AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -inarL_bsub_opreg_100.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 nasF 60 uroporphyrin-III C-methyltransferase #2 nasE 31 assimilatory nitrite reductase (subunit) #3 nasD 121 assimilatory nitrite reductase (subunit) #4 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #5 cysH 300 phosphoadenosine phosphosulfate #6 ylnB 48 similar to sulfate adenylyltransferase #7 ylnD 98 similar to uroporphyrin-III C-methyltransferase #8 citB 227 aconitate hydratase #9 yneN 71 similar to thiol:disulfide interchange protein #10 yoaE 300 similar to formate dehydrogenase #11 resC 135 essential protein similar to cytochrome c biogenesis protein #12 spoIIIAC 22 spoIIIAC #13 spoIIIAA 75 spoIIIAA #14 yqhV 144 alternate gene name: yqgE #15 nadB 102 L-aspartate oxidase #16 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #17 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #18 gerBA 264 gerBA #19 narJ 25 nitrate reductase (protein J) #20 narG 195 nitrate reductase (alpha subunit) #21 narK 135 nitrite extrusion protein #22 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter #23 yyaE 300 similar to formate dehydrogenase Motif number 1 TCTAAAAATTTTATGAAAAAT 3 2 0 TTATGAAAAA 0.789792 -120 ATAATTTTTAATAGGAGAAAACTTACGAGC 4 138 1 ATAGGAGAAA 0.941781 -42 TTTGTCTCCGAAAGGAGGAAAGAAGAA 5 284 1 AAAGGAGGAA 0.838866 -17 TAAGTTCGACTTATGAGAAAAATGTACCGG 8 81 0 TTATGAGAAA 0.829632 -147 TGAATCAATAGGAAGAGAAGGCATTTC 9 8 1 ATAGGAAGAG 0.771555 -64 GAGGCAGACTTTATGACAAGCCTCTCT 13 8 0 TTATGACAAG 0.71438 -68 CAATCGGTAGAAAGGAGGAGGCTCTG 13 60 1 AAAGGAGGAG 0.839399 -16 AAAGGAAAAAAGAAGTCTGT 14 1 1 AAAGGAAAAA 0.937116 -144 TTTTATACGGAAATGACAAGACTACTTCAG 14 78 1 AAATGACAAG 0.837201 -67 CCTGTAATTCTTATGAAAAATTAAGCAAGA 17 74 1 TTATGAAAAA 0.789792 -219 ATATGTTGTCATAGGAAAAAGGCAGCTTAT 18 80 0 ATAGGAAAAA 0.925823 -185 TTTGAAGGGGTAATGAAAAGATGATGCTTT 18 114 0 TAATGAAAAG 0.818307 -151 TTGTATCAAAAAAGGAGAATTATTCTTATC 18 204 0 AAAGGAGAAT 0.655291 -61 ATGTTCACACAAAGGAGAAGGAAGGCTGCG 20 75 0 AAAGGAGAAG 0.950959 -121 TCACGATCAAAAGGACAAAGTCTTCGGGC 21 10 1 AAAGGACAAA 0.9081 -126 TCTCATAAAAAAAGGACAAAGCCCGAAGAC 21 30 0 AAAGGACAAA 0.9081 -106 TGTCCTTTTTTTATGAGAAAAACGTGTGAT 21 42 1 TTATGAGAAA 0.829632 -94 AAATTTGCGTAAATGAAAAAGGATCGCTGT 22 70 0 AAATGAAAAA 0.885388 -231 ATACAGCAGTTTAGGAAAAGAGGTGAAGGG 23 22 1 TTAGGAAAAG 0.879178 -279 GATATCGTAGAAATGAAAAAACCGCATCCA 23 81 1 AAATGAAAAA 0.885388 -220 CTTACCTTCTATATGAAAAAGCATGAGTGT 23 269 0 ATATGAAAAA 0.866131 -32 ATATAGAAGGTAAGGAGAAGACGGCG 23 285 1 TAAGGAGAAG 0.918438 -16 ********** Masking position 6 Map Score: 24.4431 Number of sites scoring better than the average of aligned sites = 921 Number in coding regions = 706 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 2 AAGATTCCCCTTTCTAGACCCTCA 4 5 1 TTCCCCTTTC 0.963476 -175 TTCTTCTTTCCTCCTTTCGGAGACAAA 5 284 0 TTCCTCCTTT 0.704397 -17 TCTCCAAAATCCCCCTTCAGATCAGATC 8 210 0 ATCCCCCTTC 0.939499 -18 GGCCCAGTTCCTCTCTCTAGTTAGATA 10 284 0 TTCCTCTCTC 0.901885 -17 CATGACATCACTCCCTTTTCGC 11 3 0 CTCCCTTTTC 0.747011 -133 TTTATTTTTGCTCCCCTCACGT 12 3 0 CTCCCCTCAC 0.884874 -20 CAGAGCCTCCTCCTTTCTACCGATTG 13 60 0 CTCCTCCTTT 0.834609 -16 GATAGCCCCTCTCCCTCTAGTAA 16 21 0 AGCCCCTCTC 0.858603 -13 ATCTGTCTCCCCTCTCTCCTGCGTAT 17 7 1 CTCCCCTCTC 0.98899 -286 TTCTGTAATCCTCCCCCCTGTTTGAGCTAT 17 40 0 CTCCCCCCTG 0.968793 -253 TTTCATTTTACTCCTCCCTCAAAAGGGCGT 17 181 0 CTCCTCCCTC 0.969042 -112 TACTTTACCCCCTGTTTGATAAGT 17 279 0 TTACCCCCTG 0.593928 -14 TTTCCCGGTGCGCCCCTCTTACAAACGCCC 18 48 1 CGCCCCTCTT 0.901049 -217 CATCTTTTCATTACCCCTTCAAAGAAAACG 18 121 1 TTACCCCTTC 0.808877 -144 TTGGCTTGCCCCTTTCAATGATTCAA 21 120 0 TGCCCCTTTC 0.911624 -16 TATTTCTCCCCCTTTTATTTAAACA 22 6 1 CTCCCCCTTT 0.958825 -295 ********** Masking position 4 Map Score: 17.8118 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 323 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 3 CTTTTCGTATATTTTGTTACATTTTATAACATGT 3 33 1 ATTTTGAATT 0.815097 -89 TTAACAATGCATTGTGACATAATTTTTAATAGGA 4 120 1 ATTGTGAAAT 0.94431 -60 TAGAATTGTGCTAAAATTTACTACAAAT 5 5 1 ATTGTGAAAT 0.944296 -296 AATGGAATTCATTTTGCTGGAAGTAGCACCTTAC 5 102 0 ATTTTGGAAT 0.624512 -199 AATGAATTCCATTTTGAAAGATAAGGGCTGCATG 5 123 1 ATTTTGAATA 0.775848 -178 GGCTTCTTTTATTGTGTTATATGAGAGAGCGTAA 8 34 1 ATTGTGAATA 0.847695 -194 CTTATGTATGATTTTGTTTTAATATGAAATTGTG 8 139 1 ATTTTGTAAA 0.690049 -89 TTAATATGAAATTGTGAGAAAATTGTGATGGAAT 8 157 1 ATTGTGAAAT 0.944296 -71 TCCGCAGCACATTGTGTCATAAAAAGAAGAGAAA 9 40 0 ATTGTGAAAA 0.930138 -32 CTAGTTAGATATTTTGTAAGAATTATAACATTTC 10 261 0 ATTTTGAAAT 0.913369 -40 ATAAGTGCGAAATGTGCTAAATCTCTTCCCCCAC 17 251 0 AATGTGAATT 0.638051 -42 GGTTTTTATTAATTTGTATCAAAAAAGGAGAATT 18 213 0 AATTTGTAAA 0.356354 -52 TTGTGTGAACATTTTGTGAAAAAAGCAGAGTGTG 20 93 1 ATTTTGAAAA 0.892185 -103 GCCAAACAGGATTGTGAATTACATCACACGTTTT 21 60 0 ATTGTGTACT 0.612428 -76 GTAAAAATTAATTGTGAAATACTTCACAATATCG 22 235 1 ATTGTGAACT 0.854581 -66 CCGAGAAGAGAATTTGAAAGAAAACTAAAAAAAG 23 195 1 AATTTGAAAA 0.6731 -106 ****** * ** * Masking position 5 Map Score: 11.3219 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 169 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 GCTGTGCTACGCTGGAAAAAACATTTGATAAG 3 86 1 GCGGAAAAAC 0.976027 -36 ACCATTATTTTCTGGAAAAGACATGTGTAAGT 4 67 1 TCGGAAAGAC 0.811354 -113 AATTCATTTTGCTGGAAGTAGCACCTTACAAA 5 99 0 GCGGAATAGC 0.835142 -202 TTTCAATCCGGCGGAAAGAAAGACAGGAACAG 5 157 0 GCGAAAAAAG 0.935611 -144 ACAGGCAGACGCCGGTATAAACCTTGCTTTCC 10 43 1 GCGGTAAAAC 0.922554 -258 GCTAGCGCTTGCTGGAATTGGCACAATAATGT 10 85 1 GCGGAATGGC 0.821644 -216 TAACGTCAATTCTGAAAAAAAGAGATTGACAT 10 223 0 TCGAAAAAAG 0.627927 -78 GGGGCCATACGCGGGAATAAAGATAAAAAGGG 11 102 1 GCGGAAAAAG 0.968525 -34 CTGTTTTTGGGCACAAAAAAAGCCTGCTCCCA 14 38 0 GCCAAAAAAG 0.805534 -107 GTATATTATAGCTCAAACAGGGGGGAGGATTA 17 33 1 GCCAAAAGGG 0.714139 -260 TCTTACAAACGCCCGTATAAGCTGCCTTTTTC 18 64 1 GCCGTAAAGC 0.691524 -201 CGAGGAAAAGGCTGAAACAAAGCTTGAAAAGC 18 173 0 GCGAAAAAAG 0.935611 -92 ATGAAAGAAAGCAGGAAAAGACA 22 288 1 GCGGAAAGAC 0.973705 -13 AAGGGTCTTGGCGGATAAAGACTTTGGCCTGA 23 47 1 GCGATAAGAC 0.836537 -254 ** **** **** Masking position 7 Map Score: 12.2158 Number of sites scoring better than the average of aligned sites = 1201 Number in coding regions = 1117 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 TCAAAAGACCGGATCACTTTTC 1 3 1 AAAAGACCGG 0.715373 -58 CCGGCGGAAAGAAAGACAGGAACAGCATGC 5 152 0 GAAAGACAGG 0.885138 -149 AAAGACAACCGGCAGAAAGCTACTGTTTGT 5 255 1 GGCAGAAAGC 0.866701 -46 CCGGCATCTGAGAAGAACGCAGCAGATCAT 7 13 0 AGAAGAACGC 0.870337 -86 CGAATCTTCTGGAAGAACTCGAATAGATCG 7 68 1 GGAAGAACTC 0.616688 -31 AAATACACAAGAAAGGCCGCATAAAGAAAA 11 50 0 GAAAGGCCGC 0.968598 -86 GAAGCCAATCGGTAGAAAGGAGGAGGCTCT 13 55 1 GGTAGAAAGG 0.611489 -21 AACGGATGGAGGAAGACCGG 15 1 0 GGAAGACCGG 0.951129 -102 TGTCATAGGAAAAAGGCAGCTTATACGGGC 18 74 0 AAAAGGCAGC 0.840519 -191 ACATATAATAGATAGGAAGCGTTTTCTTTG 18 140 0 GATAGGAAGC 0.713832 -125 ATCTTTGAATGAAAGGCAGCTAATGACCCA 20 30 1 GAAAGGCAGC 0.957128 -166 GCTGCGTTCAGGCAGGACGCTTGGGTCATT 20 51 0 GGCAGGACGC 0.906931 -145 CAAAGGAGAAGGAAGGCTGCGTTCAGGCAG 20 66 0 GGAAGGCTGC 0.879715 -130 GCTCAATCATGAAAGAAAGCAGGAAAAGAC 22 280 1 GAAAGAAAGC 0.918423 -21 GAAGGTAAGGAGAAGACGGCG 23 290 1 AGAAGACGGC 0.70228 -11 ********** Masking position 4 Map Score: 9.82722 Number of sites scoring better than the average of aligned sites = 1432 Number in coding regions = 1290 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 6 AAGATTCCCCTTTCTAGACCCTCA 4 1 1 AAGTCCCTTC 0.915865 -179 CGCTGTGATGATGTTCTCGCTTGCATTCCGGCAT 7 36 0 ATGTCGCTTC 0.980833 -63 CCTATCTTTCAAGCTAGCGCTTGCTGGAATTGGC 10 73 1 AAGTCGCTTC 0.986828 -228 TTTCAGAATGAAGAATACGTTTATCATAAAGAAG 10 179 1 AAGACGTTTT 0.656113 -122 TTTATATGATATGCTCTAGCTTGCTGAAGTAGTC 14 97 0 ATGTAGCTTC 0.817211 -48 ATTATAATTTATGTACGCGTTTTCTTGACGCCCT 17 154 1 ATGACGTTTC 0.937171 -139 ACGCCCGTATAAGCTGCCTTTTTCCTATGACAAC 18 72 1 AAGTCTTTTC 0.758124 -193 TACCCCTTCAAAGAAAACGCTTCCTATCTATTAT 18 132 1 AAGACGCTTC 0.980833 -133 TATTCAGATTAAGAATACGCTTTCATCATAAATC 22 135 1 AAGACGCTTC 0.980833 -166 ATCATAAATCATGATAGCGTTTTCGTCAACTATT 22 159 1 ATGTCGTTTC 0.956213 -142 *** * ***** * Masking position 11 Map Score: 7.68644 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 176 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 GTCCATTCCTCCTCAATGATAGTTTT 2 16 0 TCCTTCCTAA 0.625429 -16 CAGATGATCCGCTCCTTATCAAATGTTTTTTC 3 100 0 TCCCTCCTAA 0.925937 -22 AGCTCGTAAGTTTTCTCCTATTAAAAATTATGTCA 4 134 0 TTTCTCCTAA 0.753713 -46 AGATAGCCTTTTTACCTCTTAAAATAAAAAACTTT 5 186 0 TTTCCTCTAT 0.699745 -115 AATATCCATCTCCTCCTAGTTAACTTATAAAAT 6 26 0 TCTCTCCTAA 0.798648 -23 CGAAATGCCTTCTCTTCCTATTGATTCA 9 4 0 TCTTTCCTAT 0.551182 -68 GCATTTCGCTTTCTCTTCTTTTTATGACACAATGT 9 31 1 TTCCTTCTAT 0.899532 -41 GGCCAGTCCCTCCACCTCTCTGGATAGAAAATATT 10 133 1 TCCCCTCTAT 0.904948 -168 CAGAGCCTCCTCCTTTCTACCGATTGGCTTCTTT 13 52 0 CTCTTTCTAT 0.432065 -24 GATAGCCCCTCTCCCTCTAGTAATCTAGTACTC 16 10 0 TCTCCTCTAT 0.751276 -24 TCTGTCTCCCCTCTCTCCTGCGTATATTATAGCTC 17 12 1 CTCCTCCTAT 0.934327 -281 AATCTCTTCCCCCACTTCTTTCAATTGTAAGCACT 17 231 0 CCCCTTCTAT 0.880708 -62 GATCCGTACCCCTCCCCTGTAAATAACTGATCAT 18 10 1 CCCCCCCTAT 0.937996 -255 AGTTTCTCTCCTTCTTAAACATATTGAC 18 247 0 TTCCTCCTAA 0.906068 -18 GAGAGTTCACTCCTTCCGAGTCAGGTGATG 20 176 0 TTCCTCCTAG 0.779104 -20 TTGGCTTGCCCCTTTCAATGATTCAATAA 21 117 0 CTTCCCCTAT 0.787375 -19 TATTTCTCCCCCTTTTATTTAAACAAAA 22 4 1 TTCCCCCCAT 0.672971 -297 TTCTTTCAAATTCTCTTCTCGGAATCATAACACTG 23 182 0 TTCCTTCTAT 0.899532 -119 *** ***** ** Masking position 14 Map Score: 13.0096 Number of sites scoring better than the average of aligned sites = 701 Number in coding regions = 491 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 8 AAACTTATCAAGAGCGGCTGAGGGACTGGACCT 5 43 1 AAGCGGGAGG 0.980315 -258 TGTGTCATAAAAAGAAGAGAAAGCGAAATGCCT 9 29 0 AAGAAGAAAG 0.850697 -43 TTTTCTATCCAGAGAGGTGGAGGGACTGGCCCT 10 131 0 AAGAGGGAGG 0.985469 -170 GCCAATCGGTAGAAAGGAGGAGGCTCTG 13 58 1 AAAAGGGAGG 0.887348 -18 TACTAGATTACTAGAGGGAGAGGGGCTATC 16 14 1 CAGAGGGAGG 0.908198 -20 CTTACAATTGAAAGAAGTGGGGGAAGAGATTTA 17 235 1 AAGAAGGGGG 0.823684 -58 CACTTATCAAACAGGGGGTAAAGTA 17 278 1 AAGGGGAAAG 0.715616 -15 AATTATTCTTATCGAGGAAAAGGCTGAAACAAA 18 184 0 ACGAGGAAGG 0.906617 -81 AAATGTTCACACAAAGGAGAAGGAAGGCTGCGT 20 74 0 AAAAGGAAGG 0.885452 -122 TGTGACTGGTAAAGCAGGCAAGACCTAAAATTT 22 94 0 AAGCAGAAGA 0.584161 -207 ATCATGAAAGAAAGCAGGAAAAGACA 22 285 1 AAGCAGAAAG 0.807094 -16 TACAATAGATACAGCAGTTTAGGAAAAGAGGTG 23 14 1 AAGCAGTAGG 0.784388 -287 CAGTTTAGGAAAAGAGGTGAAGGGTCTTGGCGG 23 28 1 AAGAGGAAGG 0.985197 -273 GCTTTTTCATATAGAAGGTAAGGAGAAGACGGC 23 277 1 AAGAAGAAGG 0.969162 -24 * ***** **** Masking position 7 Map Score: 12.1674 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 418 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 9 TATCATTGAGGAGGAATGGAC 2 21 1 GAGGAAGGAC 0.967819 -11 TCACATTACATGGGAAAAGACAACCGGCAGA 5 240 1 TGGGAAAGAC 0.965351 -61 TGCTCCCATTTGGGAACAGACTTCTTTTTTC 14 15 0 TGGGAAAGAC 0.965351 -130 AGTTTTTTATGGAGAACGGATGGAGGAAGAC 15 14 0 GGAGAAGGAT 0.820748 -89 GAAAGAAGTGGGGGAAGAGATTTAGCACATT 17 244 1 GGGGAAAGAT 0.973174 -49 TTACAGGGGAGGGGTACGGATC 18 2 0 GGGGTAGGAT 0.880421 -263 TATTCTTATCGAGGAAAAGGCTGAAACAAAG 18 183 0 GAGGAAAGGC 0.845149 -82 TGAAAGAAAGCAGGAAAAGACA 22 289 1 CAGGAAAGAC 0.84267 -12 ATTATACGCATGGGAATGGATATTCGAATTA 23 132 1 TGGGAAGGAT 0.94807 -169 ****** **** Masking position 6 Map Score: 3.8714 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 214 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 10 ATTTTTCATAAAATTTTTAGAACTTTTC 3 9 1 TAAAATTTTT 0.678953 -113 AAAAGACATGTGTAAGTTTTTGTGACACGT 4 82 1 TGTAAGTTTT 0.83764 -98 TGCATTGTGACATAATTTTTAATAGGAGAA 4 127 1 CATAATTTTT 0.588599 -53 TGGCGAAGCTCGTAAGTTTTCTCCTATTAA 4 145 0 CGTAAGTTTT 0.619761 -35 AGCCGCTCTTGATAAGTTTTTAGATTTGTA 5 32 0 GATAAGTTTT 0.536479 -269 TCCGCCGGATTGAAAGTTTTTTATTTTAAG 5 174 1 TGAAAGTTTT 0.707789 -127 AAAATGTACCGGTAATTTTTACTGTTTACG 8 63 0 GGTAATTTTT 0.810411 -165 TGTGATGGAATGTAATGTTCATCTGAGAAT 8 180 1 TGTAATGTTC 0.535763 -48 ATATTGAGTATGTAATTTTCAGAATGAAGA 10 163 1 TGTAATTTTC 0.900981 -138 TCGGAAATGTTATAATTCTTACAAAATATC 10 258 1 TATAATTCTT 0.548705 -43 AGAGCTGAGCGGAAATTTTCTTTATGCGGC 11 35 1 GGAAATTTTC 0.651316 -101 AGAATGATCCTGTAATTCTTATGAAAAATT 17 66 1 TGTAATTCTT 0.713791 -227 ATTGATAAAATAAAATTTTTCAATCAACTA 17 111 1 TAAAATTTTT 0.678953 -182 GTACATAAATTATAATTTTCCGAATTGATT 17 140 0 TATAATTTTC 0.815502 -153 AGGAGTAAAATGAAATTGTCAATAAATCTT 17 196 1 TGAAATTGTC 0.383939 -97 TTCCCATGCGTATAATTTTCCAGCTGTTCG 23 118 0 TATAATTTTC 0.815502 -183 ********** Masking position 5 Map Score: 3.06459 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 338 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 11 CATAATATGGCTTCTTTTATTGTGTTATAT 8 26 1 CTTCTTTTAT 0.850833 -202 TGAGCGGAAATTTTCTTTATGCGGCCTTTC 11 40 1 TTTTCTTTAT 0.588141 -96 TGGGAGCAGGCTTTTTTTGTGCCCAAAAAC 14 38 1 CTTTTTTTGT 0.694867 -107 AAACAGAATCTTTCTTTTATACGGAAATGA 14 64 1 TTTCTTTTAT 0.781505 -81 CCAACCTCCCATTTTTTTATATGATATGCT 14 116 0 ATTTTTTTAT 0.783491 -29 AACTCTTGAGTTTATTTTATCCTTGTGTAA 15 41 1 TTTATTTTAT 0.698098 -62 ATTGAAAAATTTTATTTTATCAATATATAT 17 105 0 TTTATTTTAT 0.698098 -188 AATAATTCTCCTTTTTTGATACAAATTAAT 18 210 1 CTTTTTTGAT 0.821346 -55 TAGAGCCGGTTTTTTTTGATCTTTGAATGA 20 12 1 TTTTTTTGAT 0.742462 -184 GGGCTTTGTCCTTTTTTTATGAGAAAAACG 21 36 1 CTTTTTTTAT 0.9299 -100 TTCGTCAACTATTTTTTTAGTTAAATAGTT 22 180 1 ATTTTTTTAG 0.556374 -121 TTGACTAGTACTTTTTTTAGTTTTCTTTCA 23 209 0 CTTTTTTTAG 0.821346 -92 ********** Masking position 6 Map Score: 2.74006 Number of sites scoring better than the average of aligned sites = 788 Number in coding regions = 517 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 286 Fraction of orfs with sites within 600 bp upstream = 0.0459364 Motif number 12 AAGGGCTGCATGCTGTTCCTGTCTTTCTTTCCG 5 145 1 TGCTGTCCTC 0.941495 -156 GAAGGCATTTCGCTTTCTCTTCTTTTTATGACA 9 27 1 CGCTTTTCCT 0.835308 -45 TGTATTTAATCGCTGTCCCAATCTTCGGCGGGG 11 73 1 CGCTGTCCTC 0.9623 -63 CAAGGAAACACGCTGTCTCTGTTTATAGTGAAC 20 139 1 CGCTGTTCTT 0.974038 -57 AAAGTCTTCGGGCTTTGTCCTTTTTTTATGAGA 21 27 1 GGCTTTTCTT 0.844319 -109 GAAAAAGGATCGCTGTGTCCTTTATTCGTTGGC 22 53 0 CGCTGTTCTT 0.974038 -248 AGGTCTTGCCTGCTTTACCAGTCACAATCCCGC 22 101 1 TGCTTTCCTC 0.891197 -200 TTTCCTAAACTGCTGTATCTATTGTACAA 23 7 0 TGCTGTTCTT 0.959437 -294 CCGACACTCATGCTTTTTCATATAGAAGGTAAG 23 266 1 TGCTTTTCAT 0.683292 -35 ****** ** ** Masking position 6 Map Score: 2.89822 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 329 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 CATTATCACCTCAATCATAATATGGC 8 6 1 TCACCTCATC 0.968758 -222 CCCCTTCAGATCAGATCATTCTCAGATGAAC 8 196 0 TCAGATCATC 0.898566 -32 AAAAAGAGATTGACATCAATCTGAGTCTTCT 10 208 0 TGACATCATC 0.960135 -93 AGCTCTGCCATGACATCACTCCCTTTTCGC 11 10 0 TGACATCATC 0.960135 -126 AAAGTCTGCCTCACATCATACATTTTAAAGA 13 26 1 TCACATCAAC 0.952485 -50 GAACTTAGCATCACCTGACTCGGAAGGAGTG 20 168 1 TCACCTGATC 0.856345 -28 GGATTGTGAATTACATCACACGTTTTTCTCA 21 55 0 TTACATCAAC 0.793444 -81 ******** ** Masking position 8 Map Score: 1.38281 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 100 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 ATTCCCCTTTCTAGACCCTCATTATTTTAC 4 14 1 CTAGACCCTC 0.946915 -166 CTTCATAGGTCCAGTCCCTCAGCCGCTCTT 5 52 0 CCAGTCCCTC 0.994275 -249 TTTCATAGGGCCAGTCCCTCCACCTCTCTG 10 125 1 CCAGTCCCTC 0.994275 -176 GGCCCAGTTCCTCTCTCTAGTTA 10 288 0 CCAGTTCCTC 0.964117 -13 GATAGCCCCTCTCCCTCTAGTAATCTA 16 17 0 CCTCTCCCTC 0.907616 -17 CTTTATCCGCCAAGACCCTTCACCTCTTTT 23 37 0 CAAGACCCTT 0.734007 -264 ********** Masking position 9 Map Score: 3.72367 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 46 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 ********** No masking Map Score: -5.99455e-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