AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifnr_ecoli_bsub_100.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 cydA 300 cytochrome d terminal oxidase, polypeptide subunit I #2 pflA 191 pyruvate formate lyase activating enzyme 1 #3 pflB 54 formate acetyltransferase 1 #4 focA 300 probable formate transporter (formate channel 1) #5 ndh 300 respiratory NADH dehydrogenase #6 narK 300 nitrite extrusion protein #7 narG 300 nitrate reductase 1, alpha subunit #8 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #9 ansB 175 periplasmic L-asparaginase II #10 nirB 261 nitrite reductase (NAD(P)H) subunit #11 nirC 300 nitrite reductase activity #12 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #13 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #14 nrfE 79 formate-dependent nitrite reductase; possible assembly function #15 yccC 216 similar to asparaginase #16 nasF 60 uroporphyrin-III C-methyltransferase #17 nasE 31 assimilatory nitrite reductase (subunit) #18 nasD 121 assimilatory nitrite reductase (subunit) #19 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #20 yjlC 300 yjlC #21 yjlD 39 similar to NADH dehydrogenase #22 cysH 300 phosphoadenosine phosphosulfate #23 ylnB 48 similar to sulfate adenylyltransferase #24 ylnD 98 similar to uroporphyrin-III C-methyltransferase #25 resC 135 essential protein similar to cytochrome c biogenesis protein #26 yrhG 262 similar to formate dehydrogenase #27 yumB 300 similar to NADH dehydrogenase #28 yutJ 262 similar to NADH dehydrogenase #29 gerBA 264 gerBA #30 narJ 25 nitrate reductase (protein J) #31 narG 195 nitrate reductase (alpha subunit) #32 narK 135 nitrite extrusion protein #33 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter #34 cydA 300 cytochrome bd ubiquinol oxidase (subunit I) Motif number 1 GAAATTTGACGTTAAACAATTTACAACGTGAATATA 9 98 0 GTATTTACAA 0.892566 -78 GGTGTGTCCGGTGAACAGTTCAGAACCGGCGATAA 11 276 0 GTATTCAGAA 0.86505 -25 GTAAATGATTGTGCATGAATTCACAATCCTTATTCT 20 191 1 GGATTCACAA 0.989097 -110 TAGAATTGTGCTAAAATTTACTACAAATCTAAA 22 8 1 GGATTTACTA 0.700991 -293 GATTGGGACAGCGATTAAATACACAAGAAAGGCCGC 25 60 0 GGATACACAA 0.906141 -76 TAGTGCTACGGGTAAGGACTTCACAAAAAACTTTTC 27 178 1 GTATTCACAA 0.984999 -123 AGCAGAGTGTGTGACATAGTTCACAAGGAAACACGC 31 116 1 GGATTCACAA 0.989097 -80 CGAGTCAGGTGATGCTAAGTTCACTATAAACAGAGA 31 154 0 GTATTCACTA 0.930611 -42 AGAAAAACGTGTGATGTAATTCACAATCCTGTTTGG 32 57 1 GGATTCACAA 0.989097 -79 GCACGATATTGTGAAGTATTTCACAATTAATTTTTA 33 236 0 GGATTCACAA 0.989097 -65 AAAAAATATTGCTCAATATTTCACAAATGTGTCAAA 34 182 0 GTATTCACAA 0.984999 -119 CCGAGACTTTGATCAGTAATTCACAAAATAGACGAA 34 217 0 GTATTCACAA 0.984999 -84 CTGTTAATTTGCTCACTACTTCACAAATAGAACCGA 34 249 0 GTATTCACAA 0.984999 -52 * * * ******* Masking position 8 Map Score: 20.197 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 13 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 TAATTATCCTAAAGGGGTATCTTAGGAATT 7 150 1 AAAGGGGTAT 0.645901 -151 ACCCCTGAAAAAAGAGGAAAGCA 8 219 1 AAAGAGGAAA 0.789919 -13 TGCTGTTGAAAAAGAGGAAGATACTGACTA 12 108 1 AAAGAGGAAG 0.949714 -193 TGAAAAGACAAAAAAAGAAGGATATGACAA 15 103 1 AAAAAAGAAG 0.759586 -114 GTAGCACAGCAAAAAGGAATATTTAAGATA 18 66 0 AAAAAGGAAT 0.724861 -56 GAGGGTCTAGAAAGGGGAATCTT 19 4 0 AAAGGGGAAT 0.940292 -176 TGCTTATAGTAAAGGAGAATTGGAT 20 286 1 AAAGGAGAAT 0.877571 -15 TTTGTCTCCGAAAGGAGGAAAGAAGAA 22 284 1 AAAGGAGGAA 0.542943 -17 AATAAAGATAAAAAGGGCAGGCCAAACCG 25 117 1 AAAAGGGCAG 0.919474 -19 AAAGGCAATAAAAAAGGCAGCACTCAAATA 26 198 0 AAAAAGGCAG 0.838636 -65 AACTGTGAGAAAAGAAGAAGTAATGGAGGC 26 235 1 AAAGAAGAAG 0.895793 -28 CAAAAGCAAAAAAAGAGAAGGTGGATGTG 27 282 1 AAAAGAGAAG 0.87408 -19 TCTTCGGATTAAAGGGGAATTCAA 28 249 1 AAAGGGGAAT 0.940292 -14 TTGTCATAGGAAAAAGGCAGCTTATACGGG 29 75 0 AAAAAGGCAG 0.838636 -190 TTGTATCAAAAAAGGAGAATTATTCTTATC 29 204 0 AAAGGAGAAT 0.877571 -61 ATGTTCACACAAAGGAGAAGGAAGGCTGCG 31 75 0 AAAGGAGAAG 0.949714 -121 ACATTTTGTGAAAAAAGCAGAGTGTGTGAC 31 101 1 AAAAAAGCAG 0.702871 -95 TGAATCATTGAAAGGGGCAAGCCAA 32 121 1 AAAGGGGCAA 0.860823 -15 TGTTTAAATAAAAGGGGGAGAAATA 33 6 0 AAAGGGGGAG 0.929124 -295 ********** Masking position 3 Map Score: 17.0063 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 385 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 3 AACCTTTCTTTACGCCGTTTTTGTGTGCATTCAC 1 175 1 TGCTTTTTGT 0.904634 -126 CCTACCTTCTTAAGTGGATTTTTTATTTACTGCG 3 25 0 TGTATTTTTT 0.895303 -30 AATTAACAAATGAGTTGAATTTTTTCCGCATCCT 4 112 0 TGTAATTTTT 0.852349 -189 GCTATAAAATTCAGCTTAATTTTTAACGGCAAGA 8 28 0 TGCAATTTTT 0.798832 -204 ACCCGCTCATTTTGTCTATTTTTTGCACAAACAT 10 86 1 TGTATTTTTT 0.895303 -176 TAAACTTTTTGTTTTATTTTTTGTTTTTATT 11 8 1 TGTTATTTTT 0.852349 -293 AGCTTTTCTCTCAGTATTTTTTGTTGTCATATCC 15 122 0 TGTTTTTTGT 0.932386 -95 TTTAGAACTTTTCGTATATTTTGTTACATTTTAT 18 26 1 TGTATTTTGT 0.932386 -96 GGTAATCGAATTGGAGTTTTTTGTGTTTGCTATT 20 53 1 TGATTTTTGT 0.787592 -248 CTTGCCATATTCAGTATTATTTTTATCTAAAAAT 20 126 0 TGTTATTTTT 0.852349 -175 CTATAAGCAGTTTGCTGATTTTTTTGGAAAGGGT 20 261 0 TGCATTTTTT 0.854702 -40 TCATATCAAATGTGACAAATTTGTGTCAATGACA 26 17 0 TGAAATTTGT 0.714536 -246 TTCTCCTTTGTGTGAACATTTTGTGAAAAAAGCA 31 86 1 TGAATTTTGT 0.787592 -110 GTCTTCGGGCTTTGTCCTTTTTTTATGAGAAAAA 32 30 1 TGTTTTTTTT 0.895303 -106 TGGCGAATTTTAGGTCTTTTTTGTTTAAATAAAA 33 23 0 TGTTTTTTGT 0.932386 -278 GTGACGGATTTTTGTCTATTTTGTTGCTTATTTA 34 18 0 TGTATTTTGT 0.932386 -283 TTAGGTATTTTAGGCTTTATTTTTGAAATGAATC 34 67 1 TGCTATTTTT 0.798832 -234 TGTGAAATATTGAGCAATATTTTTTTCGTCTATT 34 193 1 TGCTATTTTT 0.798832 -108 CAATATTTTTTTCGTCTATTTTGTGAATTACTGA 34 207 1 TGTATTTTGT 0.932386 -94 GATCAAAGTCTCGGTTCTATTTGTGAAGTAGTGA 34 239 1 TGTTATTTGT 0.902997 -62 * ** ******* Masking position 10 Map Score: 20.3718 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 75 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 AGGCTCCCACAGGAGAAAACCG 7 289 1 AGGAGAAAAC 0.923696 -12 GGGGGAAGAGAGGAAAAGGCCGGACGACGA 10 33 0 AGGAAAAGGC 0.970697 -229 AATTCATTGTATGAAAAGACAAAAAAAGAA 15 92 1 ATGAAAAGAC 0.672333 -125 TGTGCTACGCTGGAAAAAACATTTGATAAG 18 88 1 TGGAAAAAAC 0.762568 -34 CATTATTTTCTGGAAAAGACATGTGTAAGT 19 69 1 TGGAAAAGAC 0.876474 -111 AATTTTTAATAGGAGAAAACTTACGAGCTT 19 140 1 AGGAGAAAAC 0.923696 -40 CACATTACATGGGAAAAGACAACCGGCAGA 22 241 1 GGGAAAAGAC 0.856401 -60 ATTCTTATCGAGGAAAAGGCTGAAACAAAG 29 183 0 AGGAAAAGGC 0.970697 -82 GTTCACACAAAGGAGAAGGAAGGCTGCGTT 31 73 0 AGGAGAAGGA 0.689718 -123 TCATAAAAAAAGGACAAAGCCCGAAGACTT 32 28 0 AGGACAAAGC 0.799304 -108 GAAAGAAAGCAGGAAAAGACA 33 290 1 AGGAAAAGAC 0.966213 -11 CCGGAAATGGAGGAGAAAGC 34 291 1 AGGAGAAAGC 0.933435 -10 ********** Masking position 6 Map Score: 9.55802 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 157 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 TTTATTAACATGTTTGCAACCTTTCTTTACGCC 1 158 1 TGTGCACCTT 0.960754 -143 AGGCCCCACTTTCGTGGAGCCTTTATTGTACGC 2 41 0 TTTGGGCCTT 0.853665 -151 GAGAATAACATGAATGGTGCATTGGTCATACCA 5 178 0 TGTGGGCATT 0.672942 -123 CTCGTTTCGATGTCTGCCACCTTAGTGTCTGTA 6 264 0 TGTGCACCTT 0.960754 -37 AGGCGTGCAATGCGCGCAGCGTTAGCCGCACAC 11 82 0 TGCGCGCGTT 0.889074 -219 CCTTTGGTGATGGGCGCGACCTTTGGTATCGCC 11 230 1 TGCGCACCTT 0.938771 -71 GGAAATTTTCTTTATGCGGCCTTTCTTGTGTAT 25 45 1 TTTGCGCCTT 0.960754 -91 ACCAGGCGTTTGAATGCTGCCTAACTTGTATGC 26 154 0 TGTGCGCCTA 0.926238 -109 ACAGGTTATTTGAGTGCTGCCTTTTTTATTGCC 26 192 1 TGTGCGCCTT 0.989983 -71 TTTTCAAGCTTTGTTTCAGCCTTTTCCTCGATA 29 175 1 TTTTCGCCTT 0.658571 -90 GCGTCCTGCCTGAACGCAGCCTTCCTTCTCCTT 31 61 1 TGCGCGCCTT 0.984101 -135 ** *** ***** Masking position 12 Map Score: 8.26865 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 227 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 TCAGCCAATTTGATCGAGAACAATTTATCT 1 8 0 TGATAAACAA 0.888598 -293 AGGCGAGATATGATCTATATCAATTTCTCATCT 4 228 1 TGATAATCAA 0.969832 -73 CAACAAAACTTGATTAACATCAATTTTGGTATG 5 152 1 TGATAATCAA 0.969832 -149 CTATGGGTAATGATAAATATCAATGATAGATAA 6 191 1 TGATAATCAA 0.969832 -110 TCTTATCGTTTGATTTACATCAAATTGCCTTTA 6 229 1 TGATAATCAA 0.969832 -72 GCGTGGGAATTGATAACGATCAAGAGTGATGGG 7 196 0 TGATCATCAA 0.858237 -105 CTACCGCTATTGAGGTAGGTCAATTTGCGAAGG 8 100 1 TGAGAGTCAA 0.791309 -132 CGTTGTAAATTGTTTAACGTCAAATTTCCCATA 9 106 1 TGTTAGTCAA 0.718971 -70 AAGGTGAATTTGATTTACATCAATAAGCGGGGT 10 191 1 TGATAATCAA 0.969832 -71 CACTTACAATTGATTAAAGACAACATTCACAGT 12 161 1 TGATAGACAA 0.833218 -140 TCTCCTTTTTTGATACAAATTAATAAAAACCGT 29 216 1 TGATAATTAA 0.716956 -49 **** * ***** Masking position 12 Map Score: 7.69972 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 29 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 ATTACGCCGCAAAATCCTTACAATAAACAGGTTT 1 100 0 AAAACTCAAT 0.965817 -201 ATCGTACAGTAAAAAGCGTACAATAAAGGCTCCA 2 26 1 AAAACTCAAT 0.965817 -166 CACAAACATGAAATATCAGACAATTCCGTGACTT 10 111 1 AAATCGCAAT 0.77969 -151 CTCTTAAAATAAAAAACTTTCAATCCGGCGGAAA 22 172 0 AAAACTCAAT 0.965817 -129 AATAAAACGCCTCCATTACTTCTTCTT 26 246 0 AAAACTCATT 0.765951 -17 GGACTTCACAAAAAACTTTTCAATATATTTCATA 27 193 1 AAAATTCAAT 0.669673 -108 TATATTTCATAAAATCCCGCCAATAAGCTGAAGC 27 216 1 AAAACGCAAT 0.94046 -85 AATAGTTTCAAAATAACCTACAATTTAGCCTGAA 28 134 0 AAATCTCAAT 0.863584 -129 CCCTTCAAAGAAAACGCTTCCTATCTATTATATG 29 135 1 AAAACTCTAT 0.765951 -130 TACAAATTAATAAAAACCGTCAATATGTTTAAGA 29 229 1 TAAACGCAAT 0.646586 -36 ATTTAAACAAAAAAGACCTAAAATTCGCCAACGA 33 27 1 AAAACTAAAT 0.669673 -274 AAATGTGTCAAAAAGTCATCCAATATGATGCAAG 34 160 0 AAAACTCAAT 0.965817 -141 **** * * **** Masking position 3 Map Score: 7.37089 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 16 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 ACACAAAAACGGCGTAAAGAAAGGTTGCAAA 1 170 0 GGCGTAAGAA 0.716574 -131 TCACGTAACTGGAGGAATGAA 9 165 1 GGAGGAAGAA 0.951479 -11 ACGTAGCGGGGGAAGAGAGGAAAAGGCCGGA 10 39 0 GGAAGAGGGA 0.864368 -223 CGCCCGCCATGGCGGAGCTGACCCAAAAGCC 11 134 0 GGCGGAGTGA 0.910861 -167 CCCCTTGCGAGGCGGAACGGGG 13 2 0 GGCGGAAGGG 0.921487 -37 CTATCATTGAGGAGGAATGGAC 17 20 1 GGAGGAAGGA 0.973303 -12 CTTTCAATCCGGCGGAAAGAAAGACAGGAAC 22 159 0 GGCGGAAGAA 0.952341 -142 GTCTCCGAAAGGAGGAAAGAAGAA 22 287 1 GGAGGAAGAA 0.951479 -14 AAGTTAACTAGGAGGAGATGGATATT 23 33 1 GGAGGAGTGG 0.760082 -16 GTGATGTCATGGCAGAGCTGAGCGGAAATTT 25 22 1 GGCAGAGTGA 0.563866 -114 GAGAAAAGAAGAAGTAATGGAGGCGTTTTAT 26 241 1 GAAGTAAGGA 0.478714 -22 ATATGTTTAAGAAGGAGAGAAACT 29 251 1 GAAGGAGGAA 0.8436 -14 ACCTGACTCGGAAGGAGTGAACTCTC 31 180 1 GAAGGAGGAA 0.8436 -16 ******* *** Masking position 6 Map Score: 6.69612 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 551 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 AAATTCAACTCATTTGTTAATTTTTAAAATTT 4 124 1 CATTTGTATT 0.966431 -177 ATTTATTAACCAATTGTTAATTAATGGTTATT 5 265 0 CAATTGTATT 0.958963 -36 TGTCTGTAAACATTTGATTATCCTTTAAAAAA 11 40 0 CATTTGTATC 0.870577 -261 TTTTTCTTGACAATTGATGATTGAATCAAGAT 15 62 0 CAATTGTATT 0.958963 -155 TCCTTACATCCATATGATGATTAATCATTGTA 15 186 0 CATATGTATT 0.900968 -31 TTGACTTATTCAATTGTTTATTTTTAGATAAA 20 107 1 CAATTGTATT 0.958963 -194 AAGATCATTTCATTTGGTTATTATCGTAGCGG 27 106 0 CATTTGTATT 0.966431 -195 GAAGCTAACACAAATGATGATTTTATTATGGG 27 245 1 CAAATGTATT 0.880732 -56 GAGATTGTGTCATTTGGTCAGTCTGGCAATCT 34 130 1 CATTTGTAGT 0.870577 -171 ****** * *** Masking position 5 Map Score: 5.69202 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 26 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 GATCAAATTGGCTGAAAGGCGGTAATTTAG 1 26 1 GCTGAAAGGC 0.933665 -275 TTGGTGCGCAGCTCGAAGGCTACGTCGAGT 2 134 0 GCTCGAAGGC 0.927228 -58 TTATCAGAGGGCCGACAGGCTCCCACAGGA 7 273 1 GCCGACAGGC 0.869313 -28 TTGCTCATGCCGGACGGCACTATCGTCG 10 9 1 GCCGGACGGC 0.601303 -253 AGAGGAAAAGGCCGGACGACGATAGTGCCG 10 25 0 GCCGGACGAC 0.915697 -237 CGGGTTATTTGCCGACAGGCGTGCAATGCG 11 101 0 GCCGACAGGC 0.869313 -200 CTTCTCAGATGCCGGAATGCAAGCGAGAAC 24 28 1 GCCGGAATGC 0.944633 -71 AAAGGACAAAGCCCGAAGACTTTGTCCTTT 32 20 0 GCCCGAAGAC 0.927243 -116 ********** Masking position 2 Map Score: 5.10955 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 502 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 11 CATGTTTGCAACCTTTCTTTACGCCGTTTTTGT 1 166 1 ACCTCTTTCG 0.708178 -135 CGAAAGTGGGGCCTTTTTTAGCGCGAGAGCCTT 2 60 1 GCCTTTTACG 0.959851 -132 TAGCGCGAGAGCCTTTTTTGTCAGCTATCTATA 2 78 1 GCCTTTTGCA 0.951319 -114 GCTACGTCGAGTCTGTTTTGGCAGTCACCTTAA 2 113 0 GTCTTTTGCA 0.796489 -79 ATCATATCTCGCCTGGCTTATAGGCCCGTAACT 4 209 0 GCCTCTTAAG 0.547087 -92 CGGTAAAGTCGCCTATCTTTTCAGCAACAAAAC 5 128 1 GCCTCTTTCA 0.86507 -173 AAAGAGTTACTCCTTATTTGCCGTGTGGTTAGT 6 82 1 TCCTTTTGCG 0.83772 -219 TCGCTGTTTTGTCTCTCTTGCCGTTAAAAATTA 8 13 1 GTCTCTTGCG 0.888251 -219 TGCTTTCCTCTTTTTTCAGGGGTATTAC 8 214 0 TCCTTTTTCA 0.454711 -18 TTCTATTACCGCCTACCTTAACGATTCAGCAAC 10 222 0 GCCTCTTACG 0.955254 -40 GTATCAGACCTCCTTTGGCGAAGCTCGTAA 19 160 0 ACCTTTTGCG 0.880908 -20 TGCTGTTCCTGTCTTTCTTTCCGCCGGATTGAA 22 155 1 GTCTCTTTCG 0.74492 -146 GCATTCAAACGCCTGGTTTGACACAGGTTATTT 26 170 1 GCCTTTTGCA 0.951319 -93 TTTGAGTGCTGCCTTTTTTATTGCCTTTCTTGC 26 200 1 GCCTTTTATG 0.704607 -63 CTTGTTACACCTCATTTATCAAAAG 30 5 0 ACCTTTTACA 0.636277 -21 TTTAGGTCTTGCCTGCTTTACCAGTCACAATCC 33 98 1 GCCTTTTACA 0.913129 -203 ACGGATTTTTGTCTATTTTGTTGCTTATTTATG 34 16 0 GTCTTTTGTG 0.470376 -285 **** **** ** Masking position 8 Map Score: 10.0572 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 663 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 12 GTTTATTGTAAGGATTTTGCGGCGTAATAT 1 106 1 AGGATTTTGC 0.890162 -195 CTGATATTTCATGTTTGTGCAAAAAATAGA 10 100 0 ATGTTTGTGC 0.650506 -162 ACGCAAAAGTAGAATTGTGCAAATAAACGG 12 13 1 AGAATTGTGC 0.890162 -288 GAGAGAGTAAAGGATTTTGACTTATTCAAT 20 91 1 AGGATTTTGA 0.775713 -210 ATTTTTGTAAATGATTGTGCATGAATTCAC 20 185 1 ATGATTGTGC 0.929715 -116 CATAAGAATAAGGATTGTGAATTCATGCAC 20 201 0 AGGATTGTGA 0.952396 -100 TAGAATTGTGCTAAAATTTAC 22 2 1 AGAATTGTGC 0.890162 -299 CTAGCCAAACAGGATTGTGAATTACATCAC 32 67 0 AGGATTGTGA 0.952396 -69 CTGAATAAGCGGGATTGTGACTGGTAAAGC 33 112 0 GGGATTGTGA 0.806665 -189 GCTTTCTTTCATGATTGAGCATAGTATGGC 33 270 0 ATGATTGAGC 0.650506 -31 ********** Masking position 5 Map Score: 5.88204 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 131 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 TTACCGGGTGAGATCAAAAAACAGAGTTTA 5 104 0 AGATCAAAAA 0.894828 -197 TTTTTGCGCGAAATCAAAAAGAACATCTGT 8 151 0 AAATCAAAAA 0.841315 -81 AACAAAAAATAAAACAAAAAGTTTA 11 6 0 AAAACAAAAA 0.626223 -295 TTAAAAAATAAAAACAAAAAATAAAACAAA 11 18 0 AAAACAAAAA 0.626223 -283 TTGATTCAGAAAATGTAAAATAATGAGGGT 19 28 0 AAATGTAAAA 0.630686 -152 GAATATGGCAAGATGAAAAACTGGGTAGTA 20 148 1 AGATGAAAAA 0.827735 -153 AATTTACTACAAATCTAAAAACTTATCAAG 22 25 1 AAATCTAAAA 0.751484 -276 TTTTATTTTAAGAGGTAAAAAGGCTATCTG 22 192 1 AGAGGTAAAA 0.572575 -109 GGGTCTAACAAAAGCAAAAAAAGAGAAGGT 27 274 1 AAAGCAAAAA 0.721567 -27 TTTCATTCAAAGATCAAAAAAAACCGGCTC 31 14 0 AGATCAAAAA 0.894828 -182 TAAACAAAAAAGACCTAAAATTCGCCAACG 33 30 1 AGACCTAAAA 0.775541 -271 AAATTTGCGTAAATGAAAAAGGATCGCTGT 33 70 0 AAATGAAAAA 0.749634 -231 AAAGCAGGCAAGACCTAAAATTTGCGTAAA 33 87 0 AGACCTAAAA 0.775541 -214 TTCACAAAATAGACGAAAAAAATATTGCTC 34 204 0 AGACGAAAAA 0.773815 -97 ********** Masking position 7 Map Score: 5.70711 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 159 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 ATTGGCTGAAGTATACCCATACCCGGAAAGAG 6 56 1 GTTACCCTAC 0.816402 -245 GCTGTAAAATCCCTACCCTTACCGATGTAAAG 6 117 0 CCTACCCTAC 0.984983 -184 TGATATTTATCATTACCCATAGTGAGTACAGT 6 181 0 CATACCCTAG 0.918272 -120 CAGGGAGAGGCACTACCCTTTCCAAAAAAATC 20 247 1 CATACCCTTC 0.932503 -54 TAACTTGTATGCATACCCATACAACAATATCA 26 134 0 GCTACCCTAC 0.958687 -129 TTTGTGAAGTCCTTACCCGTAGCACTATTATC 27 173 0 CCTACCCTAG 0.958687 -128 GATCCGTACCCCTCCCCTGTAAATA 29 4 1 CCTACCCTCC 0.959972 -261 ATCATCTTTTCATTACCCCTTCAAAGAAAACG 29 119 1 CATACCCTTC 0.932503 -146 ** ***** *** Masking position 5 Map Score: 2.79543 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 27 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 AGGTTAAATATCGGTAATTTGTATTTAATAA 4 20 1 TGGTAATTTG 0.836864 -281 AAAAGCCGAGCGGGTTATTTGCCGACAGGCG 11 110 0 CGGTTATTTG 0.967914 -191 ATTTTCACGCTCGGTAATTTGCTCGATCCAT 11 191 1 TGGTAATTTG 0.836864 -110 AATTACCCTGCCGTTTATTTGCACAATTCTA 12 22 0 CGTTTATTTG 0.921825 -279 CATTCACAGTGTGGTTATTTGTTACACATAG 12 184 1 GGGTTATTTG 0.873688 -117 CAGAAAGCTACTGTTTGTTTGTCTCCGAAAG 22 267 1 CGTTTGTTTG 0.757988 -34 TGGTTTGACACAGGTTATTTGAGTGCTGCCT 26 183 1 CGGTTATTTG 0.967893 -80 CCGGTTAAAACTGTTAATTTGCTCACTACTT 34 264 0 CGTTAATTTG 0.880246 -37 * ********* Masking position 5 Map Score: 1.57753 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 84 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295