AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifnr_ecoli_bsub_300.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 yggN 182 orf, hypothetical protein #11 yggH 160 orf, hypothetical protein #12 yhfC 270 putative transport #13 nirB 261 nitrite reductase (NAD(P)H) subunit #14 nirC 300 nitrite reductase activity #15 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #16 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #17 nrfE 79 formate-dependent nitrite reductase; possible assembly function #18 yccC 216 similar to asparaginase #19 nasF 60 uroporphyrin-III C-methyltransferase #20 nasE 31 assimilatory nitrite reductase (subunit) #21 nasD 121 assimilatory nitrite reductase (subunit) #22 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #23 yjlC 300 yjlC #24 yjlD 39 similar to NADH dehydrogenase #25 cysH 300 phosphoadenosine phosphosulfate #26 ylnB 48 similar to sulfate adenylyltransferase #27 ylnD 98 similar to uroporphyrin-III C-methyltransferase #28 resC 135 essential protein similar to cytochrome c biogenesis protein #29 resA 131 essential protein similar to cytochrome c biogenesis protein #30 ypuL 91 similar to hypothetical proteins #31 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #32 ypuI 54 similar to hypothetical proteins from B. subtilis #33 ypuG 280 similar to hypothetical proteins #34 yrhG 262 similar to formate dehydrogenase #35 yrhF 300 yrhF #36 yumB 300 similar to NADH dehydrogenase #37 yutJ 262 similar to NADH dehydrogenase #38 gerBA 264 gerBA #39 narJ 25 nitrate reductase (protein J) #40 narG 195 nitrate reductase (alpha subunit) #41 ywiD 143 ywiD #42 narK 135 nitrite extrusion protein #43 ywiB 300 ywiB #44 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter #45 cydA 300 cytochrome bd ubiquinol oxidase (subunit I) Motif number 1 CATCGGTAAGGGTAGGGATTTTACAGCACCGTGAAA 6 122 1 GTATTTACAG 0.594074 -179 GAAATTTGACGTTAAACAATTTACAACGTGAATATA 9 98 0 GTATTTACAA 0.854252 -78 GGTGTGTCCGGTGAACAGTTCAGAACCGGCGATAA 14 276 0 GTATTCAGAA 0.749081 -25 GTAAATGATTGTGCATGAATTCACAATCCTTATTCT 23 191 1 GGATTCACAA 0.983943 -110 TAGAATTGTGCTAAAATTTACTACAAATCTAAA 25 8 1 GGATTTACTA 0.70094 -293 GATTGGGACAGCGATTAAATACACAAGAAAGGCCGC 28 60 0 GGATACACAA 0.839825 -76 AACACACATGGCGGAATAGTTCACTAGCAAGTCTTA 35 80 1 GGATTCACTA 0.938419 -221 TAGTGCTACGGGTAAGGACTTCACAAAAAACTTTTC 36 178 1 GTATTCACAA 0.974429 -123 AGCAGAGTGTGTGACATAGTTCACAAGGAAACACGC 40 116 1 GGATTCACAA 0.983943 -80 CGAGTCAGGTGATGCTAAGTTCACTATAAACAGAGA 40 154 0 GTATTCACTA 0.90455 -42 CTGTACAGCAGTGATGTATTTCACAGCCTGTATGAT 41 70 0 GGATTCACAG 0.938653 -74 AGAAAAACGTGTGATGTAATTCACAATCCTGTTTGG 42 57 1 GGATTCACAA 0.983943 -79 GCACGATATTGTGAAGTATTTCACAATTAATTTTTA 44 236 0 GGATTCACAA 0.983943 -65 AAAAAATATTGCTCAATATTTCACAAATGTGTCAAA 45 182 0 GTATTCACAA 0.974429 -119 CCGAGACTTTGATCAGTAATTCACAAAATAGACGAA 45 217 0 GTATTCACAA 0.974429 -84 CTGTTAATTTGCTCACTACTTCACAAATAGAACCGA 45 249 0 GTATTCACAA 0.974429 -52 * * * ******* Masking position 8 Map Score: 22.528 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 23 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 2 ACCTTTCTTTACGCCGTTTTTGTGTGCATTCAC 1 176 1 AGCCGTTTTT 0.875325 -125 CACTTTCGTGGAGCCTTTATTGTACGCTTTTTA 2 35 0 GGCCTTTTTT 0.895596 -157 TTTAGCGCGAGAGCCTTTTTTGTCAGCTATCTA 2 76 1 GGCCTTTTTT 0.895596 -116 GTCAGGCAGTGGTGCGTTTTTCTACCGCTATTG 8 79 1 GTGCGTTTTT 0.676422 -153 TTCCGCAGCCACGGCCTTATCATGCTTGCATCC 11 79 1 AGGCCTTTCT 0.733311 -82 AGGTAAAGGGATGGCCTTGTTCTTGAAGGCTAT 12 62 0 AGGCCTTTTT 0.770335 -209 CTATCGTCGTCCGGCCTTTTCCTCTCTTCCCCC 13 30 1 CGGCCTTTCT 0.926947 -232 AAAAATTACCCTGCCGTTTATTTGCACAATTCT 15 23 0 CGCCGTTATT 0.676345 -278 AGTCGGTTTTCTGGCGTTGTTGTTAAGTCTCGG 17 50 1 CGGCGTTTTT 0.960669 -30 GAACAGCATGCAGCCCTTATCTTTCAAAATGGA 25 130 0 CGCCCTTTCT 0.943917 -171 ATATGATCTGCTGCGTTCTTCTCAGATGCCGG 27 10 1 GTGCGTTTTT 0.676422 -89 TTTCTTTATGCGGCCTTTCTTGTGTATTTAATC 28 51 1 CGCCTTTTTT 0.952714 -85 CGGTTTGGCCTGCCCTTTTTATCTTTATTCCC 28 114 0 CGCCCTTTTT 0.953555 -22 AAACGGCGTTTTTTTTAGATTTGGC 30 3 1 AGGCGTTTTT 0.841093 -89 CACTAGAGGCCGGGCGTTCTTTTTTCCTTTTAT 33 54 0 CGGCGTTTTT 0.960669 -227 TATTTGAGTGCTGCCTTTTTTATTGCCTTTCTT 34 198 1 CGCCTTTTTT 0.952714 -65 AATTTTGAATCATCCGTTGTCTTTGACGAATAG 37 52 0 CTCCGTTTCT 0.842247 -211 CCCGTATAAGCTGCCTTTTTCCTATGACAACAT 38 75 1 CGCCTTTTCT 0.942913 -190 CGAAATCCTCCTTTTTTCTTTCATTATAA 41 7 1 CTCCTTTTTT 0.801987 -137 ACAAAGTCTTCGGGCTTTGTCCTTTTTTTATGA 42 25 1 CGGCTTTTCT 0.925662 -111 AGGACACAGCGATCCTTTTTCATTTACGCAAAT 44 65 1 GTCCTTTTCT 0.585685 -236 * ****** ** * Masking position 7 Map Score: 18.1969 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 366 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 3 ACTGAAATCGTACAGTAAAAAGCGTACAATAAAGGCTCCAC 2 20 1 TAAAGAAATA 0.770988 -172 AGTCACCTTAAAGTATAGATAGCTGACAAAAAAGGCTCTCG 2 83 0 AAAAGAAAAA 0.770988 -109 TCTCACAAATTCGCTCAAATAATAAACAATAAACTCTGTTT 5 75 1 TAAAAAAATA 0.648096 -226 CTGACAGGCCAGTTAAAAAAATGCTATAAAATTCAGCTTAA 8 43 0 AAAATAAAAA 0.572248 -189 GAGATTTCCTTAACAAACAGAGCAGAAAAAAAGCAAGTGAA 12 11 1 TAAAGAAAAA 0.931134 -260 TTGCAATAAAACATTTAAACAGATCACAAAATCACCTAAAA 12 184 1 AAAAGAAAAA 0.770988 -87 TATTTCATGTTTGTGCAAAAAATAGACAAAATGAGCGGGTT 13 85 0 TAAAAAAAAA 0.880905 -177 ATCCTTTAAAAAATAAAAACAAAAAATAAAACAAAAAGTTT 14 12 0 AAAAAAAAAA 0.648096 -289 AAAAGGAATATTTAAGATACATGTTATAAAATGTAACAAAA 21 44 0 TAAATAAAAA 0.843086 -78 CCTATATCCTTGATTCAGAAAATGTAAAATAATGAGGGTCT 22 26 0 TAAAAAAATA 0.648096 -154 GTGCTTTTAGTGTACCATAGAAGGGATAAAAGGAAAAAAGA 33 29 1 TAAAAAAAAA 0.880905 -252 TTCTCACAGTTATGCAAGAAAGGCAATAAAAAAGGCAGCAC 34 205 0 TAAAGAAAAA 0.931134 -58 CACAAAAAACTTTTCAATATATTTCATAAAATCCCGCCAAT 36 199 1 TAAATAAAAA 0.843068 -102 CCGAAGAGTATGATAGATACATTGAAGAAAATACGAACTAT 37 215 0 TAAATAAAAA 0.843087 -48 TAGCTGCCTTTCATTCAAAGATCAAAAAAAACCGGCTCTAT 40 11 0 TAAATAAAAA 0.843087 -185 ACAACATAGATCTGCTAGAAAAACAAAAAAAGG 43 3 0 TAAAAAAAAA 0.880905 -298 TAAAAAGCATTTCCTTATATAGAAGAGAAAATCATATCACT 43 153 0 TAAAGAAAAA 0.931134 -148 CTCATCAGATTTGAAGATAAACCTCATAAAAAGCATTTCCT 43 179 0 TAAACAAAAA 0.662686 -122 CCGACATAAATAAGCAACAAAATAGACAAAAATCCGTCACA 45 12 1 TAAAAAAAAA 0.880905 -289 ACGATTCATTTCAAAAATAAAGCCTAAAATACCTAAAAAGT 45 62 0 TAAAGAAATA 0.770988 -239 TGATCAGTAATTCACAAAATAGACGAAAAAAATATTGCTCA 45 203 0 TAAAGAAAAA 0.931134 -98 * * * ** * **** Masking position 11 Map Score: 18.3529 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 62 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 TATTCGCCTGATGCTCCCTTTTAATTAACTGTTTTAG 4 72 1 ATCTCCCTTA 0.725596 -229 GACACCTCTGATACTCGTTTCGATGTCTGCCACCTTA 6 273 0 ATCTCGTTTC 0.690197 -28 CCCATGGGGAATACTCCTTAATACCCATCTGCATAAA 7 45 1 ATCTCCTTAA 0.767925 -256 AATTCCTAAGATACCCCTTTAGGATAATTAACAGCCA 7 143 0 ATCCCCTTTA 0.965241 -158 ACTTTGGATAATGCCCGTTTTCAGAACACTTTCACAA 11 120 1 ATCCCGTTTC 0.69104 -41 TCACCTTTATATACTCCTTAATGGGTATATTGCTGAT 13 161 0 ATCTCCTTAA 0.767925 -101 TATTTGCACAATTCTACTTTTGCGTGA 15 1 0 ATCTACTTTA 0.786972 -300 TAGTCAGTATCTTCCTCTTTTTCAACAGCATGCATAA 15 101 0 CTCCTCTTTA 0.623506 -200 TGCATGTAAAATACCACTTTAGAGTTAGTCAGTATCT 15 126 0 ATCCACTTTA 0.787633 -175 TTGTTGTCATATCCTTCTTTTTTTGTCTTTTCATACA 18 99 0 ATCTTCTTTC 0.72278 -118 AAGATTCCCCTTTCTAGACCCTCATTATTT 22 4 1 ATCCCCTTTC 0.951454 -176 ATCCAATTCTCCTTTACTATAAGCAGTTTGCT 23 279 0 ATCTCCTTTA 0.965109 -22 TTCTTCTTTCCTCCTTTCGGAGACAAACAAACAG 25 277 0 TTCTCCTTTC 0.746545 -24 GGTGCTTCCTCCTTTAATGTGCTTTTAGTGTA 33 6 1 TTCTCCTTTC 0.746545 -275 GCCTCCATTACTTCTTCTTTTCTCACAGTTATGCAAG 34 228 0 CTCTTCTTTA 0.622579 -35 TTGAATTCCCCTTTAATCCGAAGAGTATGAT 37 242 0 ATCCCCTTTA 0.965241 -21 GATAAGAATAATTCTCCTTTTTTGATACAAATTAATA 38 204 1 ATCTCCTTTA 0.965109 -61 CGCAGCCTTCCTTCTCCTTTGTGTGAACATTTTGTGA 40 75 1 CTCTCCTTTA 0.9251 -121 CGAAATCCTCCTTTTTTCTTTCATTATAAAT 41 5 1 ATCTCCTTTT 0.716887 -139 CCTTTTCATCATTCCACTTTGACTTGAATAGTATAAT 43 264 0 ATCCACTTTA 0.787633 -37 TATTTCTCCCCCTTTTATTTAAACAAAAAAGA 44 6 1 CTCCCCTTTA 0.925373 -295 ** ******* * Masking position 9 Map Score: 12.7945 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 88 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TTGCAACCTTTCTTTACGCCGTTTTTGTGTG 1 171 1 TTTTACGCCG 0.952533 -130 TGCGGTGTTTCTCCAGATGTGGCCCA 2 176 0 TTTTCTCCAG 0.706273 -16 GATAATCAAATATTTACTCCGTATTTGCATA 4 167 1 TTTTACTCCG 0.736021 -134 ACTATTAAGATTTTTATGCAGATGGGTATTA 7 63 0 TTTTATGCAG 0.802926 -238 CAGTGGTGCGTTTTTCTACCGCTATTGAGGT 8 85 1 TTTTCTACCG 0.717632 -147 GCATAATACTTTTTTATGCCGTTTAATTCTT 9 28 1 TTTTATGCCG 0.957397 -148 CGGGATAAGGTGTTTACGCCGCATCCGGCAT 10 93 1 TTTTACGCCG 0.952533 -90 TGACGATCACTTTTTATTCCGTGATCAAAAT 12 124 1 TTTTATTCCG 0.757422 -147 TTCCTGTCTTTCTTTCCGCCGGATTGAAAGT 25 160 1 TTTTCCGCCG 0.966446 -141 ACAAACAGTAGCTTTCTGCCGGTTGTCTTTT 25 254 0 GTTTCTGCCG 0.793376 -47 CGTATTTCCCCCGATCTATTCGA 27 86 0 TTTTCCCCCG 0.922139 -13 GCGGAAATTTTCTTTATGCGGCCTTTCTTGT 28 43 1 TTTTATGCGG 0.814751 -93 AAGCAAAGGCTTTTTCTCCCGCTTCTGCGCT 33 108 1 TTTTCTCCCG 0.929888 -173 TCCTTACGATTTTTTCTGCTGACTCGTCAAT 36 36 0 TTTTCTGCTG 0.698283 -265 TTCTTGAAAATATTTCCGCAGGCCGCTACGA 36 84 1 TTTTCCGCAG 0.839276 -217 ACTATTATCATGTTTATCCGGCTGGCCCAAG 36 151 0 TTTTATCCGG 0.643933 -150 TTTTGTTGCTTATTTATGTCGGC 45 3 0 TTTTATGTCG 0.52707 -298 * ********* Masking position 5 Map Score: 13.5037 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 421 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 6 TTACTTTATTCGCCTGATGCTCCCTTTTAA 4 66 1 CGCCTGATGC 0.938625 -235 ATGCCTGATGCGCTTCTTATC 5 2 1 TGCCTGATGC 0.980277 -299 AATGCAAAACTGCCTGATGCGCTACGCTTA 10 32 1 TGCCTGATGC 0.980277 -151 GCGTTTTCCATGCCGGATGCGGCGTAAACA 10 103 0 TGCCGGATGC 0.990352 -80 CAAAGTTAGTTGCCGGATGCAAGCATGATA 11 96 0 TGCCGGATGC 0.990352 -65 TTACAAACTATGCAGGTTGCCGGGCTTCAT 25 76 0 TGCAGGTTGC 0.852778 -225 AGTAGCTTTCTGCCGGTTGTCTTTTCCCAT 25 249 0 TGCCGGTTGT 0.852778 -52 ********** Masking position 8 Map Score: 7.59566 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 169 Number in noncoding regions = 418 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 7 TCAGCCAATTTGATCGAGAACAATTTATCT 1 8 0 TGATAAACAA 0.86508 -293 AGGCGAGATATGATCTATATCAATTTCTCATCT 4 228 1 TGATAATCAA 0.959752 -73 CAACAAAACTTGATTAACATCAATTTTGGTATG 5 152 1 TGATAATCAA 0.959752 -149 CTATGGGTAATGATAAATATCAATGATAGATAA 6 191 1 TGATAATCAA 0.959752 -110 TCTTATCGTTTGATTTACATCAAATTGCCTTTA 6 229 1 TGATAATCAA 0.959752 -72 GCGTGGGAATTGATAACGATCAAGAGTGATGGG 7 196 0 TGATCATCAA 0.763894 -105 TTTTATTCCGTGATCAAAATCACCTCTTAAAAT 12 135 1 TGATAATCAC 0.935122 -136 AAGGTGAATTTGATTTACATCAATAAGCGGGGT 13 191 1 TGATAATCAA 0.959752 -71 CACTTACAATTGATTAAAGACAACATTCACAGT 15 161 1 TGATAGACAA 0.669495 -140 TGTCCATCAGTTATGAATAACAATTATATTTCT 31 57 0 TTATAAACAA 0.407667 -66 GTCTATCGTTTTATAAAAATCAAGGATTGGTCT 35 121 0 TTATAATCAA 0.719069 -180 TCTCCTTTTTTGATACAAATTAATAAAAACCGT 38 216 1 TGATAATTAA 0.574332 -49 ACAGCCTGTATGATGAATGTCACTTATCAGGAG 41 51 0 TGATAGTCAC 0.819938 -93 TGTACAGCAGTGATGTATTTCACAGCCTGTATG 41 72 0 TGATATTCAC 0.746442 -72 GAAAAACGTGTGATGTAATTCACAATCCTGTTT 42 58 1 TGATATTCAC 0.746442 -78 **** * ***** Masking position 3 Map Score: 10.1618 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 73 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 8 CGGTTTTCTCCTGTGGGAGCCT 7 289 0 GTTTTCTCCT 0.84584 -12 TGCTTTCCTCTTTTTTCAGGGG 8 220 0 CTTTCCTCTT 0.414919 -12 GTCCATTCCTCCTCAATGATAGT 20 19 0 CATTCCTCCT 0.741877 -13 AAGCTCGTAAGTTTTCTCCTATTAAAAATT 22 140 0 GTTTTCTCCT 0.84584 -40 TTCTTCTTTCCTCCTTTCGGAGACA 25 286 0 CTTTCCTCCT 0.920949 -15 TGCCCCCTTCCCCCTATTGCAGATC 29 117 0 CCTTCCCCCT 0.810485 -15 GATAGCTTCTTCCTTATATCTTAT 32 41 0 GCTTCTTCCT 0.8643 -14 GGTGCTTCCTCCTTTAATGTGCT 33 4 1 GCTTCCTCCT 0.956819 -277 GCCGGGCGTTCTTTTTTCCTTTTATCCCTT 33 49 0 CTTTTTTCCT 0.67603 -232 GTATAAGCTGCCTTTTTCCTATGACAACAT 38 78 1 CCTTTTTCCT 0.840031 -187 CTGAACGCAGCCTTCCTTCTCCTTTGTGTG 40 70 1 CCTTCCTTCT 0.772989 -126 CGAAATCCTCCTTTTTTCTTTCATTATAA 41 10 1 CCTTTTTTCT 0.378844 -134 AAGTCTTCGGGCTTTGTCCTTTTTTTATGA 42 28 1 GCTTTGTCCT 0.641308 -108 GCTTTCTCCTCCATTTCCGG 45 291 0 GCTTTCTCCT 0.932466 -10 ********** Masking position 4 Map Score: 6.83533 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 213 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 9 ATTGGCTGAAGTATACCCATACCCGGAAAGAGT 6 56 1 GTTACCCTCC 0.920205 -245 GCTGTAAAATCCCTACCCTTACCGATGTAAAGC 6 116 0 CCTACCCTCC 0.98989 -185 CAGGGAGAGGCACTACCCTTTCCAAAAAAATCA 23 247 1 CATACCCTCC 0.979342 -54 TAACTTGTATGCATACCCATACAACAATATCAA 34 133 0 GCTACCCTCA 0.932272 -130 GCTGATTACCCCTTCCGATATTGCCT 35 285 0 GATACCCTCC 0.96682 -16 TTTGTGAAGTCCTTACCCGTAGCACTATTATCA 36 172 0 CCTACCCTGC 0.941878 -129 GATCCGTACCCCTCCCCTGTAAATAA 38 4 1 CCTACCCTCC 0.98989 -261 ATCATCTTTTCATTACCCCTTCAAAGAAAACGC 38 119 1 CATACCCTCA 0.915563 -146 ** ***** * ** Masking position 5 Map Score: 5.26161 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 27 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 TGTTCTCGATCAAATTGGCTGAAAGGCGGTAATT 1 19 1 CAAATTGCAA 0.911656 -282 TCGAAAAATGCAAATTTGCTTCAACAAAAACCTG 1 73 1 CAAATTGCAA 0.911656 -228 ATCACTCTCACAAATTCGCTCAAATAATAAACAA 5 70 1 CAAATTGCAA 0.911656 -231 TGGTCATACCAAAATTGATGTTAATCAAGTTTTG 5 155 0 AAAATTATAA 0.690527 -146 TAGCTAAAGGCAATTTGATGTAAATCAAACGATA 6 232 0 CAATTTATAA 0.589097 -69 TCTGTATGGGAAATTTGACGTTAAACAATTTACA 9 109 0 AAATTTACAA 0.560953 -67 GTGACTTAAGAAAATTTATACAAATCAGCAATAT 13 138 1 AAAATTATAA 0.690527 -124 AAAGTTCTAAAAATTTTATGAAAAAT 21 3 0 AAATTTATAA 0.470947 -119 ATTCACGTTCAAATTTTGTTCAAAAAGTGTTATC 23 11 1 AAATTTGTAA 0.640412 -290 TCTCAGATTCAAATTGATATAAAGGACGGAGGA 24 10 1 CAAATTATAA 0.782306 -30 GAATTGTGCTAAAATTTACTACAAATCTAAAAAC 25 13 1 AAAATTACAA 0.762051 -288 TCAAATGTGACAAATTTGTGTCAATGACAAATAT 34 12 0 CAAATTGTAA 0.877896 -251 CGAATAGTGAAAAATTCGCGATAATGGACATATG 37 25 0 AAAATTGCAA 0.865 -238 AAATAACCTACAATTTAGCCTGAAAACACAAATT 37 124 0 CAATTTGCAA 0.804569 -139 GATTTTAGATCAAATTCGATATAATTCTAGATGT 37 173 1 CAAATTGAAA 0.502898 -90 TTTTTTGATACAAATTAATAAAAACCGTCAATAT 38 221 1 CAAATTATAA 0.782306 -44 GGCAAGACCTAAAATTTGCGTAAATGAAAAAGGA 44 77 0 AAAATTGCAA 0.865 -224 CATGTAGACAAAAATTCGTAAAAATTAATTGTGA 44 218 1 AAAATTGTAA 0.816989 -83 ****** ** ** Masking position 6 Map Score: 10.6689 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 69 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 11 CGATCAAATTGGCTGAAAGGCGGTAATTTAG 1 25 1 GGCTGAAGGC 0.914968 -276 TATCTCGCCTGGCTTATAGGCCCGTAACTCG 4 207 0 GGCTTAAGGC 0.747383 -94 CGTTCGGTAGGCCTGATAAGAAGCGCATCAG 5 15 0 GCCTGAAAGA 0.922966 -286 TTTATCAGAGGGCCGACAGGCTCCCACAGGA 7 272 1 GGCCGAAGGC 0.829069 -29 ACGCACCACTGCCTGACAGGCCAGTTAAAAA 8 65 0 GCCTGAAGGC 0.612504 -167 ATCTTTCCAGGCCTGATAAGCGTAGCGCATC 10 47 0 GCCTGAAAGC 0.979643 -136 GCCAGAAAAGAGGTGGTTTCT 17 1 1 GCCAGAAAGA 0.826822 -79 TAACAACAACGCCAGAAAACCGACTTCAGGA 17 44 0 GCCAGAAACC 0.822834 -36 TTATTCTTATGCCTTAAAAGCGTGAGACAGG 23 220 1 GCCTTAAAGC 0.868201 -81 TCACAGTTATGCAAGAAAGGCAATAAAAAAG 34 212 0 GCAAGAAGGC 0.663635 -51 CTACAATTTAGCCTGAAAACACAAATTAGTA 37 120 0 GCCTGAAACA 0.720306 -143 CTGAAACAAAGCTTGAAAAGCTGCACATATA 38 163 0 GCTTGAAAGC 0.798812 -102 ****** **** Masking position 6 Map Score: 4.93947 Number of sites scoring better than the average of aligned sites = 836 Number in coding regions = 603 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 12 ATATTACGCCGCAAAATCCTTACAATAAAC 1 106 0 GCAAAATCCT 0.889077 -195 GAATGTATCGTCACATTCATTAA 6 4 0 TCACATTCAT 0.679817 -297 CCGTTTATTTGCACAATTCTACTTTTGCGT 15 13 0 GCACAATTCT 0.889077 -288 ATTGAATAAGTCAAAATCCTTTACTCTCTC 23 91 0 TCAAAATCCT 0.895514 -210 GTGAATTCATGCACAATCATTTACAAAAAT 23 185 0 GCACAATCAT 0.832918 -116 GTGCATGAATTCACAATCCTTATTCTTATG 23 201 1 TCACAATCCT 0.97191 -100 GTAAATTTTAGCACAATTCTA 25 2 0 GCACAATTCT 0.889077 -299 CACGTTCATTTCACATTTCTTACTTTTTGA 29 69 0 TCACATTTCT 0.773439 -63 ACAAGCTTTTTCAAATTCCTATGCCAAATC 30 28 0 TCAAATTCCT 0.773439 -64 GTGATGTAATTCACAATCCTGTTTGGCTAG 42 67 1 TCACAATCCT 0.97191 -69 GCTTTACCAGTCACAATCCCGCTTATTCAG 44 112 1 TCACAATCCC 0.866949 -189 ********** Masking position 5 Map Score: 5.48472 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 72 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 TTTTTAGCGCGAGAGCCTTTTTTGTCAGCTA 2 74 1 GAAGCCTTTT 0.923035 -118 CTGATATACAGATAGCCTTTTTACCTCTTAA 25 199 0 GAAGCCTTTT 0.92302 -102 GTGAAATTTAGAAAGCGTTTTTACCGTGATC 29 31 0 GAAGCGTTTT 0.975231 -101 CCCTTTTTCAGGGAGAGTTTTTTTATGTTTG 31 21 1 GGAGAGTTTT 0.710098 -102 AGTATTGGACGAGAGCTTTTTGGTGGCTTAT 33 203 1 GAAGCTTTTT 0.814718 -78 AAGAAGTAATGGAGGCGTTTTATT 34 249 1 GGGGCGTTTT 0.853948 -14 ATAATAGATAGGAAGCGTTTTCTTTGAAGGG 38 135 0 GGAGCGTTTT 0.96556 -130 TATAAACAGAGACAGCGTGTTTCCTTGTGAA 40 135 0 GAAGCGTGTT 0.901961 -61 GATTTATGATGAAAGCGTATTCTTAATCTGA 44 138 0 GAAGCGTATT 0.861251 -163 CATAAATCATGATAGCGTTTTCGTCAACTAT 44 161 1 GAAGCGTTTT 0.975233 -140 ** ******** Masking position 8 Map Score: 7.37971 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 53 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 AAATTGATCACCGTCGAAAAATGCAAATTT 1 60 1 CCGTCGAAAA 0.690884 -241 TTTTACAGCACCGTGAAAAATCTCATAATT 6 140 1 CCGTGAAAAA 0.846612 -161 GTCTCTCTTGCCGTTAAAAATTAAGCTGAA 8 23 1 CCGTTAAAAA 0.710117 -209 GCAGTAATACCCCTGAAAAAAGAGGAAAGC 8 211 1 CCCTGAAAAA 0.846612 -21 AGTCTTCCCTCAAGAAAAATCAGGCC 10 167 0 CCCTCAAGAA 0.817415 -16 TTCTAAATAGCCTTCAAGAACAAGGCCATC 12 56 1 CCTTCAAGAA 0.862783 -215 GATTGGCCTGCGTTCAAAAATAAAATGGCA 12 251 0 CGTTCAAAAA 0.660198 -20 ATTTGATTATCCTTTAAAAAATAAAAACAA 14 31 0 CCTTTAAAAA 0.774799 -270 TTGTTGCTGACCTTCAAAAATTACCCTGCC 15 41 0 CCTTCAAAAA 0.952158 -260 TTTCACATAACCTTCAAAAAGTAAGAAATG 29 56 1 CCTTCAAAAA 0.952158 -76 AAAAAACTCTCCCTGAAAAAGGGAGAGTAA 31 14 0 CCCTGAAAAA 0.846612 -109 TGTACAAACTCCTTCAAAACAGGATATGAA 33 171 1 CCTTCAAAAC 0.7584 -110 TTTCATTACCCCTTCAAAGAAAACGCTTCC 38 126 1 CCTTCAAAGA 0.758377 -139 ********** Masking position 7 Map Score: 5.08446 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 69 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 AGGGTCACACGCATGCCCCAATAGAAATTT 1 233 0 GCATGCCCCA 0.912476 -68 GCCAGCATTTGCTGGCCCCAGATTGATAAC 10 140 0 GCTGGCCCCA 0.977732 -43 ATTTTTGAACGCAGGCCAATC 12 260 1 GCAGGCCAAT 0.800214 -11 CCATGGCGGAGCTGACCCAAAAGCCGAGCG 14 129 0 GCTGACCCAA 0.84976 -172 TCATGACATTGCTCGCCCCTATGTGTAACA 15 203 0 GCTCGCCCCT 0.859459 -98 GTATTTAATCGCTGTCCCAATCTTCGGCGG 28 74 1 GCTGTCCCAA 0.762331 -62 GATAAAAAGGGCAGGCCAAACCG 28 123 1 GCAGGCCAAA 0.826378 -13 TAACTTGTATGCATACCCATACAACAATAT 34 136 0 GCATACCCAT 0.530547 -127 AAATATTTCCGCAGGCCGCTACGATAATAA 36 91 1 GCAGGCCGCT 0.81877 -210 TGTTTATCCGGCTGGCCCAAGAAACATTCA 36 142 0 GCTGGCCCAA 0.970342 -159 TTGGCTTGCCCCTTTCAATGATT 42 123 0 GCTTGCCCCT 0.912476 -13 ********** Masking position 6 Map Score: 4.32026 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 289 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925