AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_mjan_reg_300.orf -o00330_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 MJ0002 300 M. jannaschii predicted coding region MJ0002 #2 MJ0102 300 Phenylacrylic acid decarboxylase #3 MJ0237 300 arginyl-tRNA synthetase (argS) #4 MJ0309 129 agmatinase (speB) #5 MJ0310 39 conserved hypothetical protein #6 MJ0311 243 M. jannaschii predicted coding region MJ0311 #7 MJ0312 300 M. jannaschii predicted coding region MJ0312 #8 MJ0313 142 spermidine synthase (speE) #9 MJ0429 167 argininosuccinate synthetase (argG) #10 MJ0535 300 acetylpolyamine aminohydrolase (aphA) #11 MJ0684 68 aspartate aminotransferase (aspB2) #12 MJ0791 300 argininosuccinate lyase (argH) #13 MJ0881 300 ornithine carbamoyltransferase (argF) #14 MJ1159 36 replication factor A related protein #15 MJ1160 56 amidase #16 MJ1231 255 oxaloacetate decarboxylase alpha chain (oadA) #17 MJ1232 113 conserved hypothetical protein #18 MJ1238 90 prolyl-tRNA synthetase (proS) #19 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 CAAAATACCAATTATAAAAAATTATATAAA 1 204 1 ATTATAAAAA 0.851928 -97 TATAAAAAATTATATAAAAAATTACATAAG 1 216 1 TATATAAAAA 0.694942 -85 AATTTTGGAGATATTAAAAATCCAATAGC 1 282 1 ATATTAAAAA 0.792278 -19 TAAATCTAAAAAAATAAATATAACAACCTA 2 213 0 AAAATAAATA 0.922864 -88 AAATAAATACTATTTAAAAATAGTTAATCC 2 244 0 TATTTAAAAA 0.561455 -57 TAAGATTTAAAAAATAAATACTATTTAAAA 2 255 0 AAAATAAATA 0.922864 -46 TAATTAAATTTATTTAAAAACCCATTGGGT 3 104 1 TATTTAAAAA 0.561455 -197 TACTATGGAAAATATAAAAACCCAATGGGT 3 123 0 AATATAAAAA 0.942096 -178 TTAATTTATTAATTTAAATAAATGATAGAA 3 217 0 AATTTAAATA 0.845804 -84 TTAAATTAATAAATTAAAAAGAAGGTATTT 3 230 1 AAATTAAAAA 0.916241 -71 TTTTTTATTTAATTTAAAAATTGGGGATTT 3 265 0 AATTTAAAAA 0.90161 -36 AAAATAAAAAAATTAAATTT 4 1 1 AAAATAAAAA 0.950388 -129 CTAATCATTAAAAATAAAAAAGATTGTTTA 4 40 0 AAAATAAAAA 0.950388 -90 AGCACATATAAAAATATATATCCTAATCAT 4 62 0 AAAATATATA 0.83714 -68 GTTGAAATAAAAAATGGAAAGAA 5 4 1 GAAATAAAAA 0.838237 -36 AAAATGGAAAGAAATAAAAATGGGATAGT 5 21 1 GAAATAAAAA 0.838237 -19 CTTTCTACTAAATTTATATAATATTGAATT 6 19 1 AATTTATATA 0.704349 -225 GTATAGGGGGTATATAAATACCACAAATAA 6 98 1 TATATAAATA 0.554401 -146 TATATATAGAATTATATATAAGAGCATTAT 6 147 0 ATTATATATA 0.602384 -97 AGACTTTCATATAATAAATACTTTGTTGTT 6 199 0 ATAATAAATA 0.806643 -45 TTAAACATGTATTTTATAAAAGTAAAAACT 7 22 1 ATTTTATAAA 0.583013 -279 ACATTCATATAATATATAAATGTAAATCCA 7 57 1 AATATATAAA 0.875617 -244 TGTTCAATATTTTATAAAAATTTGTATTTT 7 90 1 TTTATAAAAA 0.525136 -211 AAAACCAAAAATTTTATATAGTCGATTATA 7 202 1 ATTTTATATA 0.457509 -99 CTAAACACTTAATATATAAACTGTGAAAGT 7 281 0 AATATATAAA 0.875617 -20 TACACCTCCTAAAATAAATAAGGTGATGTA 8 121 1 AAAATAAATA 0.922864 -22 ACTCACCTATTATATATAAACTGCTAATAA 9 54 0 TATATATAAA 0.548718 -114 ATCTTACATAAAATTATAAATCCTTAAACT 9 122 0 AAATTATAAA 0.824552 -46 TTTTATGTAAGATATAAAAATATTTTGTGA 9 139 1 GATATAAAAA 0.818661 -29 TCTCTTTTGGGATATAAAAAATTATTTAGG 10 257 0 GATATAAAAA 0.818661 -44 TTTAAATCATAATATATATAGAGGTTTTGT 12 105 0 AATATATATA 0.810678 -196 GTTAAATAGTAAATTATATATGTTAAAATT 12 135 1 AAATTATATA 0.745868 -166 AATTGTTTTATTATTAAAAATTCTAATAAG 12 170 0 TTATTAAAAA 0.574984 -131 TTTTGATATAAAATTATAAAATAGTTAAAA 12 223 0 AAATTATAAA 0.824552 -78 CAGTTAATTTATTATAAAAAATACAATAAT 13 19 1 ATTATAAAAA 0.851928 -282 ACAAAGTTAATAAATAAAAAGAATTACAAA 13 90 1 TAAATAAAAA 0.871907 -211 TTATTGAATGAAATTAAATAAATAAGGGCA 13 165 0 AAATTAAATA 0.872306 -136 AAACTACAACAATATAAATAATGGCTCATG 13 241 1 AATATAAATA 0.907905 -60 ATGGCTCATGATAATATAAAATAGTTTTTA 13 261 1 ATAATATAAA 0.741563 -40 CAAAAAATAAATAAATATAAGTC 15 4 1 AAAATAAATA 0.922864 -53 TATTTATTTTGATTTAAAAAAGGCACAGCC 16 220 0 GATTTAAAAA 0.719349 -36 TTTTTAAATCAAAATAAATATTTGTGAGGG 16 230 1 AAAATAAATA 0.922864 -26 TTATGGCAATAAAATAAATATATACTTATC 17 25 0 AAAATAAATA 0.922864 -89 AAAAACCCCCTTATTAAAAATACTAATGAT 17 94 0 TTATTAAAAA 0.574984 -20 ACTGTCATTTTAAATAAAAATTAATATTTA 18 41 1 TAAATAAAAA 0.871907 -50 TTATAGCAAATTAATAAATATTAATTTTTA 18 55 0 TTAATAAATA 0.595444 -36 TAGTCCTCTAAAATTATAAAACAATCTCTT 19 217 0 AAATTATAAA 0.824552 -84 ********** Masking position 5 Map Score: 54.8294 Number of sites scoring better than the average of aligned sites = 2413 Number in coding regions = 1547 Number in noncoding regions = 866 Number of orfs with sites within 600 bp upstream = 555 Fraction of orfs with sites within 600 bp upstream = 0.0891423 Motif number 2 TGCGTCAACAAACAATCCAAATAAACCTTTAATTA 1 95 1 ACAATAATAA 0.881269 -206 ACCAATTATAAAAAATTATATAAAAAATTACATAA 1 210 1 AAAATTAAAA 0.855923 -91 TATAACAACCTAAAATAAAATAATAAAATGGTGCC 2 190 0 TAAATAAAAA 0.700145 -111 TAGTTAATCCATAAATCTAAAAAAATAAATATAAC 2 219 0 AAAATAAAAA 0.955321 -82 GTTAAGATTTAAAAAATAAATACTATTTAAAAATA 2 252 0 AAAAAAAACA 0.774573 -49 GGGTTTTTAAATAAATTTAATTACATACCTAAACT 3 92 0 AAAATAATAA 0.952538 -209 ATTAATTTAAATAAATGATAGAAAAGTTTATATAT 3 205 0 AAAATTAAAA 0.855924 -96 ATTTAAATTAATAAATTAAAAAGAAGGTATTTAAA 3 228 1 AAAATAAAGA 0.660801 -73 TCCCCAATTTTTAAATTAAATAAAAAATGAGAGAG 3 268 1 TAAATAAAAA 0.700132 -33 AAACCATAGCACATATAAAAATATATATCCTAATC 4 64 0 AATATAATAA 0.596904 -66 TAACCACCTCAACAAAGAAAATATACTAAAAGAAG 4 104 0 ACAAAAATAA 0.581973 -26 GTTGAAATAAAAAATGGAAAGAAATAAAAATGGG 5 10 1 AAAATAAGAA 0.824077 -30 TTATAGGAGTATATATAGAATTATATATAAGAGCA 6 151 0 AATATAATAA 0.596903 -93 CATATAATATATAAATGTAAATCCAACTTGTTCAA 7 62 1 AAAATAATCA 0.945042 -239 TAATTATCCTATAAAAAAAATTCCSCCCCCCCCCC 7 134 1 AAAAAAATCS 0.763333 -167 CCCCCCCCCGAAAAATCCAAAAAAATCGGAAAAAC 7 172 1 AAAATAAAAA 0.955321 -129 ACTGTCAATAATCAATCTAAATAGAAATTTTTGGG 9 17 0 ACAATAATAA 0.881269 -151 CAAAACTATAAGCAATAAAATACAAAAAGTTTAAG 9 95 1 ACAATAAACA 0.871374 -73 ATCCCAAAAGAGAAATATTAAACTAAAAACCTATT 10 274 1 AAAATTAACA 0.83579 -27 GCACCATACAAAAAATTAAAGAATAGTTGGCGATG 12 33 0 AAAATAAAAA 0.955321 -268 CACATTTTTCACAAATGTAATAATACAAAACCTCT 12 81 1 AAAATAAAAA 0.955321 -220 ATTTTATATCAAAAAATGAAATATAACATAATCAA 12 239 1 AAAAAAATAA 0.79012 -62 ATTTATTATAAAAAATACAATAATAAAACAGTTCT 13 25 1 AAAATAAAAA 0.955321 -276 TATAGCACTGAAAAATATAACACAAAGTTAATAAA 13 69 1 AAAATAAACA 0.948237 -232 AAGTTAATAAATAAAAAGAATTACAAAAACATCAA 13 93 1 AAAAAAATAA 0.79012 -208 CAAAAAATAAATAAATATAAGTCAATATTATAACC 15 11 1 AAAATAATCA 0.945042 -46 TATCATTTCAATCAATACTACACTACGGCTATAAA 16 33 1 ACAATTAACA 0.653047 -223 TGTGCCTTTTTTAAATCAAAATAAATATTTGTGAG 16 223 1 TAAATAATAA 0.686701 -33 ACTAATGATTATAAATTATAATAGATTATTGACAT 17 68 0 AAAATTATAA 0.847944 -46 GAGAAAAATCCTAATCTATATAACAATG 19 4 1 AAAATTATCA 0.826921 -297 AAAATAATACACAAATAAAAGTCCATTGTTATATA 19 27 0 AAAATAATCA 0.945042 -274 CCTCCTCAAAATCAATATTAAGAGATAGTTCTTCA 19 104 0 ACAATTAGAA 0.324918 -197 ATAGTCCTCTAAAATTATAAAACAATCTCTTAAAT 19 213 0 AAATTAAACA 0.42619 -88 * **** ** ** * Masking position 10 Map Score: 35.5336 Number of sites scoring better than the average of aligned sites = 785 Number in coding regions = 597 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 3 TCCAGCTATGAAAACTCTTTTAGTTTTCATTTAAC 2 76 1 AAAATTTTTT 0.898055 -225 ATACTATTTAAAAATAGTTAATCCATAAATCTAAA 2 233 0 AAAAATTAAA 0.820098 -68 TTCACCATTAAAAACTGTTAAGTTAAGATTTAAAA 2 273 0 AAAATTTAAA 0.905799 -28 AAAATAAAAAAATTAAATTTATCAAATTTT 4 6 1 AAAAATTAAT 0.877905 -124 TCAAAATGTTAAAATTCTTAATGCTCCTATGTATA 6 68 1 AAAATTTAAT 0.939028 -176 TGATTTCTAAAAAAATATTATTTGTGGTATTTATA 6 110 0 AAAATTTATT 0.918677 -134 AGCACCATGCAAAAATTTTTATAGACAAAAGGTTT 8 53 1 AAAATTTTAA 0.879114 -90 TTTTATAGACAAAAGGTTTAATTAACATTACTCCA 8 69 1 AAAAGTTAAA 0.720778 -74 AATAAAATACAAAAAGTTTAAGGATTTATAATTTT 9 108 1 AAAAGTTAAT 0.805241 -60 TGTAAGATATAAAAATATTTTGTGAGGGATTGTC 9 144 1 AAAATTTTTA 0.846153 -24 CCTAATCTCTAAAATTGTTTAAGGAGAACAGTATT 10 102 1 AAAATTTTAA 0.879114 -199 TATTGTATCAAAAACTCTTTTTTATCCACTCTAAA 10 218 1 AAAATTTTTT 0.898055 -83 TGGGATATAAAAAATTATTTAGGATATTTTAGAGT 10 245 0 AAAATTTTAT 0.920935 -56 TGCCACCACGAAAAGTATTATTAATTAATAATAAT 11 15 1 AAAATTTATT 0.920934 -54 TATATATGTTAAAATTTTTAACTTATTAGAATTTT 12 149 1 AAAATTTAAA 0.905799 -152 TTTTAATAATAAAACAATTATAACTTTAAAAAAGT 12 181 1 AAAAATTATT 0.846673 -120 ATAAAATTATAAAATAGTTAAAAATAATTTACTTT 12 211 0 AAAAATTAAT 0.879538 -90 AACAGTTCTTAAAAAACTTATAGCACTGAAAAATA 13 51 1 AAAAATTATA 0.775161 -250 TATACTATTAAAAACTATTTTATATTATCATGAGC 13 264 0 AAAATTTTTT 0.898055 -37 ATCACCATAAAAAATTATTTTGAATAGAATT 14 7 0 AAAATTTTTT 0.898055 -30 TATTATAACCAAAAAAATTTACGGTGATGAG 15 36 1 AAAAATTTAT 0.846673 -21 **** * **** * Masking position 8 Map Score: 21.4281 Number of sites scoring better than the average of aligned sites = 816 Number in coding regions = 557 Number in noncoding regions = 259 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 4 AACTTAACAGTTTTTAATGGTGAATTT 2 284 1 TTTTATGGTG 0.991887 -17 CTATAAAAATTTTTGCATGGTGCTATTTATGG 8 45 0 TTTTATGGTG 0.991887 -98 AATATAATAGTTATAAATGGAGTAATGTTAAT 8 89 0 TTATATGGAG 0.858967 -54 ACCTTATTTATTTTAGGAGGTGTAAATATAAT 8 113 0 TTTTGAGGTG 0.90404 -30 ATTAATAATACTTTTCGTGGTGGCATAAA 11 8 0 CTTTGTGGTG 0.933169 -61 CTTTTAGTGTTTATAAATGGTGATGTC 11 52 1 TTATATGGTG 0.97477 -17 TTCTTTAATTTTTTGTATGGTGCCCCTATTAT 12 45 1 TTTTATGGTG 0.991887 -256 TTCAAAATAATTTTTTATGGTGATGATTT 14 18 1 TTTTATGGTG 0.991887 -19 TTATTTAAAGTTTTTCATGGTGGGGCA 18 6 0 TTTTATGGTG 0.991887 -85 **** ****** Masking position 4 Map Score: 13.1647 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 28 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 TGAGAACTGATTATGGAGAATATTTAGCGTTT 1 133 0 TTATGGGAAA 0.940239 -168 TTTCTAATAATTTTGGAGATATTAAAAATCCA 1 274 1 TTTTGGGATT 0.860446 -27 TATAAGAGCATTATGGTGATTTCTAAAAAAAT 6 129 0 TTATGGGATT 0.846235 -115 ATGGTGCTATTTATGGGTAAGAAAAATCCTAA 8 29 0 TTATGGTAAA 0.646306 -114 AAATAGAAATTTTTGGGGATAAA 9 2 0 TTTTGGGATA 0.976078 -166 TTGCTTATAGTTTTGGAGTATATATAACTCAC 9 78 0 TTTTGGGTAA 0.803044 -90 CCTTAAACAATTTTAGAGATTAGGGGGGAGCC 10 94 0 TTTTAGGATA 0.853846 -207 CTAAAATTGTTTAAGGAGAACAGTATTGTATG 10 110 1 TTAAGGGAAA 0.717501 -191 AATATTTCTCTTTTGGGATATAAAAAATTATT 10 261 0 TTTTGGATAA 0.40425 -40 TAATAATTCCTTTTAGTGTTTATAAATGGTGA 11 43 1 TTTTAGGTTA 0.574714 -26 AGGGCAATATTTATGGGAATTAACAATTAACT 13 139 0 TTATGGAATA 0.858563 -162 AAATAATTTTTTATGGTGATGATTT 14 22 1 TTATGGGATA 0.973314 -15 CCGTAAATTTTTTTGGTTATAATATTGACTTA 15 28 0 TTTTGGTATA 0.825652 -29 CCAAAAAAATTTACGGTGATGAG 15 44 1 TTACGGGATA 0.831903 -13 AAATTTAAGATTTAGGAGATAAAATTGAGTTT 16 99 0 TTTAGGGATA 0.868354 -157 TGATAAATATTTATGGCAATAAAATAAATATA 17 33 0 TTATGGAATA 0.852134 -81 TTTTAGACACTTTTAGAGATGAGGCTATAAGC 19 58 1 TTTTAGGATA 0.853846 -243 ****** *** * Masking position 2 Map Score: 12.8866 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 324 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 6 TATCCCTCCCTCGGCACCATTTTATTATTT 2 178 1 TCGGCACCAT 0.84744 -123 ATTTTTTTAGAAATCACCATAATGCTCTTA 6 129 1 AAATCACCAT 0.783416 -115 TTACCCATAAATAGCACCATGCAAAAATTT 8 41 1 ATAGCACCAT 0.870312 -102 TCTACATCACCTTATTTATTTTA 8 130 0 ACATCACCTT 0.942828 -13 GACATCACCATTTATAAACAC 11 58 0 ACATCACCAT 0.976416 -11 CTCAGCTCCATATAGGGAGCG 12 2 1 TCAGCTCCAT 0.877949 -299 TTTATCACCTTTTATACTATT 13 290 0 TTATCACCTT 0.808331 -11 AAATCATCACCATAAAAAATTAT 14 24 0 TCATCACCAT 0.979576 -13 CTCATCACCGTAAATTTTTTT 15 46 0 TCATCACCGT 0.918075 -11 GATATCACCTTTTATTTTATA 18 80 0 ATATCACCTT 0.784502 -11 CTCTTTTTTAACAGCTCCATTAATTCCTCC 19 134 0 ACAGCTCCAT 0.861288 -167 ATCTAAATAATCATCAACATAGTCCTCTAA 19 236 0 TCATCAACAT 0.759565 -65 CCTACTGAATTCATCACCCTCATCTAAATA 19 257 0 TCATCACCCT 0.918075 -44 ********** Masking position 10 Map Score: 11.7524 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 127 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 ACAATCCAAATAAACCTTTAATTAACTAAACGC 1 106 1 TAAACTAATT 0.773055 -195 TTTAATTAACTAAACGCTAAATATTCTCCATAA 1 122 1 TAAACAAATA 0.890761 -179 CCATAAATCTAAAAAAATAAATATAACAACCTA 2 213 0 AAAAAAAATA 0.834891 -88 AGTTAAGATTTAAAAAATAAATACTATTTAAAA 2 255 0 TAAAAAAATA 0.802982 -46 AAAATAAAAAAATTAAATTTATCAAATTT 4 7 1 AAAAAAAATT 0.765711 -123 TTATAAAAGTAAAAACTATAATACATTCATATA 7 35 1 AAAAATAATA 0.765711 -266 AAGATATCGAAAAAATACAAATTTTTATAAAAT 7 98 0 AAAAAAAATT 0.765711 -203 AAAAATCGGAAAAACCAAAAATTTTATATAGTC 7 192 1 AAAACAAATT 0.867352 -109 CTAAACACTTAATATATAAACTGT 7 287 0 TAAACTAATA 0.840518 -14 CTATTATATATAAACTGCTAATAATAACTGTCA 9 45 0 TAAACTAATA 0.840518 -123 TTGTTCTTCTTAAACACGAAATATAGGGTTGGA 10 185 0 TAAACAAATA 0.890761 -116 TTTTATTATTAAAAATTCTAATAAGTTAAAAAT 12 162 0 AAAAATAATA 0.765711 -139 TTATAACTTTAAAAAAGTAAATTATTTTTAACT 12 198 1 AAAAAAAATT 0.765711 -103 ATTTTATATCAAAAAATGAAATATAACATAATC 12 239 1 AAAAAAAATA 0.834891 -62 TTCTTAAACAGTTAATTTATTATAAAA 13 5 1 TAAACTAATT 0.773055 -296 AAGAATTACAAAAACATCAAATATTATTAATAG 13 108 1 AAAACAAATA 0.910045 -193 AATAACCACATAAACGTGTAATTTTGCAAATAT 13 190 1 TAAACTAATT 0.773055 -111 CCCACCATGAAAAACTTTAAATAACCAACTGTC 18 14 1 AAAACAAATA 0.910045 -77 ***** ***** Masking position 12 Map Score: 22.6062 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 159 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 8 ATACCTAAACTTTGATGATTGATTGTTTTG 3 73 0 TTTGATGATT 0.96316 -228 AATAAGTTTATTTGATGATTGATTGTAGCA 3 153 1 TTTGATGATT 0.96316 -148 CTTTTTTATTTTTAATGATTAGGATATATA 4 48 1 TTTAATGATT 0.837352 -82 AAATCCTAAAATTGATGATTTGAAATT 8 8 0 ATTGATGATT 0.8882 -135 ATTAATAATATTTGATGTTTTTGTAATTCT 13 109 0 TTTGATGTTT 0.804745 -192 AATTTTTTATGGTGATGATTT 14 26 1 GGTGATGATT 0.952986 -11 TAAATAATAAGTTAATGATTCATTATCAAC 19 188 0 GTTAATGATT 0.8909 -113 AGAGGACTATGTTGATGATTATTTAGATGA 19 238 1 GTTGATGATT 0.976453 -63 TTTAGATGAGGGTGATGAATTCAGTAGGGG 19 259 1 GGTGATGAAT 0.761644 -42 ********** Masking position 5 Map Score: 7.75146 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 101 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 TGGTGAAAACCATTATCAACAAACCATGGGAACG 1 18 1 CATTATAAAC 0.692578 -283 AAACGCTAAATATTCTCCATAATCAGTTCTCAAT 1 133 1 TATTCTAATC 0.562834 -168 ATGAAGATGATATTATAAGAACACTGCTACAATC 3 173 0 TATTATACAC 0.866542 -128 TCCTATAAGGTGTTATCACGTAACAACAAAGTAT 6 178 1 TGTTATTAAC 0.581896 -66 TATTAACTCATATTATTAACAAACTATACATTAT 7 230 1 TATTATAAAC 0.943178 -71 CATTTATAACTATTATATTTACACCTCCTAAAAT 8 102 1 TATTATACAC 0.866542 -41 ATAACTCACCTATTATATATAAACTGCTAATAAT 9 53 0 TATTATAAAC 0.94315 -115 ATGTAACCGATATTATCGATAAACGTTTA 10 6 0 TATTATAAAC 0.94315 -295 CATACAACAATGTTCTTCTTAAACAGACTATCAG 10 40 0 TGTTCTAAAC 0.936685 -261 AGAAGAACATTGTTGTATGGAAACGGGAGGTGTG 10 55 1 TGTTGTAAAC 0.861928 -246 CATACAATACTGTTCTCCTTAAACAATTTTAGAG 10 108 0 TGTTCTAAAC 0.936685 -193 AGGAGAACAGTATTGTATGGAAACCCATCATAGT 10 123 1 TATTGTAAAC 0.864365 -178 GATACAATATTGTTCTTCTTAAACACGAAATATA 10 193 0 TGTTCTAAAC 0.936685 -108 ACATAATCAATATTATTTAAACACGATTAAAATG 12 264 1 TATTATACAC 0.866542 -37 ATAATAAAACAGTTCTTAAAAAACTTATAGCACT 13 44 1 AGTTCTAAAC 0.575249 -257 TATAAGTCAATATTATAACCAAAAAAATTTACGG 15 26 1 TATTATAAAA 0.467416 -31 ****** **** Masking position 6 Map Score: 14.2736 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 64 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GTTTCGTTTGTATCCCTCCCTCGGCACCAT 2 168 1 TATCCCTCCC 0.979695 -133 GTGGTATTTATATACCCCCTATACATAGGA 6 92 0 TATACCCCCT 0.827733 -152 AACTATGCCTCCTTTAATTAGAT 6 231 0 TATGCCTCCT 0.798327 -13 AAAAAAATTCCSCCCCCCCCCCCCCCCCCC 7 147 1 CSCCCCCCCC 0.97835 -154 CSCCCCCCCCCCCCCCCCCCCCCCGAAAAA 7 157 1 CCCCCCCCCC 0.904067 -144 CTATTATATTTACACCTCCTAAAATAAATA 8 111 1 TACACCTCCT 0.914979 -32 GACAATCCCTCACAAAATATTTT 9 155 0 AATCCCTCAC 0.738657 -13 GAGCCGCCCTCACACCTCCCGTTTCCATAC 10 69 0 CACACCTCCC 0.95413 -232 CAATCATAGTTACCCCTCATCAAAAATTGA 16 137 0 TACCCCTCAT 0.902582 -119 AGCTATCCCTCACAAATATTTAT 16 243 0 TATCCCTCAC 0.931573 -13 ********** Masking position 5 Map Score: 4.06122 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 116 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 ATACTACCAATTAGAATTTCTAATAATTTTG 1 258 1 TTAGATTTCT 0.870412 -43 CTATTTTTAAATAGTATTTATTTTTTAAATC 2 251 1 ATAGATTTAT 0.65141 -50 TTTTTAATGATTAGGATATATATTTTTATAT 4 56 1 TTAGATATAT 0.795479 -74 TATTCTTCTTTTAGTATATTTTCTTTGTTGA 4 100 1 TTAGATATTT 0.841109 -30 ATAGGAGCATTAAGAATTTTAACATTTTGAA 6 67 0 TAAGATTTTA 0.308647 -177 ACGTAACAACAAAGTATTTATTATATGAAAG 6 195 1 AAAGATTTAT 0.378259 -49 TTTATAAAAATTTGTATTTTTTCGATATCTT 7 100 1 TTTGATTTTT 0.717779 -201 TTCCGATTTTTTTGGATTTTTCGGGGGGGGG 7 172 0 TTTGATTTTT 0.717779 -129 ATCATCAATTTTAGGATTTTTCTTACCCATA 8 19 1 TTAGATTTTT 0.955077 -124 CTTTTGTCTATAAAAATTTTTGCATGGTGCT 8 53 0 TAAAATTTTT 0.530306 -90 ACAAAAAGTTTAAGGATTTATAATTTTATGT 9 116 1 TAAGATTTAT 0.83568 -52 AAAAAATTATTTAGGATATTTTAGAGTGGAT 10 241 0 TTAGATATTT 0.841109 -60 GGTTTTTAGTTTAATATTTCTCTTTTGGGAT 10 274 0 TTAAATTTCT 0.522885 -27 ATAATTCCTTTTAGTGTTTATAAATGGTGAT 11 45 1 TTAGGTTTAT 0.59893 -24 ATTATATATGTTAAAATTTTTAACTTATTAG 12 147 1 TTAAATTTTT 0.776156 -154 TTTTAACTTATTAGAATTTTTAATAATAAAA 12 164 1 TTAGATTTTT 0.955076 -137 ATTAAATCGATAAGTATATATTTATTTTATT 17 17 1 TAAGATATAT 0.558749 -97 CAATAATCTATTATAATTTATAATCATTAGT 17 72 1 TTATATTTAT 0.436488 -42 TTTATAATCATTAGTATTTTTAATAAGGGGG 17 88 1 TTAGATTTTT 0.955077 -26 TAAATAAAAATTAATATTTATTAATTTGCTA 18 51 1 TTAAATTTAT 0.71821 -40 GTTATATAGATTAGGATTTTTCTC 19 4 0 TTAGATTTTT 0.955077 -297 **** ****** Masking position 7 Map Score: 16.6204 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 443 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 12 GGTTTATTTGGATTGTTTGTTGACGCATTG 1 92 0 GATTGTTTGT 0.900044 -209 AAACTTTGATGATTGATTGTTTTGTGGGCT 3 67 0 GATTGATTGT 0.952121 -234 TTTATTTGATGATTGATTGTAGCAGTGTTC 3 159 1 GATTGATTGT 0.952121 -142 AAATAAAAAAGATTGTTTAAAATTTGATAA 4 29 0 GATTGTTTAA 0.735857 -101 TTTCTATTTAGATTGATTATTGACAGTTAT 9 25 1 GATTGATTAT 0.939195 -143 TTTTGTATTTTATTGCTTATAGTTTTGGAG 9 92 0 TATTGCTTAT 0.601162 -76 GTTTAAATAATATTGATTATGTTATATTTC 12 256 0 TATTGATTAT 0.850185 -45 CGTAGTGTAGTATTGATTGAAATGATATAT 16 30 0 TATTGATTGA 0.744253 -226 TATCTCTTAATATTGATTTTGAGGAGGAAT 19 112 1 TATTGATTTT 0.71171 -189 ATAAGTTAATGATTCATTATCAACCTCTGT 19 182 0 GATTCATTAT 0.643342 -119 TTATTTAAGAGATTGTTTTATAATTTTAGA 19 211 1 GATTGTTTTA 0.547903 -90 ********** Masking position 2 Map Score: 4.19316 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 102 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 GGTTTTTATATTTTCCATAGTAAATAAGTTTATT 3 131 1 TTTCATAAAA 0.899176 -170 TAAATTTCAGAATTCAATATTATATAAATTTAGT 6 25 0 ATTCATAATA 0.615428 -219 TATAGTTTTTACTTTTATAAAATACATGTTTAAA 7 21 0 ATTTATAATA 0.616231 -280 AAATCCAACTTGTTCAATATTTTATAAAAATTTG 7 80 1 TTTCATATTA 0.696332 -221 AATTTGTATTTTTTCGATATCTTACATAATTATC 7 108 1 TTTCATATTA 0.696321 -193 GGGGGAATTTTTTTTATAGGATAATTATGTAAG 7 128 0 TTTTATAATA 0.788253 -173 ACTATGATGGGTTTCCATACAATACTGTTCTCCT 10 123 0 GTTCATAATA 0.573515 -178 TAAAAAAGAGTTTTTGATACAATATTGTTCTTCT 10 208 0 TTTTATAATA 0.899158 -93 CTTATTAGAATTTTTAATAATAAAACAATTATAA 12 170 1 TTTTATAAAA 0.900914 -131 TATATTTCATTTTTTGATATAAAATTATAAAATA 12 230 0 TTTTATAAAA 0.899158 -71 TATTATTGTATTTTTTATAATAAATTAACTGTTT 13 16 0 TTTTATAAAA 0.786501 -285 ACATCAAATATTATTAATAGTTAATTGTTAATTC 13 121 1 TATTATATAA 0.274209 -180 TATAAAATAGTTTTTAATAGTATAAAAGGTGATA 13 275 1 TTTTATAATA 0.900976 -26 GAGTTTAAATTAATTAATACAAAAATCTCTATCC 16 71 0 TATTATAAAA 0.602291 -185 TATCACCTTTTATTTTATAGCAAATTAATAAATA 18 65 0 TTTTATAAAA 0.788253 -26 AAGAGATAGTTCTTCAATATCAAAACCAAAGCTT 19 86 0 TTTCATAAAA 0.902157 -215 * *** *** *** Masking position 7 Map Score: 12.1782 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 158 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 14 TTAAATGAAAACTAAAAGAGTTTTCATAGCTGG 2 77 0 ATAAAGATTT 0.530646 -224 TTAATTTAAAAATTGGGGATTTTCTTTAAATAC 3 254 0 ATGGGGATTT 0.864185 -47 TCCTTTAATTAGATAGAGACTTTCATATAATAA 6 212 0 AAAGAGATTT 0.96411 -32 AGTAAGGGGTTTTAAACATGTAT 7 1 1 ATAGGGGTTT 0.875721 -300 TGAAAGTCCTATAGAGAGACTTTAATAATGTAT 7 255 0 AAAGAGATTT 0.96411 -46 TAATCAATCTAAATAGAAATTTTTGGGGATAAA 9 11 0 AAAGAAATTT 0.772665 -157 AGAGTGGATAAAAAAGAGTTTTTGATACAATAT 10 217 0 AAAGAGTTTT 0.790762 -84 ATCATAATATATATAGAGGTTTTGTATTATTAC 12 97 0 AAAGAGGTTT 0.937569 -204 CTATAAACAAGGATAGAGATTTTTGTATTAATT 16 61 1 GAAGAGATTT 0.809048 -195 TCAAAAATTGATTAAGAAAATTTAAGATTTAGG 16 115 0 ATAGAAATTT 0.684721 -141 AGTATTTTTAATAAGGGGGTTTTT 17 100 1 AAGGGGGTTT 0.847721 -14 GGAGCTGTTAAAAAAGAGATTTTAAAGTTCCCA 19 146 1 AAAGAGATTT 0.964109 -155 TGATGAATTCAGTAGGGGAGTTTTAGATGCATT 19 271 1 ATGGGGATTT 0.864185 -30 * * ***** *** Masking position 11 Map Score: 5.39738 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 419 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 15 ATTGTTTGTTGACGCATTGATTGGATATATTA 1 79 0 GAGCATTGTT 0.93685 -222 TAAGAGGCATTGCCGAGCGTAGCGA 2 4 1 GAGCATTGCG 0.985722 -297 ATCAAAATAGGATGCATTGCCTCGCTACGCTC 2 25 0 GAGCATTGCT 0.97773 -276 CTGGGAGAGCGCCGCATTGGCTGTGCGGAGGC 3 24 0 GCGCATTGCT 0.973261 -277 ACACGATTAAAATGCATTGGTGAAATA 12 284 1 AAGCATTGTG 0.887417 -17 AAATAACGGAACTGCATTGCCGTTTTATTTGG 16 190 1 ACGCATTGCG 0.950834 -66 ** ****** ** Masking position 6 Map Score: 1.07744 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 11 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084