AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00770_mjan_reg_300.orf -o00770_mjan_300.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 Input sequences: #1 MJ0161 300 acetolactate synthase small subunit (ilvN) #2 MJ0277 183 acetolactate synthase large subunit (ilvB) #3 MJ0278 82 peptidyl-prolyl cis-trans isomerase, FKBP-type rotamase (slyD) #4 MJ0535 300 acetylpolyamine aminohydrolase (aphA) #5 MJ0663 27 acetolactate synthase large subunit (ilvB) #6 MJ1008 100 branched-chain amino acid aminotransferase (ilvE) #7 MJ1009 51 phosphate transport system regulatory protein (phoU) #8 MJ1010 300 M. jannaschii predicted coding region MJ1010 #9 MJ1276 217 dihydroxy-acid dehydratase (ilvD) #10 MJ1277 123 3-isopropylmalate dehydratase (leuD) #11 MJ1279 181 M. jannaschii predicted coding region MJ1279 #12 MJ1543 193 ketol-acid reductoisomerase (ilvC) Motif number 1 GATTAAAAGAAAATTTTCATAGTTTTTCGTA 1 34 1 AAATTTTATA 0.964123 -267 GAGGGTGTTCAATTTTTCATAACTAAATTTA 1 72 0 AATTTTTATA 0.976362 -229 TTGATTTGCATATTTTTGATAGGATATGACA 1 198 0 TATTTTTATA 0.922951 -103 TGATACCTGAAATTTTTGATTTGCATATTTT 1 213 0 AATTTTTATT 0.948751 -88 CTACTAAATATCTATTTTATTATTTTTAAAT 1 264 1 TCTATTTATT 0.555415 -37 TCTTTAATTCTATTTTTTATTTTTAGTCTTT 2 17 1 TATTTTTATT 0.842948 -167 GTTGGTATTTAATATTTAATTACTAATCTTA 2 47 0 AATATTTATT 0.892403 -137 AAATACCAACACTTTTTTATATCAAACTTTT 2 68 1 ACTTTTTATA 0.955447 -116 CTTAGTATAAAAATTTTTATATATGATTTCA 2 122 1 AAATTTTATA 0.964123 -62 GATAAAAAAGAGTTTTTGATACAATATTGTT 4 213 0 AGTTTTTATA 0.900489 -88 TATCCTAAATAATTTTTTATATCCCAAAAGA 4 254 1 AATTTTTATA 0.976357 -47 TTGCAAATAGACAATTTTATATATTAAATAT 6 39 1 ACAATTTATA 0.86213 -62 AAATAAAATGAATATTTAATATATAAAATTG 6 50 0 AATATTTATA 0.94874 -51 TTTTTATTTTTAATTTTAATAACTTTTGCAA 8 70 0 TAATTTTATA 0.886277 -231 GGGGGCGTTCAAATTTTTATTTTTAATTTTA 8 83 0 AAATTTTATT 0.923338 -218 AAAGAGATATACTTTTTAATTACTGGCAAAA 8 247 1 ACTTTTTATT 0.905762 -54 AAATTTACTATATATTTCATATCATTTTTTT 8 274 0 TATATTTATA 0.842984 -27 TCTTATATTTAGATTTTCATATTAAACAATA 10 25 1 AGATTTTATA 0.854805 -99 TTAAATATACAAATTTTTATATTTAAAACTA 11 27 1 AAATTTTATA 0.964123 -155 TTAAAAATTTAAAATTTTATATTAGTTTTAA 11 49 0 AAAATTTATA 0.923338 -133 AATACAGTAGAAATTTTTATATAGTTGAATG 11 92 1 AAATTTTATA 0.964123 -90 GCCATAATAAAATTTTTAATACTTTAAACTA 11 159 0 AATTTTTATA 0.97635 -23 ACTATTTAATTTTAGGATAAT 12 1 1 ACTATTTATT 0.811598 -193 ******* *** Masking position 6 Map Score: 39.8052 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 527 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 259 Fraction of orfs with sites within 600 bp upstream = 0.0415997 Motif number 2 AAATTAAGTTAAGATTAAAAGAAAATTTTCA 1 22 1 AAGATAAAAG 0.441176 -279 ATTAATTAACAAAAGAAAAATTAAGCCTTGT 1 170 1 AAAAAAAAAT 0.920786 -131 AGTAAGATTTAAAAATAATAAAATAGATATT 1 270 0 AAAATAATAA 0.828589 -31 CTTAAAGACTAAAAATAAAAAATAGAATTAA 2 20 0 AAAATAAAAA 0.920533 -164 ATCATATATAAAAATTTTTATACTAAGGATT 2 118 0 AAAATTTTAT 0.475233 -66 AAGTAATGATAAAATTGAAATCATATATAAA 2 137 0 AAAATGAAAT 0.945298 -47 CCAATCACCAAAAAATGTTAAGGGTAAAGTA 2 163 0 AAAATGTTAA 0.412354 -21 TTTGTCCATAAAAAATAATAACAAAAAACTA 3 21 1 AAAATAATAA 0.828589 -62 TTTATATCCCAAAAGAGAAATATTAAACTAA 4 269 1 AAAAAGAAAT 0.89317 -32 CTATTTGCAAAAAATAAAAATAGAGTCTATT 6 18 0 AAAAAAAAAT 0.920786 -83 TTGTCAAAATAAAAATAAAATGAATATTTAA 6 62 0 AAAATAAAAT 0.960042 -39 TTGGCAATATAAAAGTAAAATAAAGTATAG 7 10 0 AAAATAAAAT 0.960042 -42 TATATTGCCAAAAAATTATATGGAGGGAAAT 7 30 1 AAAATTATAT 0.817968 -22 AACTTTTGCAAAAACTATAAACACATCTTCA 8 50 0 AAAATATAAA 0.70041 -251 ATTAAAATTAAAAATAAAAATTTGAACGCCC 8 81 1 AAAAAAAAAT 0.920786 -220 ATGTTTTGCAAAAACTATAATGTTGCTATTG 8 151 1 AAAATATAAT 0.829027 -150 ATGACTTTAGAAAAGAGATATACTTTTTAAT 8 236 1 AAAAAGATAT 0.777228 -65 TTACTGGCAAAAAAATGATATGAAATATATA 8 266 1 AAAATGATAT 0.878214 -35 AATTACCACCAAAAAATAAAA 9 1 0 AAAAATAAAA 0.715248 -217 CTGGAATTTCAAAAGTTAAAGTTATCGTCTG 9 41 0 AAAATTAAAG 0.74375 -177 ATTTATTGATAAAAATAAATTCAAAAAGGAG 9 73 1 AAAATAAATT 0.654403 -145 AAATTTCATCAAGAAAAAAATCTTGGGAGAG 9 109 1 AAGAAAAAAT 0.586278 -109 AGATGTTGAAAAAATTGAAAAAGAATGTGAA 9 168 1 AAAATGAAAA 0.892838 -50 AATTTAGAAAAAAATTCAAATTCAGAAA 9 200 1 AAAATCAAAT 0.740941 -18 TAAATATAAGAAAATAGAAATAACA 10 5 0 AAAAAGAAAT 0.89317 -119 GATTATAACTAAAATAAAAAGTAAGTGAATA 10 74 0 AAAAAAAAAG 0.758051 -50 TTTTATATTTAAAACTAATATAAAATTTTAA 11 41 1 AAAATAATAT 0.909301 -141 ATATTGCTTAAAAATTTAAAATTTTATATTA 11 56 0 AAAATTAAAA 0.838495 -126 TTAAAGTATTAAAAATTTTATTATGGCAA 11 163 1 AAAATTTTAT 0.475432 -19 GCATTATCCTAAAATTAAATAGT 12 3 0 AAAATAAATA 0.477247 -191 AAATAAATTTAAAACATAAATGTTGGTTATA 12 60 0 AAAAATAAAT 0.838964 -134 **** ****** Masking position 4 Map Score: 37.022 Number of sites scoring better than the average of aligned sites = 2425 Number in coding regions = 1628 Number in noncoding regions = 797 Number of orfs with sites within 600 bp upstream = 439 Fraction of orfs with sites within 600 bp upstream = 0.0705108 Motif number 3 TTTCGTAAAGTTGTTAAATTTAGTTATGAAA 1 58 1 TTTTAAATTT 0.872312 -243 TGTCCTTTATCTTTAGAATATTTGCAAAAAC 1 122 1 CTTAGAATAT 0.599544 -179 ATGGTGAGTTCTACTAAATATCTATTTTATT 1 254 1 CTCTAAATAT 0.79609 -47 TATATCAAACTTTTTAAAGTTCTTCAAATGC 2 85 1 TTTTAAAGTT 0.707481 -99 AGTATAAAAATTTTTATATATGATTTCAATT 2 125 1 TTTTATATAT 0.624008 -59 TTTTTATCCACTCTAAAATATCCTAAATAAT 4 236 1 CTTAAAATAT 0.588279 -65 AAAATCTTTCTTGCTAAGTATCTTTGAAACT 8 19 0 TTCTAAGTAT 0.649015 -282 GCAAGAAAGATTTTTGAAGATGTGTTTATAG 8 36 1 TTTTGAAGAT 0.733921 -265 TTTATAGTTTTTGCAAAAGTTATTAAAATTA 8 60 1 TTCAAAAGTT 0.660672 -241 TTTTCGCATCTTTCTAAATATTTTCCTATAT 8 197 0 TTCTAAATAT 0.916861 -104 CTAAAGTCATTTGCAGAATTTTCGCATCTTT 8 215 0 TTCAGAATTT 0.852126 -86 CTCCTCAAATTTACTATATATTTCATATCAT 8 280 0 TTCTATATAT 0.711102 -21 AATTCTGGAATTTCAAAAGTTAAAGTTATCG 9 45 0 TTCAAAAGTT 0.660672 -173 ACTTTTGAAATTCCAGAATTTATTGATAAAA 9 56 1 TTCAGAATTT 0.852126 -162 TTCAAGCTCCTTTTTGAATTTATTTTTATCA 9 79 0 TTTTGAATTT 0.877424 -139 TTCCATAAGTTTATAGAATTTCTCTCCCAAG 9 130 0 TTTAGAATTT 0.795307 -88 TTTCTGAATTTGAATTTTTTT 9 207 0 TTCTGAATTT 0.913916 -11 TATTTCTATTTTCTTATATTTAGATTTTCAT 10 14 1 TTTTATATTT 0.603931 -110 TATTTCACCTTTTGAATATGATTAATGTA 10 105 0 CTTTGAATAT 0.733921 -19 AATATACAAATTTTTATATTTAAAACTAATA 11 30 1 TTTTATATTT 0.603931 -152 ATAGAAATAATTTTAAAGTATTTATTAGGTA 11 125 0 TTTAAAGTAT 0.403599 -57 CTCCGTGTAATTGCTAAATATCGTTTATAAC 12 35 1 TTCTAAATAT 0.916861 -159 ATAGTATCGATTTCTGAATATCAAATTAAAC 12 152 1 TTCTGAATAT 0.920352 -42 ** ******** Masking position 2 Map Score: 21.2519 Number of sites scoring better than the average of aligned sites = 1313 Number in coding regions = 1020 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 4 ATTTGCAAAAACCAATAATTTAGATGCCAAT 1 141 1 ACCAATATTT 0.9356 -160 AAATATGCAAATCAAAAATTTCAGGTATCAT 1 214 1 ATCAAAATTT 0.855576 -87 AATATTAAATACCAACACTTTTTTATATCAA 2 62 1 ACCAACATTT 0.696178 -122 GAAATCATATATAAAAATTTTTATACTAAGG 2 121 0 ATAAAAATTT 0.8452 -63 TTTCAATTTTATCATTACTTTACCCTTAACA 2 148 1 ATCATTATTT 0.74293 -36 TGAAGGGTATATAAATAGTTTTTTGTTATTA 3 36 0 ATAAATATTT 0.966779 -47 CCTAACCTTTCCAAATACTTTTTGTGAAGGG 3 60 0 CCAAATATTT 0.849902 -23 CTAAAATATCCTAAATAATTTTTTATATCCC 4 248 1 CTAAATATTT 0.924837 -53 CACCGTTTAAATCAATATTTTT 5 16 1 ATCAATATTT 0.969296 -12 TCGCATCTTTCTAAATATTTTCCTATATTGG 8 194 0 CTAAATATTT 0.924837 -107 ATTTATTTTTATCAATAAATTCTGGAATTTC 9 62 0 ATCAATAATT 0.756521 -156 AAGTAAGTGAATAAATAAGTTTTGTTTTCTG 10 56 0 ATAAATAGTT 0.809348 -68 TGGATACCTAATAAATACTTTAAAATTATTT 11 121 1 ATAAATATTT 0.966779 -61 AACTATTTATAGAAATAATTTTAAAGTATTT 11 133 0 AGAAATATTT 0.833218 -49 AATTATTTCTATAAATAGTTTAAAGTATTAA 11 144 1 ATAAATATTT 0.966779 -38 ******* *** Masking position 7 Map Score: 17.08 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 203 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 ATATCTATTTTATTATTTTTAAATCTTACTATAA 1 271 1 TATTTTAAAT 0.794287 -30 ATGTAACCGATATTATCGATAAACGTTTA 4 6 0 TATTTTAAAC 0.957115 -295 CATACAACAATGTTCTTCTTAAACAGACTATCAG 4 40 0 TGTTTTAAAC 0.981251 -261 AGAAGAACATTGTTGTATGGAAACGGGAGGTGTG 4 55 1 TGTTTGAAAC 0.962382 -246 CATACAATACTGTTCTCCTTAAACAATTTTAGAG 4 108 0 TGTTTTAAAC 0.981251 -193 AGGAGAACAGTATTGTATGGAAACCCATCATAGT 4 123 1 TATTTGAAAC 0.916091 -178 GATACAATATTGTTCTTCTTAAACACGAAATATA 4 193 0 TGTTTTAAAC 0.981251 -108 TATTTCAAAATGTTTTGCAAAAACTATAATGTTG 8 142 1 TGTTTAAAAC 0.903649 -159 TAAAATTTTATATTAGTTTTAAATATAAAAATTT 11 37 0 TATTGTAAAT 0.624092 -145 AAAACATAAATGTTGGTTATAAACGATATTTAGC 12 47 0 TGTTGTAAAC 0.957454 -147 **** * ***** Masking position 4 Map Score: 10.8853 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 64 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 TCCTTTATCTTTAGAATATTTGCAAAAACCA 1 124 1 TTAGAATATT 0.419576 -177 AAATTTTTGATTTGCATATTTTTGATAGGAT 1 204 0 TTTGCATATT 0.530496 -97 TTTTATTATTTTTAAATCTTACTATAAAAAG 1 278 1 TTTAAATCTA 0.550649 -23 TATCAAACTTTTTAAAGTTCTTCAAATGCTA 2 87 1 TTTAAAGTTT 0.56203 -97 TATAAAAATTTTTATATATGATTTCAATTTT 2 127 1 TTTATATATA 0.495002 -57 TTATATATGATTTCAATTTTATCATTACTTT 2 138 1 TTTCAATTTA 0.623638 -46 AATAGACAATTTTATATATTAAATATTCATT 6 44 1 TTTATATATA 0.495002 -57 AAGAAAGATTTTTGAAGATGTGTTTATAGTT 8 38 1 TTTGAAGATT 0.663495 -263 AAATTTTTATTTTTAATTTTAATAACTTTTG 8 73 0 TTTTAATTTA 0.377915 -228 GCAAAACATTTTGAAATATATAGGATATATA 8 129 0 TTGAAATATT 0.508101 -172 TTCGCATCTTTCTAAATATTTTCCTATATTG 8 195 0 TCTAAATATT 0.744911 -106 CAAGCTCCTTTTTGAATTTATTTTTATCAAT 9 77 0 TTTGAATTTT 0.877947 -141 TCACATTCTTTTTCAATTTTTTCAACATCTA 9 167 0 TTTCAATTTT 0.686615 -51 TTTCTGAATTTGAATTTTTTTCTAAATTC 9 199 0 TTTGAATTTT 0.877947 -19 AATATGAAAATCTAAATATAAGAAAATAGAA 10 17 0 TCTAAATATA 0.688325 -107 TATTTCACCTTTTGAATATGATTAATGTAGA 10 103 0 TTTGAATATA 0.889609 -21 AATTTGTATATTTAAATATATAGGTGAAAAT 11 11 0 TTTAAATATT 0.911293 -171 TTATATTAGTTTTAAATATAAAAATTTGTAT 11 33 0 TTTAAATATA 0.885961 -149 AATATAAAATTTTAAATTTTTAAGCAATATA 11 57 1 TTTAAATTTT 0.873976 -125 ACATTTATGTTTTAAATTTATTTCACTATAA 12 68 1 TTTAAATTTT 0.873975 -126 AGTATCGATTTCTGAATATCAAATTAAACCG 12 154 1 TCTGAATATA 0.696118 -40 ********* * Masking position 9 Map Score: 14.3691 Number of sites scoring better than the average of aligned sites = 1195 Number in coding regions = 844 Number in noncoding regions = 351 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 7 TAGGAAACCAAAAATTAAGTTAAGATTAA 1 10 1 AAAAATTAAG 0.93763 -291 TTTAGTTATGAAAAATTGAACACCCTCTAT 1 76 1 AAAAATTGAA 0.733272 -225 CAAATATTCTAAAGATAAAGGACATAATAA 1 116 0 AAAGATAAAG 0.839894 -185 TTAACAAAAGAAAAATTAAGCCTTGTCATA 1 175 1 AAAAATTAAG 0.93763 -126 CTTAAAGACTAAAAATAAAAAATAGAATTA 2 21 0 AAAAATAAAA 0.934599 -163 AAAATCGTGGAAAAAGAGAGGAGGTGACTA 4 153 0 AAAAAGAGAG 0.883933 -148 TGCAAAAAATAAAAATAGAGTCTATTCACT 6 14 0 AAAAATAGAG 0.943017 -87 TTGTCAAAATAAAAATAAAATGAATATTTA 6 63 0 AAAAATAAAA 0.934599 -38 AATATAAAAGTAAAATAAAGTATAG 7 6 0 TAAAATAAAG 0.779708 -46 TATTAAAATTAAAAATAAAAATTTGAACGC 8 80 1 AAAAATAAAA 0.934599 -221 ATTACCACCAAAAAATAAAA 9 1 0 AAAAATAAAA 0.934599 -217 ATTTATTGATAAAAATAAATTCAAAAAGGA 9 73 1 AAAAATAAAT 0.779029 -145 GAAAAAATTGAAAAAGAATGTGAAGAATTT 9 175 1 AAAAAGAATG 0.619599 -43 TAACTAAAATAAAAAGTAAGTGAATAAATA 10 70 0 AAAAAGTAAG 0.873709 -54 ********** Masking position 5 Map Score: 17.099 Number of sites scoring better than the average of aligned sites = 741 Number in coding regions = 529 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 8 CAACAATGTTCTTCTTAAACAGACTATCAG 4 40 0 CTTCTTAAAC 0.97257 -261 CAATACTGTTCTCCTTAAACAATTTTAGAG 4 108 0 CTCCTTAAAC 0.941082 -193 CAATATTGTTCTTCTTAAACACGAAATATA 4 193 0 CTTCTTAAAC 0.97257 -108 CCAAAAGAGAAATATTAAACTAAAAACCTA 4 277 1 AATATTAAAC 0.777203 -24 TTTAGATTTTCATATTAAACAATACAGAAA 10 32 1 CATATTAAAC 0.957535 -92 TTCTGAATATCAAATTAAACCGAAAACCTT 12 163 1 CAAATTAAAC 0.872671 -31 ********** Masking position 5 Map Score: 2.21326 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 43 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 9 TCTTTCGATAGAGGGTGTTCAATTTTTCAT 1 83 0 GAGGGTGTTC 0.979104 -218 GCCCCCAAGTGGGGGCGTTCAAATTTTTAT 8 94 0 GGGGGCGTTC 0.996923 -207 GCCCCCACTTGGGGGCGTTCATATATATCC 8 108 1 GGGGGCGTTC 0.996923 -193 ********** Masking position 8 Map Score: 1.92651 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 ATTTAGTAGAACTCACCATATAATAATTAT 1 243 0 ACTCACCATA 0.859161 -58 TCATTACTTTACCCTTAACATTTTTTGGTG 2 159 1 ACCCTTAACA 0.870828 -25 CTATTTATATACCCTTCACAAAAAGTATTT 3 49 1 ACCCTTCACA 0.981123 -34 TTGTATGGAAACCCATCATAGTCACCTCCT 4 135 1 ACCCATCATA 0.949299 -166 AATTTCCCTCCATATAATTTTTTG 7 38 0 TCCCTCCATA 0.857402 -14 TATCTTTGAAACTCTTCATAA 8 2 0 ACTCTTCATA 0.95421 -299 TTTTTTCTAAATTCTTCACATTCTTTTTCA 9 183 0 ATTCTTCACA 0.765487 -35 ********** Masking position 8 Map Score: 1.517 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 60 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TTTATCGATAATATCGGTTACATCTGATAG 4 17 1 ATATCGGTTA 0.922432 -284 CTAATCTCTAAAATTGTTTAAGGAGAACAG 4 103 1 AAATTGTTTA 0.918294 -198 TTAATATATAAAATTGTCTATTTGCAAAAA 6 36 0 AAATTGTCTA 0.724208 -65 ATATTTTCCTATATTGGTTAGCTCATTCAC 8 181 0 ATATTGGTTA 0.954547 -120 TTTGTTTTCTGTATTGTTTAATATGAAAAT 10 37 0 GTATTGTTTA 0.833497 -87 GTATTCAGGTATATTGCTTAAAAATTTAAA 11 67 0 ATATTGCTTA 0.886802 -115 TTATTTCTATAAATAGTTTAAAGTATTAAA 11 146 1 AAATAGTTTA 0.699996 -36 TAATTGCTAAATATCGTTTATAACCAACAT 12 42 1 ATATCGTTTA 0.923853 -152 TAAAACATAAATGTTGGTTATAAACGATAT 12 52 0 ATGTTGGTTA 0.8307 -142 ********** Masking position 4 Map Score: 3.03393 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 91 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 12 AGAATATTTGCAAAAACCAATAATTTAGAT 1 136 1 CAAAAACCAA 0.954595 -165 AATTAAATATTAAATACCAACACTTTTTTA 2 57 1 TAAATACCAA 0.883365 -127 AATATTAAACTAAAAACCTATTTT 4 287 1 TAAAAACCTA 0.783287 -14 ATAACTTTTGCAAAAACTATAAACACATCT 8 53 0 CAAAAACTAT 0.881908 -248 AAATGTTTTGCAAAAACTATAATGTTGCTA 8 149 1 CAAAAACTAT 0.881908 -152 ACATAGAATTTAAATACCATTAGAACACAA 12 104 0 TAAATACCAT 0.907935 -90 ATCGATACTATAAAAACCATATAATAATAA 12 133 0 TAAAAACCAT 0.957752 -61 ********** Masking position 6 Map Score: 3.19087 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 86 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 GGGTGTTCAATTTTTCATAACTAAATTTAA 1 71 0 TTTTTCATAA 0.607004 -230 TATGACGCTTTTGTCCATAAAAAATAATAA 3 12 1 TTGTCCATAA 0.875114 -71 TAAACGTTTATCGATAATATCGGTTAC 4 8 1 TTATCGATAA 0.461774 -293 CACACCTCCCGTTTCCATACAACAATGTTC 4 59 0 GTTTCCATAC 0.941769 -242 ACTATGATGGGTTTCCATACAATACTGTTC 4 127 0 GTTTCCATAC 0.941769 -174 TATCGTCTGTGTAGCCATAATTACCACCAA 9 20 0 GTAGCCATAA 0.824885 -198 GAATTTATTTTTATCAATAAATTCTGGAAT 9 65 0 TTATCAATAA 0.539648 -153 CATCTACACCTTTTCCATAAGTTTATAGAA 9 143 0 TTTTCCATAA 0.938618 -75 TATTTATTAGGTATCCATTCAACTATATAA 11 108 0 GTATCCATTC 0.724225 -74 ********** Masking position 7 Map Score: 0.951126 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 278 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 ********** No masking Map Score: -5.49717e-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: -5.49717e-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