AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_mjan_reg_100.orf -o00630_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: MJ0266 27 pyruvate ferredoxin oxidoreductase, subunit beta (porB) Input sequences: #1 MJ0005 87 formate dehydrogenase, beta subunit #2 MJ0006 300 formate dehydrogenase, alpha subunit #3 MJ0153 239 acetyl-CoA decarbonylase/synthase, subunit alpha (cdhA) #4 MJ0154 43 acetyl-CoA decarbonylase/synthase, subunit epsilon (cdhB) #5 MJ0213 114 M. jannaschii predicted coding region MJ0213 #6 MJ0214 89 hydrogenase expression/formation protein (hypA) #7 MJ0264 41 carbon monoxide dehydrogenase, iron sulfur subunit CooF-1 (cooF1) #8 MJ0265 42 carbon monoxide dehydrogenase, iron sulfur subunit CooF-1 (cooF2) #9 MJ0267 21 pyruvate ferredoxin oxidoreductase, subunit alpha (porA) #10 MJ0269 283 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #11 MJ0516 113 carbon monoxide dehydrogenase, hydrogenase subunit CooL (cooL) #12 MJ0713 146 hydrogenase expression regulatory protein (hypF) #13 MJ1027 125 formate hydrogenlyase, subunit 5 #14 MJ1235 284 ribulose bisphosphate carboxylase, large subunit (rbcL) #15 MJ1363 300 formate hydrogenlyase, subunit 7 #16 MJ1424 202 tRNA intron endonuclease (endA) #17 MJ1425 25 malate dehydrogenase Motif number 1 TAGTAATACTTATTTAAAATTCTATCTTATTTA 2 65 1 TTTTAAATTT 0.925387 -236 CTTATTTAAGTAATAATAATTTAAATTAAGTAG 2 90 1 TATAATATTA 0.563409 -211 CAACTATCATATATAAAATTTACTACTTAATTT 2 112 0 AATAAATTTC 0.550361 -189 TTGATACCTTTTTTAATATTTATTATGTCAATG 2 172 0 TTTAATTTTT 0.886946 -129 AAATTCTCTGTGTTTATTTTTGTCTAAGTTTTA 2 248 0 TTTTATTTTT 0.918521 -53 GTTCTATTTGTCATAAAAATTCTCTGTGTTTAT 2 264 0 TATAAAATTT 0.868163 -37 ATGCCCTATCATAAACTTTATATTTTATGCC 3 9 1 TATAAATTTT 0.912198 -231 TGCCAACACTAATTTATTTTTTTAAATTAATAG 3 38 1 ATTTATTTTT 0.854829 -202 AAATTACGCATTTTAAAAATTGTTTTGTAGGGA 3 88 0 TTTAAAATTT 0.896171 -152 AAACTTTAATATATAAAGTTTGTTATGACTAAA 3 168 0 AATAAATTTT 0.844402 -72 TCATGATTAATCATTATAATTTAAGGTTAGTTT 3 204 0 TATTATATTA 0.649652 -36 TAATTCTTTTACTTTAAATTTCTGAAGTTGGTG 4 15 1 ATTTAATTTT 0.910881 -29 ATTTTATAATTCTTTTTTATAAG 5 1 1 ATTTATATTT 0.788687 -114 TTTTGATAATACATTATATTTTCTCAACATTAA 5 39 1 AATTATTTTC 0.503299 -76 AATTATTAAGATTTTTATAGTTTTG 6 3 1 TATTAAATTT 0.904418 -87 ATATTATAACTTTTTATCTTTTTTAATCCCTT 7 20 1 TTTTATTTTT 0.918521 -22 GAAAGCTGGGAGATTAAGATTTATGACAGTAAT 10 13 1 AATTAAATTA 0.627036 -271 AATGATGTTGTATTTATTTTTGAGAATGACACT 10 114 0 TTTTATTTTA 0.793156 -170 TAATCCATGTAAATTAATTTTATTTTTTCTTAT 10 164 1 AATTAATTTT 0.886251 -120 TATATATTACTTTTAATAATTGTTAATGATTGA 10 238 1 TTTAATATTT 0.83257 -46 AAGCAATGCCTCTTAAAATTTATTGGGAGGAAT 11 87 1 TTTAAATTTT 0.931589 -27 TTTTTACGTTTAATTATGTTTGAATTTGTTTTA 12 14 1 TATTATTTTA 0.745258 -133 AATTTGTTTTATATAAACTTTATCATAAAATTT 12 36 1 AATAAATTTT 0.844402 -111 TTAATATACATATTAAATTTTATGATAAAGTTT 12 50 0 TTTAAATTTT 0.931589 -97 TAATTGATATTATTAAAATTTTTAATATACATA 12 71 0 TTTAAATTTT 0.931589 -76 ATTTGATTATTATTTAATTTTTTAATATGTAGT 12 114 0 TTTTAATTTT 0.951379 -33 TTAATTTTAAATTTGATTATTATTTA 12 131 0 ATTTAATTTA 0.776619 -16 AAGGTTAAGCTAATTATCATTATTAATTATGAT 13 43 1 TATTATATTT 0.844995 -83 CCTATTATCATGTTTATAATTGTTGG 13 110 1 TTTTATATTT 0.87723 -16 TAATTCTATTTGTTAAATTTTTTCAAAATATTA 14 39 1 TTTAAATTTT 0.931589 -246 AATTGATTTGATTTTAATATTTTGAAAAAATTT 14 53 0 ATTTAAATTT 0.86628 -232 ATTAATGAATTAATAAATTTTCATTCCGAATTG 14 81 0 TATAAATTTA 0.779364 -204 ATTTATTAATTCATTAATTTTACATTCATCCTT 14 96 1 TATTAATTTC 0.771015 -189 TATATATTTAAATTAATTATTGAACAGTAAAAT 14 162 0 ATTAATATTA 0.469079 -123 GTATTAAGTATTATTAATTTTTTGTATGGTCGT 14 234 0 TATTAATTTT 0.937189 -51 AATTTTTCAATTTTAAAGTTTTATTTTTAAGAG 15 63 0 TTTAAATTTA 0.822444 -238 GTAATACTTTTTATTAATTTTCCAATACCAAAA 15 97 1 TATTAATTTC 0.771015 -204 ATCTTTCGGATTTTTAAGATTATAAGTAGGTTG 15 135 0 TTTTAAATTT 0.925387 -166 TCTATTATGCATATTAAAATTCTCAATAAAGCA 15 220 1 AATTAAATTT 0.831723 -81 AAGCATAATCTATTTATATTTTATACATCACTA 15 248 1 TTTTATTTTA 0.793157 -53 CAGTAATTTATCATTATCATTAATGAC 15 284 0 ATTTATATTT 0.788687 -17 ATTAATTCATTCATTAATTTTGTTAAATAACAT 16 119 1 TATTAATTTT 0.937189 -84 ATTTATAAAATCTTAAAATTTATTGTGGATAAT 16 173 0 TTTAAATTTT 0.931589 -30 AATTAAAAATTTTTGGAGGGATA 17 1 1 ATTAAAATTT 0.818463 -25 * ***** *** * Masking position 6 Map Score: 58.773 Number of sites scoring better than the average of aligned sites = 2608 Number in coding regions = 1762 Number in noncoding regions = 846 Number of orfs with sites within 600 bp upstream = 540 Fraction of orfs with sites within 600 bp upstream = 0.0867331 Motif number 2 ACTGTGAAAGTCCTGTTTAAAAGAAATAACTA 1 56 1 TCTTTTAAAA 0.864261 -32 TCTTATCTTCAAAATTTTTAATGG 2 3 1 TATTTCAAAA 0.892196 -298 ATATCAACTAAACCATTAAAAATTTTGAAGAT 2 15 0 ACCTTAAAAA 0.835834 -286 TTTTCAACTATCATATATAAAATTTACTACTT 2 117 0 TATTATAAAA 0.82508 -184 TTGACATAATAAATATTAAAAAAGGTATCAAA 2 174 1 AATTTAAAAA 0.890625 -127 GAGTATCTATTAATTTAAAAAAATAAATTAGT 3 45 0 TATTAAAAAA 0.83804 -195 TAATAGATACTCATTTTTAAAAATCCCTACAA 3 65 1 TATTTTAAAA 0.864599 -175 ATTTTTAAAAATCCCTACAAAACAATTTTTAA 3 77 1 ACCTACAAAA 0.816304 -163 AAAAAATTACGCATTTTAAAAATTGTTTTGTA 3 92 0 GATTTAAAAA 0.747581 -148 TATCAAAACTTACCTTATAAAAAAGAATTATA 5 15 0 TCCTATAAAA 0.746798 -100 TCCTTAATCCAACTTTTTAAAAAGGTTTAATC 6 35 0 ACTTTTAAAA 0.880974 -55 TCAACAATAAAGCTGTTTAAAAATCAAATCGG 10 46 1 ACTTTTAAAA 0.880974 -238 TTAATTGCTTAAATCTCCAAAACTTTATATAT 10 213 1 AATTCCAAAA 0.765842 -71 AAACATAATTAAACGTAAAAAATT 12 3 0 AACTAAAAAA 0.790445 -144 AATTTAATATGTATATTAAAAATTTTAATAAT 12 64 1 GATTTAAAAA 0.747581 -83 AATATCAATTAGATTTTCAAAACTACATATTA 12 93 1 AATTTCAAAA 0.905844 -54 TTTCAAAACTACATATTAAAAAATTAAATAAT 12 107 1 AATTTAAAAA 0.890625 -40 ATTAAAACAAAACTATATAAAAGGTTAAGCTA 13 23 1 ACTTATAAAA 0.845387 -103 TAATTTTATGTGCCTTTCAAAACTGTTTAATT 14 12 1 TCCTTCAAAA 0.838048 -273 TATTTTAACCAAATATAAAAAAGGATGAATGT 14 117 0 AATTAAAAAA 0.857456 -168 TATTAGAAACGACCATACAAAAAATTAATAAT 14 226 1 GCCTACAAAA 0.617775 -59 TCGAACCCTAAAACATACAAAATAAAAACAAA 15 21 1 AACTACAAAA 0.816735 -280 AACTCATAAATTCTCTTAAAAATAAAACTTTA 15 51 1 TCTTTAAAAA 0.87476 -250 AACCTACTTATAATCTTAAAAATCCGAAAGAT 15 136 1 TATTTAAAAA 0.875075 -165 AAAATCCGAAAGATTTCTAAAACCTGTTCGCT 15 154 1 AATTCTAAAA 0.716188 -147 TGACAAATAGTGATGTATAAAATATAAATAGA 15 256 0 TATTATAAAA 0.825078 -45 TTCGCAGTTTTTATATTAAAAAGGTATTTAGA 16 80 0 TATTTAAAAA 0.875067 -123 AGTTATTATTTATAAAATCTTAAAATT 16 186 0 TATTATAAAA 0.824324 -17 TATATCCCTCCAAAAATTTTTAATT 17 11 0 ACCTCCAAAA 0.67159 -15 * ** ******* Masking position 6 Map Score: 32.7381 Number of sites scoring better than the average of aligned sites = 1857 Number in coding regions = 1352 Number in noncoding regions = 505 Number of orfs with sites within 600 bp upstream = 351 Fraction of orfs with sites within 600 bp upstream = 0.0563765 Motif number 3 TACTACTATTATTAGATTTTCTAATATCAA 2 40 0 ATTAGATTTT 0.749623 -261 TTTGATACCTTTTTTAATATTTATTATGTC 2 176 0 TTTTTAATAT 0.635335 -125 TTTTGTCTAAGTTTTAATTTTGATTTCTAG 2 234 0 GTTTTAATTT 0.817178 -67 TATCATAAACTTTATATTTTATGCCAACAC 3 17 1 TTTATATTTT 0.695693 -223 ATGATTAATCATTATAATTTAAGGTTAGTT 3 205 0 ATTATAATTT 0.749934 -35 TTGATAATACATTATATTTTCTCAACATTA 5 41 1 ATTATATTTT 0.806297 -74 AAATGAAGACATTTTAATGTTGAGAAAATA 5 55 0 ATTTTAATGT 0.493954 -60 ACCAAAAACTATTTTAATTTTAGTAAAAAA 8 22 0 ATTTTAATTT 0.896928 -21 ATAATAGCCGATTTGATTTTTAAACAGCTT 10 55 0 ATTTGATTTT 0.896777 -229 ATGTAAATTAATTTTATTTTTTCTTATGCC 10 170 1 ATTTTATTTT 0.923539 -114 GTTTAATTATGTTTGAATTTGTTTTATATA 12 21 1 GTTTGAATTT 0.762748 -126 ATTATTAAAATTTTTAATATACATATTAAA 12 66 0 TTTTTAATAT 0.635335 -81 AATAATATCAATTAGATTTTCAAAACTACA 12 90 1 ATTAGATTTT 0.749623 -57 TTTGATTATTATTTAATTTTTTAATATGTA 12 116 0 ATTTAATTTT 0.492427 -31 TTAATTTTAAATTTGATTATTATTTAATTT 12 127 0 ATTTGATTAT 0.760014 -20 TTCCGAATTGATTTGATTTTAATATTTTGA 14 61 0 ATTTGATTTT 0.896777 -224 TATGAGTTTGTTTTTATTTTGTATGTTTTA 15 29 0 TTTTTATTTT 0.869004 -272 CAATTTTAAAGTTTTATTTTTAAGAGAATT 15 59 0 GTTTTATTTT 0.861188 -242 TAAGTAGGTTGTTTGATTTTGGTATTGGAA 15 116 0 GTTTGATTTT 0.816925 -185 CATAATAGATTTTTTAATTTAATTTCTTGC 15 199 0 TTTTTAATTT 0.826975 -102 TTTATTGAGAATTTTAATATGCATAATAGA 15 220 0 ATTTTAATAT 0.759933 -81 GCATAATCTATTTATATTTTATACATCACT 15 250 1 TTTATATTTT 0.695693 -51 TCTAAATACCTTTTTAATATAAAAACTGCG 16 80 1 TTTTTAATAT 0.635335 -123 TATGTTATTTATTTTATTATCCACAATAAA 16 158 1 ATTTTATTAT 0.814776 -45 ********** Masking position 3 Map Score: 30.3977 Number of sites scoring better than the average of aligned sites = 1357 Number in coding regions = 860 Number in noncoding regions = 497 Number of orfs with sites within 600 bp upstream = 358 Fraction of orfs with sites within 600 bp upstream = 0.0575008 Motif number 4 AAGTCCTGTTTAAAAGAAATAACTAAGGTGA 1 63 1 TAAAAGAATA 0.914669 -25 TAGAATTTTAAATAAGTATTACTACTATTAT 2 58 0 AATAAGATTA 0.623159 -243 TGATAGTTGAAAATAGTATTAATATATTAGT 2 136 1 AAATAGATTA 0.775713 -165 AGTATTAATATATTAGTAATATCATTGACAT 2 150 1 TATTAGAATA 0.148128 -151 ATTTTTTTGTTAAAAGAAAAATTCAGTCCTT 3 117 1 TAAAAGAAAA 0.494745 -123 ACTTTATATATTAAAGTTTTAAAAACTAACC 3 182 1 TTAAAGTTTA 0.535911 -58 AAATTTAAAGTAAAAGAATTAGGAG 4 5 0 TAAAAGATTA 0.94175 -39 TTACCTTATAAAAAAGAATTATAAAAT 5 7 0 AAAAAGATTA 0.949644 -108 CCAACTTTTTAAAAAGGTTTAATCAAAACTA 6 28 0 AAAAAGTTTA 0.934357 -62 TAAAAAAGATAAAAAGTTATAATATTACAAC 7 14 0 AAAAAGTATA 0.902343 -28 ATTTTAGTAAAAAAAGAAATTTTAA 8 5 0 AAAAAGAATT 0.520044 -38 TTTGATTTTTAAACAGCTTTATTGTTGAATT 10 43 0 AAACAGTTTA 0.54284 -241 TGTCATTCTCAAAAATAAATACAACATCATT 10 116 1 AAAAATAATA 0.584321 -168 TAACAATTATTAAAAGTAATATATAAAGTTT 10 232 0 TAAAAGAATA 0.913238 -52 CCATGATGAAAGAATTATTCAGAAACC 11 7 1 TGAAAGATTA 0.707044 -107 ATATGTATATTAAAAATTTTAATAATATCAA 12 70 1 TAAAAATTTA 0.24067 -77 CAAAACTATATAAAAGGTTAAGCTAATTATC 13 30 1 TAAAAGTTAA 0.53071 -96 ATAAACATGATAATAGGTATATGACTCACTA 13 96 0 TAATAGTATA 0.599481 -30 AAAATTTAACAAATAGAATTAAACAGTTTTG 14 29 0 AAATAGATTA 0.777321 -256 ACCAAATATAAAAAAGGATGAATGTAAAATT 14 111 0 AAAAAGATGA 0.591661 -174 AAATAGTGTTAGAAAGCTTTACCTTTAGTTT 14 194 0 AGAAAGTTTA 0.676936 -91 CGACCATACAAAAAATTAATAATACTTAATA 14 235 1 AAAAATAATA 0.583981 -50 TTTTTCAATTTTAAAGTTTTATTTTTAAGAG 15 63 0 TTAAAGTTTA 0.535911 -238 GAAAATTAATAAAAAGTATTACTAATTTTTC 15 88 0 AAAAAGATTA 0.948159 -213 TTCGCAGGAATAAATGATTTATTGAATAATG 16 36 1 TAAATGTTTA 0.371057 -167 TTTTTATATTAAAAAGGTATTTAGATGCCTA 16 74 0 AAAAAGTATT 0.449882 -129 TTGTGGATAATAAAATAAATAACATATGGTT 16 153 0 TAAAATAATA 0.549803 -50 ATATCCCTCCAAAAATTTTTAATT 17 4 0 AAAAATTTTA 0.597665 -22 ****** **** Masking position 5 Map Score: 15.2436 Number of sites scoring better than the average of aligned sites = 1521 Number in coding regions = 1242 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 5 CCTCAAGGTATTTAGATGCCTAAAAGCGTCAAT 1 15 0 TTATGCCTAA 0.871551 -73 TTAGTTGATATTAGAAAATCTAATAATAGTAGT 2 36 1 TTAAATCTAA 0.719083 -265 AGTAATATCATTGACATAATAAATATTAAAAAA 2 164 1 TTATAATAAA 0.649648 -137 AAATCTAAGATTAGTAAGATAAAGGAAAGCTAG 2 205 1 TTAAGATAAA 0.636789 -96 ACACAGAGAATTTTTATGACAAATAGAACATTT 2 268 1 TTATGACAAA 0.776791 -33 ATCTATTAATTTAAAAAAATAAATTAGTGTTGG 3 40 0 TTAAAATAAA 0.66369 -200 AAAACAATTTTTAAAATGCGTAATTTTTTTGTT 3 95 1 TTATGCGTAA 0.515031 -145 TCAGTCCTTATTTTCATACCAAACTTGGCTTTA 3 139 1 TTATACCAAA 0.745552 -101 TATATAAAGTTTGTTATGACTAAAGCCAAGTTT 3 159 0 TTATGACTAA 0.899463 -81 TATATTAAAGTTTTAAAAACTAACCTTAAATTA 3 188 1 TTAAAACTAA 0.91226 -52 TAACCTTAAATTATAATGATTAATCATGACAAT 3 208 1 TTATGATTAA 0.813516 -32 ATATAATGTATTATCAAAACTTACCTTATAAAA 5 25 0 TTAAAACTTA 0.325189 -90 ACATTATATTTTCTCAACATTAAAATGTCTTCA 5 49 1 TTAACATTAA 0.527082 -66 ATTTCTTTTTTTACTAAAATTAAAATAGTTTTT 8 16 1 TTAAAATTAA 0.833854 -27 AATAAAGCTGTTTAAAAATCAAATCGGCTATTA 10 51 1 TTAAATCAAA 0.502427 -233 TATAGTGTCATTCTCAAAAATAAATACAACATC 10 111 1 TTAAAAATAA 0.509579 -173 ATTTTATTTTTTCTTATGCCTAAACTATTTTCG 10 180 1 TTATGCCTAA 0.873526 -104 TCATTAACAATTATTAAAAGTAATATATAAAGT 10 234 0 TTAAAAGTAA 0.615561 -50 GAAAATCTAATTGATATTATTAAAATTTTTAAT 12 78 0 TTATTATTAA 0.398368 -69 AATATGTAGTTTTGAAAATCTAATTGATATTAT 12 91 0 TTAAATCTAA 0.720662 -56 CTCGATAACTTTATTAAAACAAAACTATATAAA 13 11 1 TTAAAACAAA 0.801249 -115 AATAGATAATTTATCATAATTAATAATGATAAT 13 55 0 TTATAATTAA 0.826218 -71 GTTAAATTTTTTCAAAATATTAAAATCAAATCA 14 50 1 TTAATATTAA 0.41777 -235 TTACCTTTAGTTTATATATTTAAATTAATTATT 14 174 0 TTATATTTAA 0.540519 -111 AAAAACTATTTCGAACCCTAAAACATACAAA 15 9 1 TTAACCCTAA 0.63741 -292 TTTATTAATTTTCCAATACCAAAATCAAACAAC 15 106 1 TTATACCAAA 0.745554 -195 ATTGAGAATTTTAATATGCATAATAGATTTTTT 15 214 0 TTATGCATAA 0.404989 -87 TAAAAAGGTATTTAGATGCCTAAAGGCATCATT 16 63 0 TTATGCCTAA 0.871551 -140 TTTATGTTATTTAACAAAATTAATGAATGAATT 16 122 0 TTAAAATTAA 0.835619 -81 ** ******** Masking position 6 Map Score: 23.9957 Number of sites scoring better than the average of aligned sites = 994 Number in coding regions = 739 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 6 TGATAGTTGAAAATAGTATTAATATATTAG 2 136 1 AAATAGTATT 0.796235 -165 TAAAAAAATAAATTAGTGTTGGCATAAAAT 3 32 0 AATTAGTGTT 0.886004 -208 CGCATTTTAAAAATTGTTTTGTAGGGATTT 3 85 0 AAATTGTTTT 0.892055 -155 TGGATTAAGGAAATTGTTATTAAAGGGCTA 6 56 1 AAATTGTTAT 0.689803 -34 TAAAAAAGATAAAAAGTTATAATATTACAA 7 15 0 AAAAAGTTAT 0.448662 -27 ACTAAAATTAAAATAGTTTTTGGTG 8 28 1 AAATAGTTTT 0.968428 -15 CTTAGTAATTTAGTGTTTATT 9 5 0 ATTTAGTGTT 0.574269 -17 CAATTAACGAAAATAGTTTAGGCATAAGAA 10 190 0 AAATAGTTTA 0.73793 -94 ATTATGTTTGAATTTGTTTTATATAAACTT 12 26 1 AATTTGTTTT 0.75913 -121 TAATAATATCAATTAGATTTTCAAAACTAC 12 89 1 AATTAGATTT 0.517558 -58 TTAACCTTTTATATAGTTTTGTTTTAATAA 13 21 0 ATATAGTTTT 0.842209 -105 AAATAGAATTAAACAGTTTTGAAAGGCACA 14 20 0 AAACAGTTTT 0.817731 -265 TTTCTAATATAAATAGTGTTAGAAAGCTTT 14 205 0 AAATAGTGTT 0.953259 -80 TTAGGGTTCGAAATAGTTTTT 15 2 0 AAATAGTTTT 0.968428 -299 CATTAATGACAAATAGTGATGTATAAAATA 15 264 0 AAATAGTGAT 0.845775 -37 ********** Masking position 1 Map Score: 12.9215 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 175 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 TTAAATTATTATTACTTAAATAAGATAGAAT 2 83 0 ATTCTTAAAT 0.798082 -218 TATAAAATTTACTACTTAATTTAAATTATTA 2 103 0 ACTCTTAATT 0.89956 -198 AAAAATGAGTATCTATTAATTTAAAAAAATA 3 52 0 ATCATTAATT 0.610549 -188 CACTTCTTAATTGTCATGATTA 3 228 0 ACTCTTAATT 0.899559 -12 CAACATTAAAATGTCTTCATTTTAATCTCGC 5 63 1 ATGCTTCATT 0.738088 -52 TCCTTTTTTAACTCCTTCAATATAATAGCCG 10 75 0 ACTCTTCAAT 0.761083 -209 ATTTTCGTTAATTGCTTAAATCTCCAAAACT 10 206 1 ATTCTTAAAT 0.797443 -78 TTTAAGAGGCATTGCTTCTTTGCAGAAGCAA 11 73 0 ATTCTTCTTT 0.617689 -41 AAATTTGATTATTATTTAATTTTTTAATATG 12 118 0 ATTTTTAATT 0.792148 -29 ATGATAAATTATCTATTCATTACCTTAGTGA 13 71 1 ATCATTCATT 0.655801 -55 GCCTTTCAAAACTGTTTAATTCTATTTGTTA 14 23 1 ACTTTTAATT 0.716477 -262 ATGAAAATTTATTAATTCATTAATTTTACAT 14 90 1 ATTATTCATT 0.857746 -195 TGCATAATAGATTTTTTAATTTAATTTCTTG 15 200 0 ATTTTTAATT 0.792132 -101 GAAGTTCTATATTAATTCATTCATTAATTTT 16 109 1 ATTATTCATT 0.857746 -94 *** ******* Masking position 1 Map Score: 7.65022 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 462 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 8 TAATAGATACTCATTTTTAAAAATCCCTAC 3 65 1 TCATTTTTAA 0.730501 -175 TTCTTAATTGTCATGATTAATCATTATAAT 3 217 0 TCATGATTAA 0.779383 -23 TGCTATAGTGTCATTCTCAAAAATAAATAC 10 108 1 TCATTCTCAA 0.887555 -176 TCATTATCAATCATTAACAATTATTAAAAG 10 247 0 TCATTAACAA 0.823823 -37 CCTTAAACTGTCATTATCAATCATTAACAA 10 257 0 TCATTATCAA 0.967436 -27 AAGCTAATTATCATTATTAATTATGATAAA 13 49 1 TCATTATTAA 0.93768 -77 CAGTAATTTATCATTATCATTAATGACAAA 15 281 0 TCATTATCAT 0.824095 -20 CCTAAAGGCATCATTATTCAATAAATCATT 16 48 0 TCATTATTCA 0.880795 -155 GTTATTTATTTTATTATCCACAATAAATTT 16 161 1 TTATTATCCA 0.587441 -42 ********** Masking position 4 Map Score: 3.62871 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 154 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 GATATCACCTTAGTTATTTCTTTT 1 74 0 TCACCTTAGT 0.951446 -14 AATATCACCTAAATGTTCTATTTG 2 287 0 TCACCTAAAT 0.858069 -14 TTTTAAAAACTAACCTTAAATTATAATGAT 3 198 1 TAACCTTAAA 0.776708 -42 TTATCAAAACTTACCTTATAAAAAAGAATT 5 18 0 TTACCTTATA 0.684373 -97 TTAATAACAATTTCCTTAATCCAACTTTTT 6 49 0 TTTCCTTAAT 0.716453 -41 ACACTCACCTTAAACTGTCATTAT 10 270 0 TCACCTTAAA 0.947787 -14 TATCTATTCATTACCTTAGTGAGTCATATA 13 80 1 TTACCTTAGT 0.904651 -46 AGATTCACCTCAATATTATAGAAC 16 5 1 TCACCTCAAT 0.899603 -198 ********** Masking position 8 Map Score: 1.30946 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 52 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 ********** No masking Map Score: -1.4826e-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 11 ********** No masking Map Score: -1.4826e-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 ********** No masking Map Score: -1.4826e-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