AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -icrp_mjan_opreg_300.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 MJ0081 300 methyl coenzyme M reductase II, subunit beta (mrtB) #3 MJ0084 261 CODH nickel-insertion accessory protein (cooC) #4 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #5 MJ0086 36 unspecified methyltransferase #6 MJ0087 23 hemin permease (hemU) #7 MJ0090 80 collagenase (prtC) #8 MJ0091 95 Na+/Ca+ exchanger protein, putative #9 MJ0210 86 succinyl-CoA synthetase, beta subunit #10 MJ0210.1 43 M. jannaschii predicted coding region MJ0210.1 #11 MJ0277 183 acetolactate synthase large subunit (ilvB) #12 MJ0278 82 peptidyl-prolyl cis-trans isomerase, FKBP-type rotamase (slyD) #13 MJ0667 91 thymidine phosphorylase (deoA) #14 MJ0703 24 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA2) #15 MJ0703.1 125 M. jannaschii predicted coding region MJ0703.1 #16 MJ0704 95 M. jannaschii predicted coding region MJ0704 #17 MJ0792 300 M. jannaschii predicted coding region MJ0792 #18 MJ0792.1 68 M. jannaschii predicted coding region MJ0792.1 #19 MJ0793 60 M. jannaschii predicted coding region MJ0793 #20 MJ0794 48 M. jannaschii predicted coding region MJ0794 #21 MJ0795 79 M. jannaschii predicted coding region MJ0795 #22 MJ0955 48 histidinol-phosphate aminotransferase (hisC) #23 MJ0956 145 M. jannaschii predicted coding region MJ0956 #24 MJ1022 80 alignment in /usr/local/projects/ARG/Intergenic/ARG_R428_orf1.nr #25 MJ1054 300 UDP-glucose dehydrogenase, putative #26 MJ1081 130 conserved hypothetical protein #27 MJ1083 69 iron-sulfur flavoprotein (isf) #28 MJ1084 88 shikimate 5-dehydrogenase (aroE) #29 MJ1085 25 M. jannaschii predicted coding region MJ1085 #30 MJ1243 91 conserved hypothetical protein #31 MJ1245 148 M. jannaschii predicted coding region MJ1245 #32 MJ1246 300 succinyl-CoA synthetase, alpha subunit (sucD) #33 MJ1368 122 sulfate transport system permease protein (cysT) #34 MJ1411 300 glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent (gapN) #35 MJ1672 34 conserved hypothetical protein #36 MJ1674 113 M. jannaschii predicted coding region MJ1674 Motif number 1 ATGCAATTTAAATATATTAAGGAACTT 1 8 0 AATATATTAA 0.820123 -293 ATCCGCCATAAATATATTAAGTAGCTTTAA 1 105 0 AATATATTAA 0.820123 -196 TAATATTTGCAAAATAAAAAGTGGCGTCAG 1 178 0 AAAATAAAAA 0.951477 -123 TTTATATTTAAATATATAAATTAATATTTG 1 199 0 AATATATAAA 0.828828 -102 TATATATTTAAATATAAAAATTTATATGAT 1 211 1 AATATAAAAA 0.881403 -90 TTAGGGTATAAAAATTATAAAAAGATAGCT 1 241 0 AAAATTATAA 0.939078 -60 TTAAAATGATAAAATTAAAAAAATCTTTAA 2 164 0 AAAATTAAAA 0.942425 -137 AAAAAATGTTAAAATAATAATATTAAAATG 2 186 0 AAAATAATAA 0.948628 -115 TTTTTAGGATAAAATAGAAAATTTTATATA 2 221 1 AAAATAGAAA 0.816528 -80 TAGCTGTAGTAATATATTAACAAAAAGGTT 2 271 1 AATATATTAA 0.820123 -30 TTAAAATTTTAAAATTAAAAATAAAGTCCA 3 42 0 AAAATTAAAA 0.942425 -220 TTTTAATTTTAAAATTTTAATTGGAGGGCA 3 52 1 AAAATTTTAA 0.909449 -210 TTTAGATAAAATAATATTAATGGAAGAGAC 3 113 1 ATAATATTAA 0.745692 -149 AGGTTTTAATTAAATTTAAATCAGACTGAG 3 234 1 TAAATTTAAA 0.823854 -28 AATTATATAAAAAATAGAAAAAAG 4 5 0 AAAATAGAAA 0.816528 -130 AAAATTATAAAAAATTAAAAA 5 2 0 AAAATTAAAA 0.942425 -35 TTTATCACCAAAATAAAAATTATAAAAAA 5 18 0 AAAATAAAAA 0.951477 -19 ATGACCTCATTATATAAAAAAGA 7 4 0 TATATAAAAA 0.765216 -77 AATATAATTTAAAATTTAAAAAAATTTCTA 7 60 1 AAAATTTAAA 0.914275 -21 ATTCTGCAATAATATTTAAACTTAAGCAAA 8 35 0 AATATTTAAA 0.801675 -61 TTTTTAATGCAAAATTTTAAAATTATCATA 9 42 0 AAAATTTTAA 0.909449 -45 GAAATAATATAAAATAAAAATTATTTTG 10 9 0 AAAATAAAAA 0.951477 -35 TTAAAGACTAAAAATAAAAAATAGAATTAA 11 20 0 AAAATAAAAA 0.951477 -164 GATTAGTAATTAAATATTAAATACCAACAC 11 50 1 TAAATATTAA 0.835571 -134 ATTGAAATCATATATAAAAATTTTTATACT 11 125 0 TATATAAAAA 0.765216 -59 AAGTAATGATAAAATTGAAATCATATATAA 11 138 0 AAAATTGAAA 0.787911 -46 TTGTCCATAAAAAATAATAACAAAAAACTA 12 22 1 AAAATAATAA 0.948628 -61 TATTAAAGAAAATATATAAAGTTTAGAAAA 13 32 1 AATATATAAA 0.828828 -60 TAAAGTTTAGAAAATATAAAAATTTAATAG 13 48 1 AAAATATAAA 0.927402 -44 TAAATAATAATTTAGAGGGA 14 1 1 TAAATAATAA 0.890065 -24 AAAAATAATAAAATAGTTCTA 15 115 0 AAAATAATAA 0.948628 -11 TTAAAAAAATTATTATAACTACAATATT 16 9 1 ATTATTATAA 0.59327 -87 TAGATATCCATTTATTAAAATCTCCTACAA 16 47 0 TTTATTAAAA 0.404511 -49 TTTTTGATATAAAATTATAAAATAGTTAAA 17 33 1 AAAATTATAA 0.939078 -268 ATTAGAATTTTTAATAATAAAACAATTATA 17 84 0 TTAATAATAA 0.66503 -217 TAATAAGTTAAAAATTTTAACATATATAAT 17 110 1 AAAATTTTAA 0.909449 -191 GATTTAAAGTTAAATAGTAAATTATATATG 17 130 0 TAAATAGTAA 0.647624 -171 AAAAATTATTAAAATTAAAAAAGAAAAACA 18 14 0 AAAATTAAAA 0.942425 -55 GATGATAAAATAAATAATAACTTTAACAAT 19 32 1 TAAATAATAA 0.890065 -29 TTTAACCAAAAATATTTTAAATAAGATTTC 22 25 0 AATATTTTAA 0.791953 -24 TAATAAAACAAAAATTAAAAAGAT 23 5 0 AAAATTAAAA 0.942425 -141 TAATAAAAATAAAATAATAAAACAAAAATT 23 19 0 AAAATAATAA 0.948628 -127 AATGGATAAATTAATAAAAATAAAATAATA 23 30 0 TTAATAAAAA 0.680665 -116 TTATTATTCTTTAATTTAAATGGATAAATT 23 48 0 TTAATTTAAA 0.537457 -98 AAATTAAAGAATAATAAAAACTTTTATATG 23 61 1 ATAATAAAAA 0.830377 -85 ATTTTTTAAGTAAATTTTAATTATCAAAAG 23 96 0 TAAATTTTAA 0.814954 -50 AAAAACCCACTATATAAAAAAATCTATATT 23 126 0 TATATAAAAA 0.765216 -20 ATCAACAACTTTAATTTTAAAACTCAAAAG 24 53 0 TTAATTTTAA 0.520582 -28 ATTGATAACGAAAATTATAAGTAATGCTAT 25 147 1 AAAATTATAA 0.939078 -154 ATGTAAGAGAAATATAATAATATTATACAA 25 252 1 AATATAATAA 0.87498 -49 TCTAAATTATTAAATTATAACTATAAATTA 26 13 1 TAAATTATAA 0.871138 -118 ATTATAACTATAAATTATAACTATTCAAGT 26 26 1 TAAATTATAA 0.871138 -105 AATTAAATTTTAAATATTAAACTTGAATAG 26 46 0 TAAATATTAA 0.835571 -85 ATTAGTTTTTATAATTAAAAATTGTAAATT 28 56 0 ATAATTAAAA 0.803411 -33 TATCCTATTATTTAAAAATTTGAAAA 31 7 1 ATTATTTAAA 0.502291 -142 TAAAAATTTGAAAATTATAATACGATAATT 31 23 1 AAAATTATAA 0.939078 -126 TTTTAACAGTTAAATTGTAACTTTTCCACA 31 116 1 TAAATTGTAA 0.605414 -33 GTGCCTTATAAATATATAAATTGTGAAAGT 32 224 1 AATATATAAA 0.828828 -77 AAATTACCTAATTATATAAAATTTGTGTTA 33 64 0 ATTATATAAA 0.545962 -59 CCTTAGAAATTAAATAAAAATCCTTTGAAC 34 69 1 TAAATAAAAA 0.895821 -232 ACCAAACAACAAAATTAAAAATCCTAAAAA 34 164 1 AAAATTAAAA 0.942425 -137 AAAAATCTTAATAATTATAAGCACACATAA 34 189 1 ATAATTATAA 0.793752 -112 AAGCACACATAATATATAAACATTAAATGT 34 207 1 AATATATAAA 0.828828 -94 CAAATATGAATTAATTTTAAGGTGGTAATT 36 12 0 TTAATTTTAA 0.520582 -102 TCAAATTTACAAAATAAAAAACTATTTATA 36 49 1 AAAATAAAAA 0.951477 -65 TGGAACCTTAAAAATAATAAAAAAGTCATA 36 77 0 AAAATAATAA 0.948628 -37 ********** Masking position 5 Map Score: 93.1337 Number of sites scoring better than the average of aligned sites = 2311 Number in coding regions = 1461 Number in noncoding regions = 850 Number of orfs with sites within 600 bp upstream = 557 Fraction of orfs with sites within 600 bp upstream = 0.0894635 Motif number 2 AAGTTCCTTAATATATTTAAATTGCATTC 1 7 1 CTTAAATTTA 0.506348 -294 TTAAACTTTCCTTTAAAGATTTTATTCCTGCGA 1 46 1 CTTAAATTTT 0.709286 -255 CTTAAAGCTACTTAATATATTTATGGCGGATGA 1 104 1 CTTAAATTTA 0.506348 -197 GCAAATATTAATTTATATATTTAAATATAAAAA 1 198 1 ATTAAATTTA 0.505361 -103 AGATAGCTATCATATAAATTTTTATATTTAAAT 1 216 0 CATTATTTTT 0.471618 -85 ATAGCTATCTTTTTATAATTTTTATACCCTAAT 1 239 1 TTTAATTTTT 0.932551 -62 TTTAAAATCTTTAAAAAAATTTTGAATTCCTCA 2 136 0 TTAAAATTTT 0.843046 -165 TTTAAAGATTTTAAAGATTTTTTTAATTTTATC 2 154 1 TTAAATTTTT 0.895794 -147 ATATTATTATTTTAACATTTTTTAGTAATTTTT 2 193 1 TTTAATTTTT 0.932551 -108 TAGTAATAGGTATATAAAATTTTCTATTTTATC 2 228 0 TATTAATTTT 0.663788 -73 TTTATTATCTTATTTTAAGTTTTATTTTTTGGA 3 13 1 TATTAGTTTT 0.530913 -249 TTATTTTTAATTTTAAAATTTTAATTGGAGGGC 3 48 1 TTTAATTTTA 0.853214 -214 TCAAACATTTTATCAAAAGTTTTAGATAAAATA 3 93 1 TATAAGTTTT 0.770372 -169 ATATTAGGTTTTAATTAAATTTAAATCAGACTG 3 229 1 TTATAATTTA 0.432406 -33 TTTCTATTTTTTATATAATTTTTATGAATATTG 4 15 1 TTAAATTTTT 0.895807 -120 TTTTAATATCTAATATATATTTTTCGGTAGTTT 4 74 0 TAAAAATTTT 0.784441 -61 ATATATTAGATATTAAAAATTTTTGTTCATATC 4 89 1 TATAAATTTT 0.854063 -46 TTTTTAATTTTTTATAATTTTTATTTTGGTGA 5 10 1 TTTAATTTTT 0.932551 -27 ACTATCACATTTTTTGAATTATT 6 9 0 TATAATTTTT 0.903541 -15 TTAGAAATTTTTTTAAATTTTAA 7 68 0 TTAAATTTTT 0.895807 -13 TTGGTGATAAATTTATAGGTTTA 9 1 0 ATTAAGTTTA 0.369357 -86 AAATTTTTTATATGATAATTTTAAAATTTTGCA 9 32 1 TATAATTTTA 0.797491 -55 ATTTTGCATTAAAAAGAAATTTATCATTTAAGG 9 57 1 AAAAAATTTA 0.298325 -30 CAAAATAATTTTTATTTTATATT 10 1 1 CAAAATTTTT 0.62193 -43 TTTAATTCTATTTTTTATTTTTAGTCTTTAAGA 11 19 1 TTTTATTTTA 0.662271 -165 AAAGTGTTGGTATTTAATATTTAATTACTAATC 11 50 0 TATTAATTTA 0.45356 -134 CACTTTTTTATATCAAACTTTTTAAAGTTCTTC 11 77 1 TATAATTTTT 0.903541 -107 AAATCCTTAGTATAAAAATTTTTATATATGATT 11 117 1 TATAATTTTT 0.903529 -67 TTACTTTACCCTTAACATTTTTTGGTGATTGG 11 162 1 CTTAATTTTT 0.796133 -22 TGAAGGGTATATAAATAGTTTTTTGTTATTATT 12 34 0 ATAAATTTTT 0.707477 -49 ATTTTCTAAACTTTATATATTTTCTTTAATATT 13 30 0 CTTAAATTTT 0.709286 -62 TTTCTTTATCTATTAAATTTTTATATTTTCTAA 13 54 0 TATAATTTTA 0.797491 -38 ATATTGTAGTTATAATAATTTTTTTAA 16 5 0 TATAATTTTT 0.903529 -91 GATTATGTTATATTTCATTTTTTGATATAAAAT 17 15 1 TATTATTTTT 0.759622 -286 TTTTTAACTATTTTATAATTTTATATCAAAAAA 17 32 0 TTTAATTTTA 0.853214 -269 TAGTTAAAAATAATTTACTTTTTTAAAGTTATA 17 55 1 TAATATTTTT 0.662735 -246 ATTTTTAACTTATTAGAATTTTTAATAATAAAA 17 92 0 TATAATTTTT 0.903541 -209 AAATTATATATGTTAAAATTTTTAACTTATTAG 17 109 0 TGTAATTTTT 0.399742 -192 ATCATAATATATATAGAGGTTTTGTATTATTAC 17 157 1 ATAAAGTTTT 0.464181 -144 CTTTTTTAATTTTAATAATTTTTTGATATTTTT 18 21 1 TTTAATTTTT 0.932551 -48 AGAAATCTTATTTAAAATATTTTTGGTTAAAAA 22 24 1 TTTAAATTTT 0.896245 -25 ATCTTTTTAATTTTTGTTTTATTAT 23 3 1 CTTTATTTTT 0.568491 -143 TTTGTTTTATTATTTTATTTTTATTAATTTATC 23 23 1 TATTATTTTA 0.570547 -123 AAGACTTACATATAAAAGTTTTTATTATTCTTT 23 66 0 TATAATTTTT 0.903529 -80 TATTATTTTTTAAGTAAATTTTAATTATCAAAA 23 97 0 TAATATTTTA 0.452383 -49 ACTTAAAAAATAATATAGATTTTTTTATATAGT 23 115 1 TAAAAATTTT 0.784441 -31 TATCACAAGATTAAAGAGGTTTTAAATAGATTT 25 19 1 TTAAAGTTTT 0.754856 -282 TGATAAGACCTTAATTAAATTTTAAATATTAAA 26 55 0 TTATAATTTT 0.644395 -76 CAATTAAATTTTTGATATGTTTTTGATTTGATG 26 88 0 TTTAAGTTTT 0.831984 -43 AGAAATAGGTTTTAATAGTTTTTC 27 2 0 TTTAATTTTT 0.932551 -68 GTGTTATTTGATATTTATTTTTTACCTTCTCTT 28 20 1 ATATATTTTT 0.449343 -69 TCTCTTTGTAATTTACAATTTTTAATTATAAAA 28 47 1 ATTAATTTTT 0.795491 -42 ATTATCACATTAAATTAGTTTTTATAATTAAAA 28 66 0 TAATATTTTT 0.661453 -23 AAATATTTAATAAATTTAATAGAGG 29 6 1 TTTAAATTTA 0.784088 -20 TCCTCATTTTAAATAGAAGTTTTTTGCGTTTTT 30 63 0 AAAAAGTTTT 0.369848 -29 GTATTATAATTTTCAAATTTTTAAATAATAGGA 31 13 0 TTTAATTTTA 0.853214 -136 ATGTTATTAAAAAAAGAAATTTTAACAATTATC 31 46 0 AAAAAATTTT 0.504627 -103 AAAATATAGAATATAAAGTTTTTCATTTAGTTT 31 86 0 ATAAATTTTT 0.7075 -63 AACTTTCACAATTTATATATTTATAAGGCACTT 32 222 0 ATTAAATTTA 0.505361 -79 GTAAAAGGGGATATATAAATTTTACGGTTTAAT 32 276 1 ATAAAATTTT 0.601782 -25 TTTAATAAATTTTTAATGAAAAT 33 1 1 TTTAAATTTT 0.896245 -122 CAATTTTGTTTAACACAAATTTTATATAATTAG 33 54 1 TAAAAATTTT 0.784441 -69 CTAATCAATCTTAATCATTTTTAAGGTAATTAA 33 92 0 TTATATTTTA 0.54941 -31 GTGCTTATAATTATTAAGATTTTTAGGATTTTT 34 180 0 TTATAATTTT 0.644397 -121 TAAATGTTTTTAACAAACATTTAATGTTTATAT 34 220 0 TAAAAATTTA 0.604724 -81 GCCTCTTTCATTTTAAATGTTTTTAACAAACAT 34 233 0 TTTAAGTTTT 0.831984 -68 AAAAAGTCATATAAATAGTTTTTTATTTTGTAA 36 55 0 ATAAATTTTT 0.707477 -59 ATATGACTTTTTTATTATTTTTAAGGTTCCACA 36 76 1 TTTTATTTTA 0.662271 -38 *** * * ***** Masking position 7 Map Score: 72.381 Number of sites scoring better than the average of aligned sites = 2892 Number in coding regions = 2018 Number in noncoding regions = 874 Number of orfs with sites within 600 bp upstream = 530 Fraction of orfs with sites within 600 bp upstream = 0.0851269 Motif number 3 ATTAGGGTATAAAAATTATAAAAAGATAGCTATC 1 238 0 AAAAATAAAA 0.923667 -63 ATAAAATTAAAAAAATCTTTAAAATCTTTAAAAA 2 152 0 AAAAATAAAA 0.923667 -149 TTTTATCCTAAAAATTACTAAAAAATGTTAAAAT 2 201 0 AAAATTAAAA 0.939743 -100 AAGTCCAAAAAATAAAACTTAAAATAAGATAATA 3 15 0 AATAAAAAAA 0.826075 -247 TAAAATTAAAAATAAAGTCCAAAAAATAAAACTT 3 29 0 AATAAAAAAA 0.826075 -233 AATATTCATAAAAATTATATAAAAAATAGAAAAA 4 13 0 AAAATTAAAA 0.939743 -122 GTTTATCAAAAATAATCGTTAAAAATACATCAAT 4 44 0 AATAATAAAA 0.859581 -91 TATTTTTGATAAACTACCGAAAAATATATATTAG 4 64 1 AAACTAAAAA 0.837776 -71 TGATATGAACAAAAATTTTTAATATCTAATATAT 4 89 0 AAAAATAATA 0.76256 -46 TTGTTCATATCATATAGCCTAAAATGGTGACAAT 4 111 1 CATATAAAAA 0.467369 -24 CACCAAAATAAAAATTATAAAAAATTAAAAA 5 8 0 AAAATTAAAA 0.939743 -29 AATAATTCAAAAAATGTGATAGT 6 1 1 AATAATAAAA 0.859581 -23 AATATAATTTAAAATTTAAAAAAATTTCTAA 7 60 1 AAAATTAAAA 0.939743 -21 AATAATATTTAAACTTAAGCAAAATTTTCAGTTC 8 24 0 AAACTTAAAA 0.869384 -72 ATTATTGCAGAATATATTCAAAAACAAACTTTAA 8 52 1 AATATAAAAA 0.859581 -44 TATGGGAAATAATATAAAATAAAAATTATTTTG 10 10 0 AATATAAAAA 0.859581 -34 CTTAAAGACTAAAAATAAAAAATAGAATTAAAGA 11 17 0 AAAAATAATA 0.76256 -167 ATAAAATTGAAATCATATATAAAAATTTTTATAC 11 126 0 AATCATAAAA 0.723189 -58 GTCCATAAAAAATAATAACAAAAAACTATTTATA 12 24 1 AATAATAAAA 0.859581 -59 AATGAGAAGTAATATTAAAGAAAATATATAAAGT 13 20 1 AATATTAAAA 0.887511 -72 TGATGAATTCAATCTAATGAAAAAATAAACACTA 15 26 1 AATCTAAAAA 0.723189 -100 CTTTTTACAGAAACATATTTAAAAGATGGTGTTA 15 60 1 AAACATAAAA 0.837776 -66 AAAAATAATAAAATAGTTCTATACC 15 111 0 AAAATAAATA 0.76256 -15 ATAAAATTATAAAATAGTTAAAAATAATTTACTT 17 41 1 AAAATAAAAA 0.923667 -260 TACATTTGTGAAAAATGTGGAAAATAATAGGGGC 17 187 1 AAAAATAAAA 0.923667 -114 CACCATACAAAAAATTAAAGAATAGTTGGCGATG 17 220 1 AAAATTAATA 0.80542 -81 TATCACCTAAAAAATATCAAAAAATTATTAAAAT 18 29 0 AAAATAAAAA 0.923667 -40 AAAATCCAGAAATCTTATTTAAAATATTTTTGGT 22 17 1 AATCTTAAAA 0.771021 -32 TAAATTAATAAAAATAAAATAATAAAACAAAAAT 23 20 0 AAAATAAATA 0.76256 -126 ATTACAGCTAAATAAACTCCAAAATAAACTACTC 25 198 0 AATAAAAAAA 0.826075 -103 ATCAAATCAAAAACATATCAAAAATTTAATTGGG 26 89 1 AAACATAAAA 0.837776 -42 AAATAAATATCAAATAACACAAAAGTGTT 28 6 0 CAAATAAAAA 0.634303 -83 TTCCTCAAATAAAAAACGCAAAAAACTTCTATTT 30 52 1 AAAAAAAAAA 0.903741 -40 TTATAATTTTCAAATTTTTAAATAATAGGATA 31 9 0 CAAATTAATA 0.372383 -140 CATATTAAGGAAACTAAATGAAAAACTTTATATT 31 76 1 AAACTAAAAA 0.837776 -73 TTTAACTGTTAAAAATATAGAATATAAAGTTTTT 31 96 0 AAAAATAATA 0.76256 -53 CAACAAAATTAAAAATCCTAAAAATCTTAATAAT 34 170 1 AAAAATAAAA 0.923667 -131 TGTAAATTTGAAAATATACAAATATGAATTAATT 36 26 0 AAAATAAATA 0.76256 -88 TGGAACCTTAAAAATAATAAAAAAGTCATATAAA 36 73 0 AAAATAAAAA 0.923667 -41 ****** **** Masking position 11 Map Score: 58.9774 Number of sites scoring better than the average of aligned sites = 1850 Number in coding regions = 1325 Number in noncoding regions = 525 Number of orfs with sites within 600 bp upstream = 353 Fraction of orfs with sites within 600 bp upstream = 0.0566977 Motif number 4 CGTTCCACCTTAAAAACTGATTCT 1 287 0 TCCACCTAAA 0.906162 -14 TTTATCACCAAAATAAAAATTATA 5 23 0 ATCACCAAAT 0.833941 -14 CCTATCACCTTAAATGATAAATTT 9 73 0 ATCACCTAAA 0.989435 -14 CCAATCACCAAAAAATGTTAAGGG 11 170 0 ATCACCAAAA 0.977456 -14 TTAAATCACCACTAATTTCTTTATC 13 77 0 ATCACCATAA 0.898534 -15 TGCCTACACAACCACCTTAAGAGGTGGCAAT 17 280 1 ACCACCTAAG 0.890309 -21 CACCCATTATATCACCTAAAAAATATCAAAA 18 41 0 ATCACCTAAA 0.989435 -28 AATATTAATAATCACCATTAATAAAATTAAT 24 22 0 ATCACCATAA 0.898534 -59 TTAAGGTCTTATCACATCAAATCAAAAACAT 26 74 1 ATCACATAAA 0.922178 -57 ATTATCACATTAAATTAGTTTTTA 28 75 0 ATCACATAAA 0.922178 -14 AGGTAATTTAATTACCTTAAAAATGATTAAG 33 85 1 ATTACCTAAA 0.860504 -38 AAATTACCACCTTAAAATTAATTCAT 36 6 1 ACCACCTAAA 0.979287 -108 TTCACCTCAAAAATTTGTGGA 36 103 0 TTCACCTAAA 0.95032 -11 ******* *** Masking position 4 Map Score: 14.0534 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 71 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 TCATATAAATTTTTATATTTAAATATATAAATT 1 207 0 TTTTAATTAA 0.525747 -94 TTTAAAGATTTTTTTAATTTTATCATTTTAATA 2 163 1 TTTTTATTAT 0.943622 -138 TAATTTTATCATTTTAATATTATTATTTTAACA 2 177 1 ATTTTATTAT 0.598908 -124 GTATATAAAATTTTCTATTTTATCCTAAAAATT 2 219 0 TTTTCATTAT 0.407203 -82 ACCAACCTTTTTGTTAATATATTACTACAGCTA 2 271 0 TTGTTATTTT 0.266265 -30 TCTTTATTATCTTATTTTAAGTTTT 3 3 1 TTTATATTAT 0.695182 -259 TTGGACTTTATTTTTAATTTTAAAATTTTAATT 3 41 1 TTTTTATTAA 0.92405 -221 CCATTAATATTATTTTATCTAAAACTTTTGATA 3 103 0 TATTTATTAA 0.244314 -159 CTTTTTTCTATTTTTTATATAATTTTTATGAAT 4 11 1 TTTTTATTAT 0.943595 -124 TGAACAAAAATTTTTAATATCTAATATATATTT 4 85 0 TTTTTATTTA 0.542042 -50 TTAAAAATTTTTGTTCATATCATATAGCCTAAA 4 101 1 TTGTTATTAT 0.78861 -34 TTTTTAATTTTTTATAATTTTTA 5 1 1 TTTTTATTTT 0.619496 -36 TCTTTTTTATATAATGAGGTCATAT 7 3 1 TTTTTATTAT 0.943595 -78 TTAGAAATTTTTTTAAATTTTAAATTATATTTG 7 58 0 TTTTAATTAA 0.525754 -23 TATCACCAAATTTTTTATATGATAATTTTAAAA 9 25 1 TTTTTATTAT 0.943624 -62 GATAAATTTCTTTTTAATGCAAAATTTTAAAAT 9 49 0 TTTTTATCAA 0.347782 -38 TAAAAAGAAATTTATCATTTAAGGTGATAGG 9 66 1 TTTATATTAG 0.217546 -21 CAAAATAATTTTTATTTTATATTATTTCCC 10 8 1 ATTTTATTAT 0.598923 -36 TTTAATTCTATTTTTTATTTTTAGTCTTTAAGA 11 19 1 TTTTTATTTA 0.542065 -165 ATACCAACACTTTTTTATATCAAACTTTTTAAA 11 70 1 TTTTTATTAA 0.923997 -114 GTATAAAAATTTTTATATATGATTTCAATTTTA 11 126 1 TTTTAATTAT 0.603937 -58 TATAAATAGTTTTTTGTTATTATTTTTTATGGA 12 25 0 TTTTTTTTAT 0.299394 -58 TAGTGTTTATTTTTTCATTAGATTGAATTCATC 15 27 0 TTTTTATAAT 0.734137 -99 TATTGATTATGTTATATTTCATTTT 17 3 1 TTGATATTAT 0.337024 -298 TATATTTCATTTTTTGATATAAAATTATAAAAT 17 23 1 TTTTTATTAA 0.924024 -278 ATAATTTACTTTTTTAAAGTTATAATTGTTTTA 17 64 1 TTTTTAATAT 0.449722 -237 CTTATTAGAATTTTTAATAATAAAACAATTATA 17 84 0 TTTTTATAAA 0.666528 -217 ATGTTTTTCTTTTTTAATTTTAATAATTTTTTG 18 13 1 TTTTTATTAA 0.92405 -56 TTTTTTGATATTTTTTAGGTGATATAATGGGTG 18 39 1 TTTTTAGTAT 0.648061 -30 GTTAAAGTTATTATTTATTTTATCATCATTATT 19 26 0 TTATTATTAT 0.326113 -35 TAATTTTTGTTTTATTATTTTATTTTTATTAAT 23 18 1 TTTATATTAT 0.695182 -128 TTTTTATTATTCTTTAATTTAAATGGATAAATT 23 48 0 TCTTTATTAA 0.468558 -98 TGTAAGTCTTTTGATAATTAAAATTTACTTAAA 23 89 1 TTGATATAAA 0.0564004 -57 ATCTATATTATTTTTTAAGTAAATTTTAATTAT 23 102 0 TTTTTAATAA 0.37272 -44 TAATATAGATTTTTTTATATAGTGGGTTTTT 23 125 1 TTTTTATTGT 0.720856 -21 AAAATTAAAGTTGTTGATGTGATAAA 24 65 1 TTGTTATTAT 0.788622 -16 GAATTTATTATCACAAGATTAAAGAG 25 4 1 TTTATATAAA 0.21479 -297 CTTAATTAAATTTTAAATATTAAACTTGAATAG 26 46 0 TTTTAATTAA 0.525657 -85 TTTTGATATGTTTTTGATTTGATGTGATAAGAC 26 79 0 TTTTTATTAT 0.943624 -52 TAATTTACAATTTTTAATTATAAAAACTAATTT 28 55 1 TTTTTATAAA 0.667424 -34 GTTTTTTGCGTTTTTTATTTGAGGAATTTTAGC 30 45 0 TTTTTATTAG 0.671108 -47 AAAATTTCTTTTTTTAATAACATATTAAGGAAA 31 56 1 TTTTTATAAT 0.73339 -93 GAATATAAAGTTTTTCATTTAGTTTCCTTAATA 31 78 0 TTTTTATTGT 0.720857 -71 TTTAATAAATTTTTAATGAAAATATTATACTA 33 10 1 TTTTTATAAA 0.666117 -113 ATCTTAATCATTTTTAAGGTAATTAAATTACCT 33 85 0 TTTTTAGTAT 0.648045 -38 AATCGGTCTGATTTTAATCTAAATAATCAAATT 34 29 1 ATTTTATTAA 0.520513 -272 TTCTAAGGGTTTGTTAATTTGATTATTTAGATT 34 44 0 TTGTTATTAT 0.788621 -257 AGTTCAAAGGATTTTTATTTAATTTCTAAGGGT 34 67 0 ATTTTATTAT 0.598921 -234 ATTTTTAGGATTTTTAATTTTGTTGTTTGGTTG 34 162 0 TTTTTATTGT 0.720858 -139 AATTTGTGCCTCTTTCATTTTAAATGTTTTTAA 34 240 0 TCTTTATTAA 0.468604 -61 ATATAAATAGTTTTTTATTTTGTAAATTTGAAA 36 47 0 TTTTTATTGT 0.720858 -67 GTTCCACAAATTTTTGAGGTGAA 36 101 1 TTTTTAGTAA 0.572431 -13 ***** ** * ** Masking position 7 Map Score: 56.82 Number of sites scoring better than the average of aligned sites = 1102 Number in coding regions = 818 Number in noncoding regions = 284 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 6 ATTGCATTCAACCTGTTAAACTTTCCTTTAAAG 1 31 1 ATGTTAAATT 0.963452 -270 ATTTTTTTAAAGATTTTAAAGATTTTTTTAATT 2 149 1 ATTTTAAAAT 0.779063 -152 AATAATATTAAAATGATAAAATTAAAAAAATCT 2 168 0 ATGATAAATT 0.759446 -133 AATTACTAAAAAATGTTAAAATAATAATATTAA 2 190 0 ATGTTAAATA 0.607799 -111 CCTCCAATTAAAATTTTAAAATTAAAAATAAAG 3 46 0 ATTTTAAATT 0.790293 -216 TTTTAATGCAAAATTTTAAAATTATCATATAAA 9 38 0 ATTTTAAATT 0.790293 -49 CTATCACCTTAAATGATAAATTTCTTTTTAATG 9 63 0 ATGATAAATT 0.759446 -24 TTTATATCAAACTTTTTAAAGTTCTTCAAATGC 11 83 1 ATTTTAAATT 0.921872 -101 AAATTTTTATATTTTCTAAACTTTATATATTTT 13 40 0 ATTCTAAATT 0.695144 -52 TAATTTCTTTATCTATTAAATTTTTATATTTTC 13 57 0 ATATTAAATT 0.753429 -35 CTATAACACCATCTTTTAAATATGTTTCTGTAA 15 64 0 ATTTTAAAAT 0.740142 -62 AGTAAATTATATATGTTAAAATTTTTAACTTAT 17 112 0 ATGTTAAATT 0.962721 -189 GTATTATTACATTTGTGAAAAATGTGGAAAATA 17 180 1 ATGTGAAAAT 0.779112 -121 AATATCAAAAAATTATTAAAATTAAAAAAGAAA 18 18 0 ATATTAAATT 0.751952 -51 GGTTTCACAATTGTTAAAGTTATTATTTATT 19 40 0 ATGTTAAATT 0.960832 -21 GACCTTAATTAAATTTTAAATATTAAACTTGAA 26 49 0 ATTTTAAAAT 0.671064 -82 AAGAAACACCACATGTGAAAGTTCATTT 30 6 0 ATGTGAAATT 0.924239 -86 TGTTTCTTTAATATGCTAAAATTCCTCAAATAA 30 31 1 ATGCTAAATT 0.830044 -61 TATTATTTAAAAATTTGAAAATTATAATACGAT 31 16 1 ATTTGAAATT 0.728701 -133 ATAATACGATAATTGTTAAAATTTCTTTTTTTA 31 39 1 ATGTTAAATT 0.960832 -110 GTTACAATTTAACTGTTAAAAATATAGAATATA 31 104 0 ATGTTAAAAT 0.88201 -45 TAAATATATAAATTGTGAAAGTTCTACAACGAC 32 232 1 ATGTGAAATT 0.921726 -69 CTTGTTGAATATGTTTGAAATTTGAAAATAAGA 34 120 0 ATTTGAAATT 0.805448 -181 * ******* ** Masking position 4 Map Score: 36.2844 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 246 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 7 ATTGATGGGCGAACTGACGCCACTTTTTAT 1 165 1 GAACTGACGC 0.959613 -136 TCCCACAATGGAACTTACGCAGAGGCTATA 2 22 1 GAACTTACGC 0.984845 -279 CTATTCAATAGAACTTACGCATTTTTTTGA 2 94 0 GAACTTACGC 0.984845 -207 ACAAGTGGAGGAACATACACTGGTCTGAAA 3 174 0 GAACATACAC 0.910677 -88 AAATGAACTTTCACATGTGGTGTT 30 5 1 GAACTTTCAC 0.956802 -87 TGTCGTTGTAGAACTTTCACAATTTATATA 32 236 0 GAACTTTCAC 0.956802 -65 ********** Masking position 3 Map Score: 5.49718 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 6 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 AGCTATGATGATTGATGGGCGAACTGACGCCA 1 155 1 ATGATGGGGA 0.910608 -146 ATAAAATAATATTAATGGAAGAGACTTTGAGA 3 118 1 ATAATGGAGA 0.597944 -144 TCTTTTTCTAACAAGTGGAGGAACATACACTG 3 182 0 AAAGTGGAGA 0.81486 -80 TATCATATAAAAAATTTGGTGATAAATTTATA 9 17 0 AAATTTGGGA 0.636362 -70 AGATGGTGTTATAGTTGGATGAAGTTGAGGTA 15 83 1 AAGTTGGAGA 0.899749 -43 AAAATTAAAGAATAGTTGGCGATGACGCTCCC 17 230 1 ATAGTTGGGA 0.654691 -71 TAATAAAATTAATGTTGGGAGATT 24 3 0 ATGTTGGGGA 0.965309 -78 ATAATGTTCTACAATTGGGTGAAGTCGTTAAC 25 100 1 AAATTGGGGA 0.926445 -201 TTTACAATTAATTGTTGGAGGAGTAGTTTATT 25 178 1 ATGTTGGAGA 0.899749 -123 ATTTATGTCCATAGGTGAGAGAGT 27 56 1 AAGGTGAGGA 0.683853 -14 TTATTTAAAAAATGGTGGGGGTGCTGGGATTT 32 34 1 ATGGTGGGGT 0.777372 -267 TTAGAAATGTAAAGTTGGGGGATTTAG 35 18 1 AAGTTGGGGA 0.965309 -17 * ******* ** Masking position 1 Map Score: 5.67794 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 182 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 GATACTTTTAGGCTTTCTTTATGATTCAAAA 2 69 1 GCTTTCTTTA 0.864122 -232 TTATTTTTTGGACTTTATTTTTAATTTTAAA 3 34 1 GCTTTATTTT 0.839557 -228 TTTCTTTCTTTAATTCTATTTT 11 2 1 TCTTTCTTTA 0.750191 -182 TTTAATTCTATTTTTTATTTTTAGTCTTTAA 11 19 1 TTTTTATTTT 0.749731 -165 AAACTTTATATATTTTCTTTAATATTACTTC 13 25 0 TTTTTCTTTA 0.784519 -67 GTAAAAAGTAGTGTTTATTTTTTCATTAGAT 15 37 0 GGTTTATTTT 0.894886 -89 AATTGCTTATGCTTTTCTTTAC 16 84 1 GTTTTCTTTA 0.88519 -12 AAATGTTTTTCTTTTTTAATTTTAA 18 5 1 GTTTTCTTTT 0.88519 -64 TTTGTTTTATTATTTTATTTTTATTAATTTA 23 23 1 TTTTTATTTT 0.749731 -123 GTTGGAGGAGTAGTTTATTTTGGAGTTTATT 25 191 1 TGTTTATTTT 0.800803 -110 GTTTATTTTGGAGTTTATTTAGCTGTAATTT 25 203 1 GGTTTATTTA 0.894886 -98 TAAATCCCCTGAGTTTATTTATTAATAATTG 25 279 0 GGTTTATTTA 0.894886 -22 TTCACATGTGGTGTTTCTTTAATATGCTAAA 30 20 1 GGTTTCTTTA 0.911869 -72 ATATAAATAGTTTTTTATTTTGTAAATTTGA 36 49 0 TTTTTATTTT 0.749731 -65 * ********* Masking position 6 Map Score: 9.90362 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 305 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 AAACTTTCCTTTAAAGATTTTATTCCTGCGA 1 48 1 TTAAAGATTT 0.807854 -253 GTATATATACTTAAAGCTACTTAATATATTT 1 95 1 TTAAAGCTCT 0.599057 -206 CAAAATTTTTTTAAAGATTTTAAAGATTTTT 2 145 1 TTAAAGATTT 0.807854 -156 ATTATCTTATTTTAAGTTTTATTTTTTGGAC 3 16 1 TTTAAGTTTA 0.386932 -246 ACTAAATTAATTAAAGTTTGTTTTTGAATAT 8 65 0 TTAAAGTTGT 0.792567 -31 ATCAAACTTTTTAAAGTTCTTCAAATGCTAA 11 88 1 TTAAAGTTTT 0.960357 -96 ATTTACTTTTTTAAAGTTATAATTGTTTTAT 17 67 1 TTAAAGTTTA 0.796342 -234 ATTATATATGTTAAAATTTTTAACTTATTAG 17 109 0 TTAAAATTTT 0.722215 -192 TTCACAATTGTTAAAGTTATTATTTATTTTA 19 37 0 TTAAAGTTTT 0.960355 -24 ATACAGTGTATTAAAGTTACTATAAAATGAG 21 51 1 TTAAAGTTCT 0.911052 -29 GACTTACATATAAAAGTTTTTATTATTCTTT 23 66 0 TAAAAGTTTT 0.674289 -80 AGTTTTAAAATTAAAGTTGTTGATGTGATAA 24 59 1 TTAAAGTTTT 0.960357 -22 CCTCTATTAAATTTATTAAATATTT 29 9 0 TTAAATTTTT 0.595893 -17 ACGATAATTGTTAAAATTTCTTTTTTTAATA 31 44 1 TTAAAATTCT 0.523675 -105 AATATAGAATATAAAGTTTTTCATTTAGTTT 31 86 0 ATAAAGTTTT 0.674524 -63 ATCAGAAAGATTTAAGTTATTTAAAAAATGG 32 18 1 TTTAAGTTTT 0.796356 -283 ******** ** Masking position 5 Map Score: 12.2508 Number of sites scoring better than the average of aligned sites = 533 Number in coding regions = 444 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 11 ********** No masking Map Score: -4.57346e-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 12 TGCAATTTAAATATATTAAGGAACTT 1 6 0 ATATATAAGG 0.698476 -295 AGAGATTGTTATAGATTAGGGTATAAAAATT 1 255 0 ATAGATAGGG 0.953125 -46 CGTAAGTTCTATTGAATAGGGCTCACCTCTG 2 105 1 ATTGATAGGG 0.970255 -196 ACTTTAATTAATTTAGTAGGGATAAGA 8 79 1 ATTTATAGGG 0.970827 -17 AAAATGTGGAAAATAATAGGGGCACCATACA 17 198 1 AAATATAGGG 0.788024 -103 CATATCAAAAATTTAATTGGGTATTGCGGAT 26 102 1 ATTTATTGGG 0.856399 -29 TATTTAATAAATTTAATAGAGG 29 14 1 ATTTATAGAG 0.787949 -12 AATGATTAAGATTGATTAGGGATAGGC 33 106 1 ATTGATAGGG 0.970255 -17 ***** ***** Masking position 5 Map Score: 2.64748 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 22 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 GTTATAGATTAGGGTATAAAAATTATAAAA 1 249 0 AGGGTATAAA 0.714302 -52 CTTTTTGTGAAGGGTATATAAATAGTTTTT 12 44 0 AGGGTATATA 0.92333 -39 GATATTTTTTAGGTGATATAATGGGTGATA 18 45 1 AGGTGATATA 0.851328 -24 AAATAAACTCAGGGGATTTAA 25 290 1 AGGGGATTTA 0.950507 -11 TTCCACATAAGGGGGATATT 31 139 1 GGGGGATATT 0.860478 -10 AAAAAGTAAAAGGGGATATATAAATTTTAC 32 271 1 AGGGGATATA 0.97785 -30 ATGTAAAGTTGGGGGATTTAG 35 24 1 GGGGGATTTA 0.928178 -11 ********** Masking position 6 Map Score: 1.918 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 62 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 ********** No masking Map Score: -4.57346e-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: -4.57346e-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