AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_mjan_reg_300.orf -o00500_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 Purged sequences: MJ0086 36 unspecified methyltransferase Input sequences: #1 MJ0081 300 methyl coenzyme M reductase II, subunit beta (mrtB) #2 MJ0084 261 CODH nickel-insertion accessory protein (cooC) #3 MJ0085 134 iron transport periplasmic binding protein, putative (ceuE) #4 MJ0087 23 hemin permease (hemU) #5 MJ0090 80 collagenase (prtC) #6 MJ0091 95 Na+/Ca+ exchanger protein, putative #7 MJ0448 130 conserved hypothetical protein #8 MJ0555 300 endoglucanase (celM) #9 MJ0822 300 S-layer structural protein #10 MJ0869 119 DNA repair protein RAD51 (radA) #11 MJ0968 55 copper transporting P type ATPase (copA) #12 MJ1149 59 mutator MutT protein, putative (mutT) #13 MJ1334 214 UDP-glucose pyrophosphorylase (gtaB) #14 MJ1505 178 ATP dependent RNA helicase, putative #15 MJ1574 300 ATP-dependent RNA helicase, eIF-4A family, putative #16 MJ1605 37 glucose-6-phosphate isomerase #17 MJ1606_MJ1607 167 MJ1606: glycogen synthase (glgA), MJ1607: LPS biosynthesis protein, putative #18 MJ1608 31 M. jannaschii predicted coding region MJ1608 #19 MJ1609 38 M. jannaschii predicted coding region MJ1609 #20 MJ1610 233 glucoamylase (cga) #21 MJ1611 21 alpha-amylase (amyA) Motif number 1 TCTGTGAGGAATTCAAAATTTTTTTAAAGAT 1 132 1 ATCAAAATTT 0.856439 -169 AGTAATAGGTATATAAAATTTTCTATTTTAT 1 229 0 ATTAAAATTT 0.938483 -72 AAATTTTAAAATTAAAAATAAAGTCCAAAAA 2 38 0 ATAAAAATAA 0.789675 -224 ATGCCCTCCAATTAAAATTTTAAAATTAAAA 2 52 0 ATAAAATTTT 0.952902 -210 CAAACATTTTATCAAAAGTTTTAGATAAAAT 2 94 1 ATAAAAGTTT 0.815923 -168 AGTCTCTTCCATTAATATTATTTTATCTAAA 2 113 0 ATAATATTAT 0.785891 -149 CCTCAGTCTGATTTAAATTTAATTAAAACCT 2 234 0 ATTAAATTTA 0.737273 -28 TAAAAATTATATAAAAAATAGAAAAAAG 3 8 0 ATAAAAATAG 0.755418 -127 ATCAATATTCATAAAAATTATATAAAAAATA 3 19 0 ATAAAATTAT 0.901666 -116 TCGGTAGTTTATCAAAAATAATCGTTAAAAA 3 53 0 ATAAAAATAA 0.789675 -82 TTAATATCTAATATATATTTTTCGGTAGTTT 3 74 0 ATTATATTTT 0.803498 -61 TATATTAGATATTAAAAATTTTTGTTCATAT 3 90 1 ATAAAAATTT 0.967904 -45 TTCAAATATAATTTAAAATTTAAAAAAATTT 5 56 1 ATTAAAATTT 0.938484 -25 TATGGATGAACTGAAAATTTTGCTTAAGTTT 6 17 1 CTAAAATTTT 0.64202 -79 TTTGTTATAGATTAAAAATTGGTGAATATTT 7 11 0 ATAAAAATTG 0.871823 -120 TAATCATCAAATAAATATTTTGTTATAGATT 7 29 0 ATAATATTTT 0.889901 -102 GTAGCATCAGATTTATATTTTCCCGCATTTG 7 73 0 ATTATATTTT 0.803502 -58 CATAACTGCTATAAAAAATATTTGGTGACAT 7 109 1 ATAAAAATAT 0.931854 -22 TTTCTTCACCATCAAAAATTTACCAAAATCT 8 111 0 ATAAAAATTT 0.967904 -190 TAAAACATAAATCTAAAATAGTTGGATTAGG 8 244 1 ATTAAAATAG 0.609765 -57 TTTTAAATGGATAAAAATTAATTTTGATATA 9 81 0 ATAAAATTAA 0.715827 -220 ACAAAATTTAATTTATAATATCGCTCTATTA 9 145 0 ATTATAATAT 0.734586 -156 TATCTTTGTTATACAAAATTTAATTTATAAT 9 157 0 ATCAAAATTT 0.856439 -144 TAGTTTCTGAATGAAAAATTTTATTATATCT 9 183 0 ATAAAAATTT 0.967904 -118 AGAATAGTAAATATATAATTGAGGAGGTGTA 10 14 0 ATTATAATTG 0.578888 -106 ATTTGACTATATAAAGATTTTGGTTTATAAC 10 85 0 ATAAGATTTT 0.788123 -35 ACGTTCAGATATAAAGAATTATTGTGGGAGC 11 11 0 ATAAGAATTA 0.603181 -45 AGGGAGAGATATTTAAAATTT 12 1 0 ATTAAAATTT 0.938484 -59 TAAAAACTTCATTAAAAATATAGGGAGAGAT 12 22 0 ATAAAAATAT 0.931946 -38 ATTAAAATTTTATTTCCATTT 13 1 1 ATAAAATTTT 0.952902 -214 TATAGTAGGTATAAATAATTTGGTGATGATT 13 136 0 ATAATAATTT 0.923356 -79 AATTAATTTAATAAAAATTTACTAAAGGGAG 13 191 1 ATAAAATTTA 0.84726 -24 CTCGTAATGAATAAATAATTTATTGGCAATA 14 19 1 ATAATAATTT 0.923356 -160 ATATGTCGATATCCATATTTTTGTAAAGTTA 14 47 1 ATCATATTTT 0.615238 -132 AGTTGTTAAAATTAATATTAATAATGGATAT 15 25 0 ATAATATTAA 0.501583 -276 TGGTGAAATCATTTAAAATTTAAATAACCAT 15 166 0 ATTAAAATTT 0.938484 -135 AGCATTAATCATTAAAAATTTATTTCCCAGT 15 237 1 ATAAAAATTT 0.967904 -64 AATATCATCATTTAGATTTTTAAATATAGT 17 10 1 ATTAGATTTT 0.652991 -158 ATATTATCTAATTTAAAGTATCTATTAGATA 17 66 0 ATTAAAGTAT 0.504529 -102 GATTTTAACAATAAATATTATATTATGATGT 17 117 0 ATAATATTAT 0.785507 -51 CCAAAAAAATATTTAAAATTATATTATTAAC 19 11 0 ATTAAAATTA 0.807049 -28 ACTCTCATCTCAAAAATTTAT 21 3 0 CTAAAAATTT 0.727753 -19 ** ******** Masking position 5 Map Score: 50.9281 Number of sites scoring better than the average of aligned sites = 1401 Number in coding regions = 920 Number in noncoding regions = 481 Number of orfs with sites within 600 bp upstream = 377 Fraction of orfs with sites within 600 bp upstream = 0.0605525 Motif number 2 GAGGAATTCAAAATTTTTTTAAAGATTTTAAAGATT 1 137 1 ATTTTTTAAT 0.787108 -164 AAGATTTTAAAGATTTTTTTAATTTTATCATTTTAA 1 158 1 ATTTTTTATT 0.97374 -143 TTTAATTTTATCATTTTAATATTATTATTTTAACAT 1 175 1 TTTTTATATT 0.773856 -126 TTATTTTAACATTTTTTAGTAATTTTTAGGATAAAA 1 199 1 ATTTTATATT 0.909404 -102 TCTTTATTATCTTATTTTAAGTTTTATTTTTTGG 2 9 1 ATTATTTATT 0.885317 -253 TATTTTTTGGACTTTATTTTTAATTTTAAAATTTTA 2 35 1 ATTATTTTTT 0.574899 -227 TTTTATCTAAAACTTTTGATAAAATGTTTGAATCTA 2 88 0 ATTTTGTATG 0.673446 -174 ATAAGATATTAGGTTTTAATTAAATTTAAATCAGAC 2 224 1 ATTTTATTTT 0.637464 -38 CTTTTTTCTATTTTTTATATAATTTTTATGAATA 3 9 1 TTTTTTTATT 0.926691 -126 TCTTTTTTATATAATGAGGTCATATT 5 1 1 TTTTTTTATG 0.582984 -80 TTAGAAATTTTTTTAAATTTTAAATTATAT 5 61 0 ATTTTTTATT 0.968187 -20 GATGAACTGAAAATTTTGCTTAAGTTTAAATATTAT 6 21 1 ATTTTGTTTT 0.764072 -75 CATCAAATAAATATTTTGTTATAGATTAAAAATTGG 7 20 0 ATTTTGTAAT 0.656568 -111 TGTCACCAAATATTTTTTATAGCAGTTATGTTTGTG 7 103 0 TTTTTTTAGT 0.431701 -28 GGATTGAGAATTATTATGGTATGCTTTAGACATTTC 8 41 1 TTTATGTATT 0.569786 -260 TGGAGTGTTAAGATTTTGGTAAATTTTTGATGGTGA 8 101 1 ATTTTGTATT 0.949138 -200 TTTAGAAAATAAGTTAATTTAATCTTATAAAGATTG 8 173 1 ATTAATTATT 0.341653 -128 AAACCCCCACATATTTTTATAAGTTTCTACTAAATA 9 39 1 ATTTTTTATT 0.973723 -262 ATATCAAAATTAATTTTTATCCATTTAAAAAAGTTG 9 82 1 TTTTTTTCTT 0.447441 -219 AAACATTTGTAACTTTTTTTATTTTTTAATAGAGCG 9 119 1 ATTTTTTATT 0.97374 -182 TGAATGAAAAATTTTATTATATCTTTGTTATACAAA 9 171 0 ATTATTTATT 0.885318 -130 TTTATCACCTAAGTTTTTGTATTGTTATTTGATTGA 9 273 0 ATTTTTTATT 0.973741 -28 TACTATTCTTAGGTTTTTATAAATTCTCTTCTTTTT 10 36 1 ATTTTTTATC 0.803953 -84 ATTTTTAATGAAGTTTTTATATATATAAGTGAGAGC 12 34 1 ATTTTTTAAT 0.791473 -26 ATTAAAATTTTATTTCCATTTTTTAATGCA 13 5 1 ATTTTATTTT 0.637491 -210 TGACTTCAATAGCTTTTTTTAACTTTTCCTCATCTT 13 48 1 ATTTTTTATT 0.97374 -167 TTATTAAATTAATTTATGTTACAATTATATAGTATT 13 169 0 ATTATGTATT 0.795288 -46 TCCCTTTAGTAAATTTTTATTAAATTAATTTATGTT 13 185 0 ATTTTTTTTT 0.862793 -30 GTCGATATCCATATTTTTGTAAAGTTATAAATTTAA 14 51 1 ATTTTTTATT 0.973712 -128 ACTAAAAACTATTTTTTGCTACTTTTATAATTTTTA 14 127 1 ATTTTGTATT 0.94914 -52 ATTTTAAAATTTCTTTTATTATGATTATCCTCCAAA 15 70 1 TTTTTATATT 0.773856 -231 ATCTATTAGATAGTTTTTATACCTTTCTAAGATTTA 17 42 0 TTTTTTTATT 0.926693 -126 ATATATCACAATGTTTTTATATTATCTAATTTAAAG 17 79 0 ATTTTTTATC 0.803955 -89 TTAATAATATAATTTTAAATATTTTTTTGGTGGAAT 19 12 1 ATTTAATATT 0.403208 -27 ACCTACAATATTCTTTTTATAGCCTTCACAGCCATA 20 168 0 TTTTTTTATT 0.926693 -66 ACGATATATTTTTTTAATATTCTATTGCCTT 20 213 0 ATTTTTTATT 0.973736 -21 * ***** ** ** Masking position 10 Map Score: 54.3861 Number of sites scoring better than the average of aligned sites = 942 Number in coding regions = 653 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 274 Fraction of orfs with sites within 600 bp upstream = 0.044009 Motif number 3 CTAAAAAATGTTAAAATAATAATATTAAAAT 1 187 0 TTAAAATATA 0.704426 -114 AACCTTTTTGTTAATATATTACTACAGCTAT 1 270 0 TTAATATATA 0.850768 -31 AAAACTTAAAATAAGATAATAAAGA 2 5 0 ATAAGATATA 0.910461 -257 AAAGTTTTAGATAAAATAATATTAATGGAAG 2 108 1 ATAAAATATA 0.812713 -154 TTTATACTAAATAAGATATTAGGTTTTAATT 2 214 1 ATAAGATATA 0.910461 -48 TTTTCTATTTTTTATATAATTTTTATGAATA 3 14 1 TTTATATATT 0.690563 -121 AAAAATATATATTAGATATTAAAAATTTTTG 3 83 1 ATTAGATATA 0.937745 -52 TTTGCTTAAGTTTAAATATTATTGCAGAATA 6 35 1 TTTAAATATA 0.77927 -61 CATCTTTGTAATTATATACGACTCCAGAAAT 8 72 0 ATTATATAGA 0.750048 -229 TCTCACCTTTTTTAAATAGTAGTTAATGTAT 8 276 0 TTTAAATATA 0.77927 -25 TATCGTAAGATTTATATAGTAGTTTGTCGAA 9 231 1 TTTATATATA 0.894126 -70 CACCTCCTCAATTATATATTTACTATTCTTA 10 16 1 ATTATATATT 0.802505 -104 TTTTTAATGCATTATATATGACTTCAATAGC 13 30 1 ATTATATAGA 0.750048 -185 TTATATAGTATTAATATAGTAGGTATAAATA 13 150 0 TTAATATATA 0.850768 -65 TTATGTTACAATTATATAGTATTAATATAGT 13 161 0 ATTATATATA 0.938938 -54 CAAAAGTTCTATTAGATACTAAAAACTATTT 14 110 1 ATTAGATATA 0.937745 -69 TAAAGTATCTATTAGATAGTTTTTATACCTT 17 53 0 ATTAGATATT 0.799215 -115 GATACTTTAAATTAGATAATATAAAAACATT 17 75 1 ATTAGATATA 0.937745 -93 TATGTACATCATAATATAATATTTATTGTTA 17 112 1 ATAATATATA 0.912129 -56 GTTAATAATATAATTTTAAATATTT 19 5 1 ATAATATATT 0.732839 -34 ******** ** Masking position 7 Map Score: 24.0857 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 166 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 4 ATCACTCCCACAATGGAACTTACGCAGAGGC 1 17 1 CAATGGAATT 0.333726 -284 AAAGTATCATCAATAGCAAATAGAGTATAGC 1 46 0 CAATAGCAAT 0.318879 -255 GAGCCCTATTCAATAGAACTTACGCATTTTT 1 98 0 CAATAGAATT 0.879566 -203 TTTTAGGATAAAATAGAAAATTTTATATACC 1 222 1 AAATAGAAAT 0.761641 -79 ATTACTACAGCTATAGAAAATGATAGTAATA 1 253 0 CTATAGAAAT 0.757819 -48 AAAGTCCAAAAAATAAAACTTAAAATAAGAT 2 19 0 AAATAAAATT 0.774192 -243 TATGCCCTCCAATTAAAATTTTAAAATTAAA 2 53 0 AATTAAAATT 0.76216 -209 CATAAAAATTATATAAAAAATAGAAAAAAG 3 10 0 ATATAAAAAT 0.594971 -125 ATATATTAGATATTAAAAATTTTTGTTCATA 3 89 1 TATTAAAATT 0.740959 -46 TTCAAATATAATTTAAAATTTAAAAAAATTT 5 56 1 ATTTAAAATT 0.594969 -25 AACATAACTGCTATAAAAAATATTTGGTGAC 7 107 1 CTATAAAAAT 0.758347 -24 AATGTCGAGATTTTAGAAAATAAGTTAATTT 8 162 1 TTTTAGAAAT 0.549959 -139 GGACACTTACCATTAAAACATAAATCTAAAA 8 231 1 CATTAAAAAT 0.864843 -70 GTTTATAATGAATTAGAAATTTTTTCTTTAA 9 12 0 AATTAGAATT 0.761638 -289 AATATCGCTCTATTAAAAAATAAAAAAAGTT 9 129 0 TATTAAAAAT 0.727784 -172 AACAAAGATATAATAAAATTTTTCATTCAGA 9 178 1 TAATAAAATT 0.753711 -123 AGGGAGAGATATTTAAAATTT 12 1 0 ATTTAAAATT 0.594969 -59 TAAAAAATGGAAATAAAATTTTAAT 13 5 0 AAATAAAATT 0.774187 -210 ATATATAATGCATTAAAAAATGGAAATAAAA 13 18 0 CATTAAAAAT 0.864843 -197 TAAATTAATTTAATAAAAATTTACTAAAGGG 13 189 1 TAATAAAATT 0.753711 -26 TTGCATATGACATTAGAATATTAAATTTATA 14 76 0 CATTAGAAAT 0.864507 -103 TTTTAGTATCTAATAGAACTTTTGTGTTTGC 14 103 0 TAATAGAATT 0.753177 -76 TTCAATTGTTCTTTAAAAATTATAAAAGTAG 14 145 0 CTTTAAAATT 0.758347 -34 ATAAAAGAAATTTTAAAATATAGTGTCTTTC 15 58 0 TTTTAAAAAT 0.550672 -243 TGGTGAAATCATTTAAAATTTAAATAACCAT 15 166 0 ATTTAAAATT 0.594969 -135 TAGCATTAATCATTAAAAATTTATTTCCCAG 15 236 1 CATTAAAATT 0.872546 -65 GGAAAAGATTCAATAGAAGATGATTGTC 15 283 1 CAATAGAAAT 0.872226 -18 CCACTTTATGTAATAAAAGATTTGGGGGGAA 16 15 1 TAATAAAAAT 0.740959 -23 TCGCAAAAGGCAATAGAATATTAAAAAAATA 20 207 1 CAATAGAAAT 0.872226 -27 ******** ** Masking position 4 Map Score: 30.3086 Number of sites scoring better than the average of aligned sites = 1761 Number in coding regions = 1239 Number in noncoding regions = 522 Number of orfs with sites within 600 bp upstream = 408 Fraction of orfs with sites within 600 bp upstream = 0.0655316 Motif number 5 AGGCTTTCTTTATGATTCAAAAAAATGCGTAA 1 78 1 TATTTCAAAA 0.878464 -223 AAATCTTTAAAATCTTTAAAAAAATTTTGAAT 1 142 0 AATTTAAAAA 0.861905 -159 ATTAAAATGATAAAATTAAAAAAATCTTTAAA 1 163 0 TAATTAAAAA 0.803366 -138 GTTAAAATAATAATATTAAAATGATAAAATTA 1 177 0 TAATTAAAAT 0.592919 -124 AATTACTAAAAAATGTTAAAATAATAATATTA 1 191 0 AAATTAAAAT 0.481467 -110 TGTAGTAATATATTAACAAAAAGGTTGGTGTT 1 275 1 TATACAAAAA 0.700786 -26 TCCAAAAAATAAAACTTAAAATAAGATAATAA 2 14 0 AAATTAAAAT 0.481467 -248 AAATTAAAAATAAAGTCCAAAAAATAAAACTT 2 29 0 TAATCCAAAA 0.633578 -233 ATTAAAATTTTAAAATTAAAAATAAAGTCCAA 2 41 0 TAATTAAAAA 0.803366 -221 AATACATCAATATTCATAAAAATTATATAAAA 3 23 0 TATATAAAAA 0.803361 -112 TATCAAAAATAATCGTTAAAAATACATCAATA 3 43 0 AATTTAAAAA 0.861905 -92 GGCTATATGATATGAACAAAAATTTTTAATAT 3 98 0 TATACAAAAA 0.700787 -37 AATAATTCAAAAAATGTGATAG 4 1 1 AATTTCAAAA 0.821677 -23 ATTGCTATTTTATACTTCAAATATAATTTAAA 5 41 1 TATTTCAAAT 0.720419 -40 AATATAATTTAAAATTTAAAAAAATTTCTAA 5 60 1 AAATTAAAAA 0.722572 -21 TATTGCAGAATATATTCAAAAACAAACTTTAA 6 54 1 TATTCAAAAA 0.848771 -42 ATAAATTAGTTAATCATCAAATAAATATTTTG 7 38 0 TAAATCAAAT 0.309737 -93 CACCATCAAAAATTTACCAAAATCTTAACACT 8 104 0 AATACCAAAA 0.524325 -197 TAAATTAACTTATTTTCTAAAATCTCGACATT 8 162 0 TATTCTAAAA 0.389629 -139 AACTTTTTTAAATGGATAAAAATTAATTTTGA 9 85 0 AATATAAAAA 0.722571 -216 AAAAGAAGAGAATTTATAAAAACCTAAGAATA 10 39 0 AATATAAAAA 0.722469 -81 ATAACTACAGTATGTTTCAAAAAGAAGAGAAT 10 58 0 TATTTCAAAA 0.878464 -62 ATACTGTAGTTATAAACCAAAATCTTTATATA 10 77 1 TATACCAAAA 0.633578 -43 CTCTCACTTATATATATAAAAACTTCATTAAA 12 37 0 TATATAAAAA 0.803363 -23 GAAGATGAGGAAAAGTTAAAAAAAGCTATTGA 13 53 0 AAATTAAAAA 0.722572 -162 TGAAAGACACTATATTTTAAAATTTCTTTTAT 15 57 1 TATTTTAAAA 0.526861 -244 TTATTATGATTATCCTCCAAATTTATTGAAGT 15 85 1 TATTCCAAAT 0.596312 -216 ATTTAGCATTAATCATTAAAAATTTATTTCCC 15 233 1 AATTTAAAAA 0.861905 -68 AGATTTATACTATATTTAAAAATCTAAATGAT 17 17 0 TATTTAAAAA 0.907326 -151 ATATAATATTTATTGTTAAAATCTGAAATTGA 17 125 1 TATTTAAAAT 0.777296 -43 CCACCAAAAAAATATTTAAAATTATATTATTA 19 13 0 AATTTAAAAT 0.689927 -26 *** ******* Masking position 9 Map Score: 37.1168 Number of sites scoring better than the average of aligned sites = 1274 Number in coding regions = 933 Number in noncoding regions = 341 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 6 AATTTTTTTAAAGATTTTAAAGATTTTTTTAATT 1 148 1 AATTTTAAAT 0.852322 -153 TAATAATATTAAAATGATAAAATTAAAAAAATCT 1 168 0 AATGATAAAT 0.774179 -133 TAAAATAGAAAATTTTATATACCTATTACTATCA 1 230 1 AATTATATAT 0.700185 -71 CCCTCCAATTAAAATTTTAAAATTAAAAATAAAG 2 46 0 AATTTTAAAT 0.810062 -216 TTTTTATATAATTTTTATGAATATTGATGTATTT 3 22 1 ATTTATGAAT 0.40229 -113 ATATAATTTAAAATTTAAAAAAATTTCTAA 5 61 1 AATTAAAAAT 0.526813 -20 GGAGTCGTATATAATTACAAAGATGGAGTGTTAA 8 78 1 ATTTACAAAT 0.808705 -223 TCACCATCAAAAATTTACCAAAATCTTAACACTC 8 103 0 AATTACCAAT 0.460441 -198 AAGTTAATTTAATCTTATAAAGATTGAGAAAATT 8 183 1 AATTATAAAT 0.866192 -118 TATTTAGTAGAAACTTATAAAAATATGTGGGGGT 9 41 0 AATTATAAAT 0.866192 -260 AAAAATAAAAAAAGTTACAAATGTTTGCAACTTT 9 111 0 AATTACAAAT 0.914041 -190 TTCAGAAACTATTGTTATAACCGTTTCATATCGT 9 203 1 ATTTATAACT 0.420415 -98 ATTTTTAATGAAGTTTTTATATATATAAGTGAGA 12 34 1 AATTTTATAT 0.421229 -26 AACATAAATTAATTTAATAAAAATTTACTAAAGG 13 185 1 AATAATAAAT 0.529222 -30 ATATTTTTGTAAAGTTATAAATTTAATATTCTAA 14 61 1 AATTATAAAT 0.585594 -118 TTGTTCTTTAAAAATTATAAAAGTAGCAAAAAAT 14 137 0 AATTATAAAT 0.95502 -42 GTGTCTTTCAAAGTTGTTAAAATTAATATTAATA 15 33 0 AATGTTAAAT 0.425186 -268 ATAATAAAAGAAATTTTAAAATATAGTGTCTTTC 15 58 0 AATTTAAAAT 0.508754 -243 AAAAGGAAATATGATTATAAAACTGACTTCAATA 15 108 0 ATTTATAAAT 0.900716 -193 TTAAATATCCAAGATTACAAATCTATTTAGCATT 15 209 1 AATTACAAAT 0.91444 -92 TTTAGCATTAATCATTAAAAATTTATTTCCCAGT 15 234 1 ATTTAAAAAT 0.706004 -67 GATTTATACTATATTTAAAAATCTAAATGATGAT 17 14 0 ATTTAAAAAT 0.690341 -154 ATATAGTATAAATCTTAGAAAGGTATAAAAACTA 17 34 1 AATTAGAAAT 0.752312 -134 GTTAATAATATAATTTTAAATATTTTTTTGGTG 19 10 1 ATTTTTAAAT 0.728426 -29 AAGGCAATAGAATATTAAAAAAATATATCGT 20 213 1 AATTAAAAAT 0.85978 -21 ** ******* * Masking position 5 Map Score: 26.8523 Number of sites scoring better than the average of aligned sites = 757 Number in coding regions = 505 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 7 ATTGTCACCATTTTAGGCTATATGATATGAACA 3 112 0 ATTTGGTAAT 0.956995 -23 ATTTTCCCGCATTTGAGGATAAATTAGTTAATCA 7 54 0 ATTTGGTAAT 0.957384 -77 GCTATAAAAAATATTTGGTGACATC 7 116 1 ATATGGGAAT 0.973196 -15 TTTCTACTAAATATTTGGATATATCAAAATTAAT 9 62 1 ATATGGTAAT 0.966259 -239 ATCAATTGTCATATTTGACTATATAAAGATTTTG 10 94 0 ATATGATAAT 0.795286 -26 TTCATTAAAAATATAGGGAGAGATATTTAAAATT 12 12 0 ATATGGGAAT 0.97161 -48 GTAATAAAAGATTTGGGGGGAAAT 16 24 1 ATTTGGGAAT 0.964234 -14 **** ** ** ** Masking position 11 Map Score: 3.72799 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 66 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 TAATCTATAACAAAATATTTATTTGATGAT 7 28 1 CAAAATATTT 0.859365 -103 GATGTCACCAAATATTTTTTATAGCAG 7 114 0 CCAAATATTT 0.961076 -17 AATCTTAACACTCCATCTTTGTAATTATAT 8 86 0 CTCCATCTTT 0.606093 -215 CGTCAATTTTCTCAATCTTTATAAGATTAA 8 191 0 CTCAATCTTT 0.781585 -110 TATTCCTAATCCAACTATTTTAGATTTATG 8 249 0 CCAACTATTT 0.795698 -52 TTATAAACCCCCACATATTTTTATAAGTTT 9 35 1 CCACATATTT 0.913924 -266 TTTGATATATCCAAATATTTAGTAGAAACT 9 60 0 CCAAATATTT 0.961076 -241 AGTTATAAACCAAAATCTTTATATAGTCAA 10 84 1 CAAAATCTTT 0.834205 -36 AAATATCTCTCCCTATATTTTTAATGAAGT 12 18 1 CCCTATATTT 0.909277 -42 ATGTCGATATCCATATTTTTGTAAAGTTAT 14 49 1 CCATATTTTT 0.607891 -130 CTTTGAAAGACACTATATTTTAAAATTTCT 15 54 1 CACTATATTT 0.712848 -247 CACCAGTTTACCCAATATTAAATATCCAAG 15 192 1 CCCAATATTA 0.728093 -109 ATTTCCCCCCAAATCTTTTATTACATAA 16 20 0 CCAAATCTTT 0.953083 -18 ********** Masking position 6 Map Score: 8.03509 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 328 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 AATCTTTAAAAAAATTTTGAATTCCTCACA 1 134 0 AAAATTTTGA 0.738315 -167 CATATAGCCTAAAATGGTGACAAT 3 121 1 AAAATGGTGA 0.955876 -14 AATAATTCAAAAAATGTGATAGT 4 10 1 AAAAATGTGA 0.738637 -14 TATAGATTAAAAATTGGTGAATATTT 7 7 0 AAATTGGTGA 0.955876 -124 CTATAAAAAATATTTGGTGACATC 7 117 1 TATTTGGTGA 0.43348 -14 AGATTTTGGTAAATTTTTGATGGTGAAGAA 8 111 1 AAATTTTTGA 0.738315 -190 CTACTATTTAAAAAAGGTGAGAGATT 8 285 1 AAAAAGGTGA 0.843142 -16 AGGTATAAATAATTTGGTGATGATTATGAA 13 131 0 AATTTGGTGA 0.857591 -84 AATATTGGGTAAACTGGTGAAATCATTTAA 15 181 0 AAACTGGTGA 0.887907 -120 ATAATATAAAAACATTGTGATATATGTACA 17 90 1 AACATTGTGA 0.726867 -78 ATAAATTTTTGAGATGAGAGT 21 3 1 AAATTTTTGA 0.738315 -19 ********** Masking position 2 Map Score: 4.90545 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 99 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 10 TCATTTTAATATTATTATTTTAACATTTTTTA 1 185 1 ATTATATTTA 0.633996 -116 CATATTGGTTATTGCTATTTTATACTTCAAAT 5 31 1 ATTGTATTTA 0.946436 -50 TACTAAATATTTGGATATATCAAAATTAATTT 9 66 1 TTGGTATATA 0.633613 -235 AAGTTTTTGTATTGTTATTTGATTGACGGTAT 9 267 0 ATTGTATTTA 0.946436 -34 CTACTCTTCAATTGTTCTTTAAAAATTATAAA 14 150 0 ATTGTCTTTA 0.805005 -29 AATATTAATAATGGATATTTGAACGCTCTCCT 15 11 0 ATGGTATTTA 0.972001 -290 ATTTCCTTTTATGGATATTATAGAGCGGTAGC 15 132 1 ATGGTATTAA 0.845501 -169 GCGGTAGCTTATGGTTATTTAAATTTTAAATG 15 156 1 ATGGTATTTA 0.972001 -145 ATTTGTAATCTTGGATATTTAATATTGGGTAA 15 199 0 TTGGTATTTA 0.916409 -102 **** ***** * Masking position 6 Map Score: 3.96409 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 111 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 TCTTATCCCTACTAAATTAATTA 6 83 0 TTACCCTACT 0.893003 -13 TACCAAAATCTTAACACTCCATCTTTGTAAT 8 91 0 TTACACTCCA 0.886807 -210 CTAATTCATTATAAACCCCCACATATTTTTA 9 27 1 ATAACCCCCA 0.780039 -274 GCTTACACCTCCTCAATTATATA 10 3 1 TTAACCTCCT 0.956108 -117 AGATTTTGGTTTATAACTACAGTATGTTTCA 10 71 0 TTAAACTACA 0.757537 -49 ACCAAATTATTTATACCTACTATATTAATAC 13 143 1 TTAACCTACT 0.894902 -72 GTTATCCCCCCAAAAGGTCTTA 18 20 0 TTACCCCCCA 0.950972 -12 ATAAAATTACACCTCCAAGCGTAAGCG 20 7 1 TTAACCTCCA 0.97218 -227 *** ******* Masking position 3 Map Score: 2.20284 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 91 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 12 GGAATTCAAAATTTTTTTAAAGATTTTAAAGA 1 139 1 ATTTTTTAAG 0.740219 -162 ATCCCTACTAAATTAATTAAAGTTTGTTTTTG 6 70 0 AATTATTAAG 0.905942 -26 ATAACAAAATATTTATTTGATGATTAACTAAT 7 34 1 ATTTTTTGAG 0.848442 -97 TTGTATTGTTATTTGATTGACGGTATATACCT 9 261 0 ATTTATTGAG 0.952695 -40 AATAGTAAATATATAATTGAGGAGGTGTAAGC 10 11 0 ATATATTGAG 0.739163 -109 GAACGTATATATTTAATTAATGGGGTAATT 11 36 1 ATTTATTAAG 0.905942 -20 GTGAAACTAAAATTCATTGAAGAAGATGAGGA 13 74 0 AATTATTGAG 0.95269 -141 ATTTTTATTAAATTAATTTATGTTACAATTAT 13 177 0 AATTATTTAG 0.756893 -38 ATTTAATAAAAATTTACTAAAGGGAGAGG 13 196 1 AATTACTAAG 0.681296 -19 TTATCCTCCAAATTTATTGAAGTCAGTTTTAT 15 94 1 AATTATTGAG 0.95269 -207 **** ***** * Masking position 8 Map Score: 5.69584 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 164 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 13 GTTAGAAAAAGATTTATACTAAATAAGATA 2 202 1 GATTTATACT 0.952558 -60 CCCTCAGTCTGATTTAAATTTAATTAAAAC 2 236 0 GATTTAAATT 0.664051 -26 TCTGCAATAATATTTAAACTTAAGCAAAAT 6 33 0 TATTTAAACT 0.670565 -63 TGTAGCATCAGATTTATATTTTCCCGCATT 7 75 0 GATTTATATT 0.900658 -56 AACTATTTTAGATTTATGTTTTAATGGTAA 8 237 0 GATTTATGTT 0.759043 -64 CATATCGTAAGATTTATATAGTAGTTTGTC 9 229 1 GATTTATATA 0.533635 -72 ATCACCAAATTATTTATACCTACTATATTA 13 140 1 TATTTATACC 0.631131 -75 ATACCTACTATATTAATACTATATAATTGT 13 155 1 TATTAATACT 0.763685 -60 AAATATCCATTATTAATATTAATTTTAACA 15 23 1 TATTAATATT 0.593953 -278 AATTTTTAATGATTAATGCTAAATAGATTT 15 227 0 GATTAATGCT 0.712175 -74 CCATAAACGTTATTTATACTGGGAAATAAA 15 255 0 TATTTATACT 0.900884 -46 ACCTTTCTAAGATTTATACTATATTTAAAA 17 28 0 GATTTATACT 0.952558 -140 ********** Masking position 6 Map Score: 6.85924 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 125 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 ********** No masking Map Score: -4.85057e-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: -4.85057e-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