTTTATCATCATTATTGTATAGTATA 15 16 0 TCACATTATT 0.854326 -45 CTTTTTCCCTCATTTTATAGTAACTTT 17 63 0 TCCCATTTTA 0.926162 -17 AATCTCCCAACATTAATTTTATTAATG 19 5 1 TCACATTAAT 0.349329 -76 ATAATCTCCTCATTTTAAATAGAAGTT 25 75 0 TCCCATTTTA 0.926162 -17 TACTATCAAATGTCATCAATTTTGTTTAACACA 27 38 1 TCACAATTTT 0.698891 -85 TATAAATTAGTTACAACATTCTTTTTATTTGGT 28 272 1 TCACATTCTT 0.774779 -29 CTAAATCCCCCAACTTTACATTTCTAAA 29 17 0 TCCAACTTTA 0.489963 -18 * ** ******* Masking position 8 Map Score: 6.63313 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 310 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 Motif number 10 TTGATGTATTTTTAACGATTATTTTTGATA 2 45 1 TTTAACGATT 0.814822 -90 TTTGCTTAAGTTTAAATATTATTGCAGAAT 6 35 1 TTTAAATATT 0.834922 -61 CACTAATTTCTTTATCTATTAAATTTTTAT 10 63 0 TTTATCTATT 0.71862 -29 AGTTGAGGTATAGAACTATTTTATTATTTT 11 105 1 TAGAACTATT 0.677001 -21 GTAAATTATTTTTAACTATTTTATAATTTT 13 43 0 TTTAACTATT 0.965395 -258 AAATAATAACTTTAACAATTGTGAAACC 15 43 1 TTTAACAATT 0.83962 -18 TATTTGTTACTTCAACTATTTAAATC 16 7 0 TTCAACTATT 0.802747 -42 ACAAACCAAATATAACTGTTGGAATTAGTG 17 14 0 TATAACTGTT 0.858654 -66 ATTATTAAATTATAACTATAAATTATAACT 21 18 1 TATAACTATA 0.566947 -113 AACTATAAATTATAACTATTCAAGTTTAAT 21 31 1 TATAACTATT 0.934893 -100 TTAATTAAATTTTAAATATTAAACTTGAAT 21 48 0 TTTAAATATT 0.834922 -83 AAAAAGAAATTTTAACAATTATCGTATTAT 26 39 0 TTTAACAATT 0.83962 -110 AAAGTTACAATTTAACTGTTAAAAATATAG 26 110 0 TTTAACTGTT 0.921848 -39 TATGTGTGCTTATAATTATTAAGATTTTTA 28 188 0 TATAATTATT 0.50666 -113 CCTCTTTCATTTTAAATGTTTTTAACAAAC 28 235 0 TTTAAATGTT 0.681376 -66 ********** Masking position 4 Map Score: 9.89165 Number of sites scoring better than the average of aligned sites = 474 Number in coding regions = 395 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 11 AGTTCCTTAATATATTTAAATTGCATTCAA 1 12 1 TATATTTAAA 0.929241 -289 GGTAAGTATATATACTTAAAGCTACTTAAT 1 90 1 TATACTTAAA 0.522448 -211 TATAAATTTTTATATTTAAATATATAAATT 1 207 0 TATATTTAAA 0.929241 -94 AATATTGATGTATTTTTAACGATTATTTTT 2 41 1 TATTTTTAAC 0.724969 -94 AATTTTAAATTATATTTGAAGTATAAAATA 5 46 0 TATATTTGAA 0.511965 -35 TTAGAAATTTTTTTAAATTTTAAATTA 5 64 0 TTTTTTTAAA 0.409881 -17 ATTCTGCAATAATATTTAAACTTAAGCAAA 6 35 0 AATATTTAAA 0.726516 -61 TATTGCAGAATATATTCAAAAACAAACTTT 6 54 1 TATATTCAAA 0.745726 -42 TTTTATATGATAATTTTAAAATTTTGCATT 7 37 1 TAATTTTAAA 0.528239 -50 TTTACAGAAACATATTTAAAAGATGGTGTT 11 63 1 CATATTTAAA 0.544775 -63 AAAAGTAAATTATTTTTAACTATTTTATAA 13 47 0 TATTTTTAAC 0.724969 -254 ATAATTGTTTTATTATTAAAAATTCTAATA 13 85 1 TATTATTAAA 0.528232 -216 TGTTACTTCAACTATTTAAATC 16 3 0 ACTATTTAAA 0.460108 -46 TATTAATTTATCCATTTAAATTAAAGAATA 18 44 1 TCCATTTAAA 0.259792 -102 AAATCTATATTATTTTTTAAGTAAATTTTA 18 107 0 TATTTTTTAA 0.378446 -39 TCAACAACTTTAATTTTAAAACTCAAAAGA 19 52 0 TAATTTTAAA 0.528239 -29 TACTTGGAAATCTATTTAAAACCTCTTTAA 20 29 0 TCTATTTAAA 0.808187 -272 TAAGTAATGCTATATTTACAATTAATTGTT 20 164 1 TATATTTACA 0.501889 -137 ATTCAAGTTTAATATTTAAAATTTAATTAA 21 48 1 AATATTTAAA 0.726516 -83 AATTAGTTTTTATAATTAAAAATTGTAAAT 23 57 0 TATAATTAAA 0.564974 -32 GCAAAAAACTTCTATTTAAAATGAGGAGAT 25 69 1 TCTATTTAAA 0.808187 -23 ATAATTTTCAAATTTTTAAATAATAGGATA 26 11 0 AATTTTTAAA 0.695609 -138 TTATATTCTATATTTTTAACAGTTAAATTG 26 103 1 TATTTTTAAC 0.724969 -46 TAAATGCTCTTATTTTCAAATTTCAAACAT 28 113 1 TATTTTCAAA 0.716141 -188 CATATTTGTATATTTTCAAATTTACAAAAT 30 34 1 TATTTTCAAA 0.716141 -80 ACTTTTTTATTATTTTTAAGGTTCCACAAA 30 81 1 TATTTTTAAG 0.495795 -33 ********** Masking position 6 Map Score: 15.2611 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 709 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 253 Fraction of orfs with sites within 600 bp upstream = 0.040636 Motif number 12 TGCAATTTAAATATATTAAGGAACTT 1 7 0 ATATATTAAG 0.832805 -294 TCCGCCATAAATATATTAAGTAGCTTTAAG 1 104 0 ATATATTAAG 0.832805 -197 AGAGATTGTTATAGATTAGGGTATAAAAAT 1 256 0 ATAGATTAGG 0.946812 -45 TATTCTCTTAATTGCTTATGCTTTTCTTTA 12 75 1 ATTGCTTATG 0.643707 -21 TATTGATTATGTTATATTTCA 13 2 1 ATTGATTATG 0.885487 -299 AAACCTCTATATATATTATGATTTAAAGTT 13 149 0 ATATATTATG 0.902852 -152 TTCTGATAAAATACATTAGGTCAGAATTTA 22 31 1 ATACATTAGG 0.834867 -39 AATGATTAAGATTGATTAGGGATAGGC 27 106 1 ATTGATTAGG 0.903268 -17 TTTAATGTTTATATATTATGTGTGCTTATA 28 204 0 ATATATTATG 0.902852 -97 ********** Masking position 6 Map Score: 3.67494 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 75 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 ********** No masking Map Score: -8.18302e-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: -8.18302e-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: -8.18302e-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