AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inarP_ecoli_hinf_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 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #2 ccmC 41 heme exporter protein C #3 napF 300 ferredoxin-type protein: electron transfer #4 yhfC 270 putative transport #5 nirB 261 nitrite reductase (NAD(P)H) subunit #6 nirC 300 nitrite reductase activity #7 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #8 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #9 nrfE 79 formate-dependent nitrite reductase; possible assembly function #10 HI0007 300 formate dehydrogenase, beta subunit (fdxH) #11 HI0340 82 conserved hypothetical protein #12 HI0341 84 conserved hypothetical protein #13 HI0342 205 ferredoxin-type protein (napF) #14 HI0343 180 napD protein (napD) #15 HI0345 300 ferredoxin-type protein (napG) #16 HI0936 108 cytochrome C-type biogenesis #17 HI0937 200 extragenic suppressor (suhB) #18 HI1068 43 nitrite reductase, cytochrome C-type protein (nrfB) #19 HI1069 161 nitrite reductase, cytochrome C552 (nrfA) #20 HI1074 264 conserved hypothetical protein #21 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) #22 HI1089 248 heme exporter ATP-binding protein A (ccmA) #23 HI1091 57 heme exporter protein C (ccmC) #24 HI1092 41 heme exporter protein D (ccmD) #25 HI1095 138 thiol:disulfide interchange protein (dsbE) Motif number 1 ACAATTTTACCTGCTCTTTTAGTGTTAAAT 3 14 1 CTGCTCTTTT 0.732114 -287 ACGCTTCCCGCCACTCTTTTGATCCTGCTA 3 145 1 CCACTCTTTT 0.888298 -156 CTATCGTCGTCCGGCCTTTTCCTCTCTTCC 5 30 1 CCGGCCTTTT 0.88837 -232 TTCTATAAACCCGCTCATTTTGTCTATTTT 5 78 1 CCGCTCATTT 0.981026 -184 GCAGCGTTAGCCGCACACTTATTAATAGTG 6 70 0 CCGCACACTT 0.917499 -231 CCTTTTTCTGCCGCTAATTTTTCGC 10 6 0 CCGCTAATTT 0.888298 -295 GGTATAATCGCCGCCAATTTTTTCACGAAC 11 54 1 CCGCCAATTT 0.939847 -29 TTGTGCTACGCCACCCATTTGTAATTTGAA 14 70 0 CCACCCATTT 0.939847 -111 TCCACTTTTACCGCACATTTTTTGAAGTCG 15 214 0 CCGCACATTT 0.988725 -87 TAAAAATCAACCGCACTTTATTTTCTCCCA 15 265 1 CCGCACTTTA 0.934019 -36 CAATTTTCCACCGCACTTTAACCATAAATG 17 20 1 CCGCACTTTA 0.934019 -181 GAAAAATGCACCGCACTTTTTAGTGCAAAC 18 13 1 CCGCACTTTT 0.988725 -31 AGTAGAATAGCCGCCAATTTGGATTATCTC 21 127 1 CCGCCAATTT 0.939847 -174 AGAAAAACCACCGCACTTTTATACGATGAA 23 16 0 CCGCACTTTT 0.988725 -42 TAACTTTGCTCCACCCATTTATGGGGGGAG 25 99 0 CCACCCATTT 0.939847 -40 TTTTTACCGCACTTTTTCATTAACTT 25 123 0 CCGCACTTTT 0.988725 -16 ********** Masking position 9 Map Score: 29.0605 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 251 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 2 GCACTATCGTCGTCCGGCCTTTTCCTCTCTT 5 27 1 CTCCGGCCTT 0.878211 -235 TCGATCCATCCGTACGCCCTTTGGTGATGGG 6 213 1 CTACGCCCTT 0.829504 -88 TTCACGACAGTAACCGCACCTACACTGTCAT 7 229 0 TACCGCACCT 0.969759 -72 TCCATTGTGTTTTCCGCCCCTTGCGAGGCGG 8 18 0 TTCCGCCCCT 0.931892 -21 TTTTCCACTTTTACCGCACATTTTTTGAAGT 15 216 0 TACCGCACAT 0.921611 -85 ATGTAAAAATCAACCGCACTTTATTTTCTCC 15 262 1 CACCGCACTT 0.993747 -39 CTCCAATTTTCCACCGCACTTTAACCATAAA 17 17 1 CACCGCACTT 0.993747 -184 ATGAAAAATGCACCGCACTTTTTAGTGCAA 18 10 1 GACCGCACTT 0.968306 -34 TCCATTTTTTTAACCGCACTTT 20 253 1 TACCGCACTT 0.988173 -12 AAGAGAAAAACCACCGCACTTTTATACGATG 23 18 0 CACCGCACTT 0.993747 -40 CGTAATCCCCCTTCCGCCCTTCGGGCACCTT 25 42 0 CTCCGCCCTT 0.985467 -97 TTTTTACCGCACTTTTTCATTAAC 25 125 0 TACCGCACTT 0.988173 -14 * ********* Masking position 11 Map Score: 21.1604 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 104 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 TTAAGCTGAATTTTATAGCATTTTTTTAACTGGCCT 1 43 1 TTTTATTTTT 0.717642 -189 TTTTGTGATCTGTTTAAATGTTTTATTGCAATCGGT 4 179 0 TGTTTTTTTT 0.832866 -92 GAGCGGGCGATTTTAGGTGATTTTGTGATCTGTTTA 4 199 0 TTTTATTTTT 0.717642 -72 TAAACTTTTTGTTTTATTTTTTGTTTTTATT 6 6 1 TTTTTATTTT 0.524169 -295 TTTTATTTTTTGTTTTTATTTTTTAAAGGATAATCA 6 22 1 TGTTTTTTTA 0.912128 -279 GCAATGGCGGTTTTTATTGTTTTTCACGACAGTAAC 7 246 0 TTTTTTTTTA 0.941866 -55 AAATAGGTAGTTTTTCAATTATTTGAACTTTATTTG 13 103 0 TTTTTATTTA 0.696477 -103 TATTTTGGGTTGTTTTCATTCATTCATCGTAAACAC 13 134 1 TGTTTCATTA 0.748788 -72 TTTGTTTTAGATCATTCATTGTTATTGC 14 163 0 TGTTTCATTA 0.748788 -18 CCTTTTCCACTTTTACCGCACATTTTTTGAAGTCGG 15 213 0 TTTTACATTT 0.421908 -88 TGCGGTTGATTTTTACATGGTTTTTACGCAGCCTTT 15 244 0 TTTTATTTTA 0.841125 -57 CAAGGTGCTATTTTTAATTTTATTAATGAAACATAC 16 36 1 TTTTTTATTA 0.8661 -73 GATCAAGTGATTTTTCTACCCATTCATTTATGGTTA 17 38 0 TTTTTCATTA 0.823081 -163 AAAACAGTGGTTTTTATAGGTTTTCAGAAAAACTTT 17 96 0 TTTTTTTTTA 0.941866 -105 TAAAAACCACTGTTTTATGATTTTCAACTAGTTATT 17 116 1 TGTTTTTTTA 0.912128 -85 TGGCACGGAATTTTTCTGTTCTTTAAAAGCTGGTGG 17 171 1 TTTTTCTTTA 0.920968 -30 AATATACCTCTTTTTGAGTATTTTAAAAGATAAGCT 19 69 1 TTTTTTTTTA 0.941866 -93 AAATTTACCTTTTTTTTCTTTATTGATGGTGCATTT 20 75 0 TTTTTTATTA 0.8661 -190 AGGGCTTATTTGTTATATTTTATTTAATTGACTTAG 21 22 0 TGTTATATTA 0.575227 -279 TATATAGCATTTTTTACTATTTTTTATCCTTATGTT 21 87 1 TTTTTTTTTA 0.941866 -214 ATAACTGGTGTTTTTTTAACCTTTAAAAATAATTAT 21 161 1 TTTTTCTTTA 0.920968 -140 GATCATTAAATGTTTTTCCTTTTTTAAAAAGTGAAT 22 101 1 TGTTTTTTTA 0.912128 -148 TTCTCTTTAATTTTTAAGGATTTTTT 23 42 1 TTTTTTTTTT 0.886077 -16 GTGCGGTTAGTTTTTAGCGATTTTTTATAAGGAATA 24 12 1 TTTTTTTTTT 0.886077 -30 TTTTTACCGCACTTTTTCATTAACTTT 25 122 0 TTTTACTTTT 0.646401 -17 ***** **** * Masking position 4 Map Score: 24.6112 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 190 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 4 TATTAATAAGTGTGCGGCTAACGCTGCGCG 6 73 1 TGTGCGGCTA 0.861267 -228 CAACATTCACAGTGTGGTTATTTGTTACAC 7 181 1 AGTGTGGTTA 0.903327 -120 TGACAGTGTAGGTGCGGTTACTGTCGTGAA 7 230 1 GGTGCGGTTA 0.965167 -71 CTTCAAAAAATGTGCGGTAAAAGTGGAAAA 15 217 1 TGTGCGGTAA 0.923479 -84 GAGAAAATAAAGTGCGGTTGATTTTTACAT 15 262 0 AGTGCGGTTG 0.988295 -39 TTATGGTTAAAGTGCGGTGGAAAATTGGAG 17 17 0 AGTGCGGTGG 0.985845 -184 TGCACTAAAAAGTGCGGTGCATTTTTCAT 18 10 0 AGTGCGGTGC 0.962937 -34 AAAGTGCGGTTAAAAAAATGGA 20 253 0 AGTGCGGTTA 0.991638 -12 ATCGTATAAAAGTGCGGTGGTTTTTCTCTT 23 19 1 AGTGCGGTGG 0.985845 -39 AGTGCGGTTAGTTTTTAGCG 24 1 1 AGTGCGGTTA 0.991638 -41 TTAATGAAAAAGTGCGGTAAAAA 25 126 1 AGTGCGGTAA 0.977485 -13 ********** Masking position 3 Map Score: 20.6436 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 64 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 GCCACAAAATAATCCGCCTTCGCAAATTGA 1 119 0 AATCCGCCTT 0.963119 -113 TCCGTGATCAAAATCACCTCTTAAAATGCA 4 141 1 AAATCACCTC 0.835033 -130 ATGTAAATCAAATTCACCTTTATATACTCC 5 181 0 AATTCACCTT 0.708117 -81 GCGACCTTTGGTATCGCCTTAACGCTGGTG 6 245 1 GTATCGCCTT 0.654777 -56 AAAACAATAAAAACCGCCATTGCAACAATG 7 259 1 AAACCGCCAT 0.835861 -42 CCCCGTTCCGCCTCGCAAGGGGCG 8 5 1 GTTCCGCCTC 0.749953 -34 ATACGTCCAGAAACCACCTCTTTTCTGGC 9 10 0 AAACCACCTC 0.945664 -70 CAACGCCAGAAAACCGACTTCAGGAAGGAA 9 39 0 AAACCGACTT 0.847277 -41 AATTTTTACCATATCGCCTTTTTGGATGCC 10 34 0 ATATCGCCTT 0.883664 -267 ATAAGAAATCATTTCGCCTCGACGAGATGA 15 65 0 ATTTCGCCTC 0.777454 -236 CGGACGTAATAAACCACCTCGTGGCTTAGT 15 106 1 AAACCACCTC 0.945664 -195 ATTTCAAAAGAAACCGACTTCAAAAAATGT 15 200 1 AAACCGACTT 0.847277 -101 AGGCGGTATAAAACCGCCTTAATTTTGAGT 19 21 0 AAACCGCCTT 0.982337 -141 AGGCGGTTTTATACCGCCTTAATTTATTTA 19 32 1 ATACCGCCTT 0.963123 -130 TTAAAGAGAAAAACCACCGCACTTTTATAC 23 22 0 AAACCACCGC 0.702503 -36 GGGGATACGTAATCCCCCTTCCGCCCTTCG 25 50 0 AATCCCCCTT 0.753087 -89 ********** Masking position 5 Map Score: 14.8769 Number of sites scoring better than the average of aligned sites = 654 Number in coding regions = 590 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 CTTCGCAAATTGACCTACCTCAATAGCGGTAGA 1 99 0 TGACTCTCAA 0.774806 -133 TTTTAAGAGGTGATTTTGATCACGGAATAAAAA 4 134 0 TGATTATCAC 0.751481 -137 GGTATATTGCTGATTTGTATAAATTTTCTTAAG 5 142 0 TGATTATAAA 0.70305 -120 AAGGTGAATTTGATTTACATCAATAAGCGGGGT 5 191 1 TGATTATCAA 0.962122 -71 CTTTTGTTGCTGACCTTCAAAAATTACCCTGCC 7 41 0 TGACTAAAAA 0.706275 -260 CTGTGAATGTTGTCTTTAATCAATTGTAAGTGC 7 160 0 TGTTTATCAA 0.671074 -141 TTAGATTTTTTGATCTATAACAAATAAAGTTCA 13 83 1 TGACTAACAA 0.962684 -123 TTACGATGAATGAATGAAAACAACCCAAAATAG 13 133 0 TGATGAACAA 0.729652 -73 TAACAATGAATGATCTAAAACAAA 14 167 1 TGACTAACAA 0.962684 -14 ATTTGCAAGCTGACCTGCATCAAAGAAAGTGGT 15 140 0 TGACTATCAA 0.966558 -161 CACTGTTTTATGATTTTCAACTAGTTATTTTGG 17 123 1 TGATTAACTA 0.645524 -78 CCGCCTTAATTTATTTAAAACAACAATATACCT 19 45 1 TTATTAACAA 0.678454 -117 TGCTAAAGTTTGAGCTTGATCAAGCTTATCTTT 19 94 0 TGACTATCAA 0.966558 -68 TTTATTTAATTGACTTAGATCAAATTGAC 21 7 0 TGATTATCAA 0.962123 -294 ATAAACAACATTAGTTCCAACAATGATTAACAA 21 263 0 TTATTAACAA 0.678793 -38 AAACATTTAATGATCTAAATCAATTTTTTTGCT 22 83 0 TGACTATCAA 0.966558 -166 ATAGGTTTATTGATTTAAAACAAAATTTAATAA 22 137 0 TGATTAACAA 0.957749 -112 *** ** ***** Masking position 1 Map Score: 19.1371 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 90 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 GTCAAAGATGCATACCCCGATCGGGGTAAAAC 3 178 0 CATCCCGATC 0.880442 -123 ACCTTCCATCATTAACGCGCTCTGAAAATTGA 3 275 0 ATTCGCGCTC 0.933645 -26 AATCACCTAAAATCGCCCGCTCGCGGCATATC 4 213 1 AATCCCGCTC 0.984434 -58 CCGCTCGCGGCATATCCCGCTATGCCATTTTA 4 229 1 CATCCCGCTA 0.956354 -42 CTTTTCCTCTCTTCCCCCGCTACGTGCATCTA 5 45 1 CTTCCCGCTA 0.961404 -217 ATCTATTTCTATAAACCCGCTCATTTTGTCTA 5 72 1 ATACCCGCTC 0.868101 -190 CCTGTCGGCAAATAACCCGCTCGGCTTTTGGG 6 112 1 AATCCCGCTC 0.984434 -189 GATCATCCTGATTTTCACGCTCGGTAATTTGC 6 181 1 ATTCACGCTC 0.837625 -120 ACGCTCGGTAATTTGCTCGATCCATCCGTACG 6 197 1 ATTCTCGATC 0.356383 -104 TGCCAAGATAATTGTCCAGCTAATGCGATTCG 14 37 1 ATTCCAGCTA 0.565074 -144 GCCTTTTCCACTTTTACCGCACATTTTTTGAA 15 218 0 CTTACCGCAC 0.831827 -83 ACCATGTAAAAATCAACCGCACTTTATTTTCT 15 259 1 AATACCGCAC 0.800436 -42 ATGAAAAATGCACCGCACTTTTTAGTGC 18 7 1 AATACCGCAC 0.800436 -37 ATTGATGGTGCATTTCGCGCTAGCCAAATTGC 20 58 0 CATCGCGCTA 0.810904 -207 CTTCGGGCACCTTCCCCCGCAAGCAGGGGAAG 25 23 0 CTTCCCGCAA 0.904692 -116 *** ******* Masking position 9 Map Score: 9.86771 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 896 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 8 TGCTTTCCTCTTTTTTCAGGGGT 1 219 0 TTTCCTCTTT 0.972879 -13 CGTCCGGCCTTTTCCTCTCTTCCCCCGCTA 5 37 1 TTTCCTCTCT 0.8603 -225 TAGTCAGTATCTTCCTCTTTTTCAACAGCA 7 108 0 CTTCCTCTTT 0.939115 -193 TGCATGTAAAATACCACTTTAGAGTTAGTC 7 133 0 ATACCACTTT 0.728438 -168 GGCTTAGTATTTACCACTTTCTTTGATGCA 15 128 1 TTACCACTTT 0.9061 -173 TACGCAGCCTTTTCCACTTTTACCGCACAT 15 226 0 TTTCCACTTT 0.948993 -75 CTTCCTCTTTTATTGATGGG 15 291 0 CTTCCTCTTT 0.939115 -10 AAACAACAATATACCTCTTTTTGAGTATTT 19 62 1 ATACCTCTTT 0.837975 -100 TTCCTCAAATTTACCTTTTTTTTCTTTATT 20 87 0 TTACCTTTTT 0.804196 -178 TTTACCAAAATTTCCATTTTTTTAACCGCA 20 241 1 TTTCCATTTT 0.804196 -24 ATTAAATGTTTTTCCTTTTTTAAAAAGTGA 22 105 1 TTTCCTTTTT 0.887878 -144 GTGCGGTGGTTTTTCTCTTTAATTTTTAAG 23 30 1 TTTTCTCTTT 0.720194 -28 ********** Masking position 8 Map Score: 11.3314 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 165 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 TGTCTCTCTTGCCGTTAAAAATTAAGCTGAA 1 22 1 GCCGTAAAAA 0.970418 -210 TACCTCAATAGCGGTAGAAAAACGCACCACT 1 86 0 GCGGTGAAAA 0.905728 -146 AAAATAATCCGCCTTCGCAAATTGACCTACC 1 113 0 GCCTTGCAAA 0.826577 -119 GAGATTTCCTTAACAAACAGAGCAGAA 4 7 1 TCCTTACAAA 0.426508 -264 ATTCTAAATAGCCTTCAAGAACAAGGCCATC 4 55 1 GCCTTAAGAA 0.790131 -216 GATTGGCCTGCGTTCAAAAATAAAATGGCA 4 251 0 GCGTTAAAAA 0.93087 -20 CATTTGATTATCCTTTAAAAAATAAAAACAA 6 31 0 TCCTTAAAAA 0.772443 -270 TTTGTTGCTGACCTTCAAAAATTACCCTGCC 7 41 0 ACCTTAAAAA 0.829482 -260 AGTTATGCATGCTGTTGAAAAAGAGGAAGAT 7 99 1 GCTGTGAAAA 0.597799 -202 TGCGGTTACTGTCGTGAAAAACAATAAAAAC 7 242 1 GTCGTAAAAA 0.619315 -59 AATCAACCTTGGAAAAAATTTGCCCT 11 6 1 ACCTTGAAAA 0.769915 -77 TATAGAATATGCCTTCAAATATAACCTTAAT 12 52 1 GCCTTAAATA 0.70532 -33 AAAAGAAACCGACTTCAAAAAATGTGCGGTA 15 205 1 GACTTAAAAA 0.610663 -96 TGGTTAAAGTGCGGTGGAAAATTGGAGCGTT 17 13 0 GCGGTGAAAA 0.905728 -188 ATAAATTAAGGCGGTATAAAACCGCCTTAAT 19 28 0 GCGGTTAAAA 0.597799 -134 AAAGTGCGGTTAAAAAAATGGAAATT 20 249 0 GCGGTAAAAA 0.933186 -16 TGTTTTTTTAACCTTTAAAAATAATTATGTA 21 169 1 ACCTTAAAAA 0.829482 -132 ACAAGGCGATGCCTTAAATAATCCCTAATTA 21 236 0 GCCTTAATAA 0.717535 -65 ***** ***** Masking position 5 Map Score: 9.47728 Number of sites scoring better than the average of aligned sites = 770 Number in coding regions = 675 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 10 GCATAATTAATAAGCCATTTTTATAGCCGCT 3 227 0 TAAGCATTTT 0.868958 -74 GCTTATTAATTATGCGGTTTATTTGGTCGCT 3 243 1 TATGCGTTTA 0.866635 -58 CACCTCTTAAAATGCAATTTAGCAACCGATT 4 155 1 AATGCATTTA 0.568707 -116 CATATCCCGCTATGCCATTTTATTTTTGAAC 4 239 1 TATGCATTTT 0.943337 -32 CACGGTTACCTTTGCCATTTAATGCCTTCAT 10 175 0 TTTGCATTTA 0.805206 -126 CAATTTTGACTATGCTGTTTTCAATTTAGA 13 10 0 TATGCGTTTT 0.912486 -196 TCAAAATTGCTATGCTGTTTTGTTTTAATCC 13 32 1 TATGCGTTTT 0.912486 -174 CATCTAGTGTTAAGCTATTTGCAAGCTGACC 15 158 0 TAAGCATTTG 0.866663 -143 TAGAATGTTATATGCGATTTGGGTAGTGGGT 20 18 1 TATGCATTTG 0.942258 -247 GGGTGTATTGTTTGCAATTTGGCTAGCGCGA 20 45 1 TTTGCATTTG 0.866664 -220 CGGTTAGTTTTTAGCGATTTTTTATAAGGAA 24 15 1 TTAGCATTTT 0.725376 -27 ***** ***** Masking position 8 Map Score: 6.33445 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 63 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 11 TCTACCGCTATTGAGGTAGGTCAATTTGCGAA 1 99 1 TTGAGTAGTC 0.722541 -133 ACCCCGCTTATTGATGTAAATCAAATTCACCT 5 192 0 TTGATTAATC 0.95667 -70 GTGTGGTTATTTGTTACACATAGGGGCGAGCA 7 192 1 TTGTTCAATA 0.638511 -109 TGAACTTTATTTGTTATAGATCAAAAAATCTA 13 84 0 TTGTTTAATC 0.948926 -122 TTTGTTTTAGATCATTCATTGTT 14 168 0 TTGTTTAATC 0.948926 -13 ACCACTTTCTTTGATGCAGGTCAGCTTGCAAA 15 140 1 TTGATCAGTC 0.841452 -161 AGGTATATTGTTGTTTTAAATAAATTAAGGCG 19 46 0 TTGTTTAATA 0.8215 -116 GTCAATTTGATCTAAGTCAATTAAATAA 21 7 1 TTGATTAGTC 0.932561 -294 GATCACATTTTTGATATAAATACAAAAATAGG 21 55 0 TTGATTAATA 0.845414 -246 AGCAAAAAAATTGATTTAGATCATTAAATGTT 22 83 1 TTGATTAATC 0.95667 -166 TTATTAAATTTTGTTTTAAATCAATAAACCTA 22 137 1 TTGTTTAATC 0.948926 -112 ***** ** *** Masking position 8 Map Score: 8.59555 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 45 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 ACCCACATACGCGCCCGCCATGGCGGAGCT 6 146 0 GCGCCCGCCA 0.960066 -155 ACCAAAGGTCGCGCCCATCACCAAAGGGCG 6 227 0 GCGCCCATCA 0.971137 -74 GGTGTACGACACGCCCATCAATTTCGAGAT 10 119 0 ACGCCCATCA 0.942165 -182 AGGTTGTGCTACGCCACCCATTTGTAATTT 14 73 0 ACGCCACCCA 0.924226 -108 CACTTTATTTTCTCCCATCAATAAAAGAGG 15 278 1 TCTCCCATCA 0.802558 -23 TAATTACTCAACTCCAATCAGCTAAGTTTA 21 212 0 ACTCCAATCA 0.800584 -89 CTTCGCGACAGCTCCCCCCATAAATGGGTG 25 88 1 GCTCCCCCCA 0.975979 -51 CATTAACTTTGCTCCACCCATTTATGGGGG 25 102 0 GCTCCACCCA 0.940766 -37 ********** Masking position 10 Map Score: 4.38612 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 365 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 TTTCTGCTGGTTTGCTCTCTCATTAGAATTTAA 3 38 0 TTTGCCCTCT 0.957301 -263 AAAACGGGCTTTTGCTCACATTTCAAATGGTTA 3 108 0 TTTGCCCATT 0.859472 -193 TTGTCTATTTTTTGCACAAACATGAAATATCAG 5 97 1 TTTGCCAACT 0.897712 -165 CGCTGCGCGCATTGCACGCCTGTCGGCAAATAA 6 94 1 ATTGCCCCTT 0.84589 -207 CGCTCGGTAATTTGCTCGATCCATCCGTACGCC 6 198 1 TTTGCCATCA 0.856079 -103 CTGCCGTTTATTTGCACAATTCTACTTTTGCGT 7 13 0 TTTGCCATTT 0.946989 -288 CTGTCATGACATTGCTCGCCCCTATGTGTAACA 7 203 0 ATTGCCCCCT 0.880468 -98 CTTCATCCGAATTGCGCCATTGTTGCAATGGCG 7 273 0 ATTGCCATTT 0.87678 -28 TTGGAAAAAATTTGCCCTATTATACGAGAAAAA 11 19 1 TTTGCCATTT 0.946989 -64 TTTGCTATTATTTGCTCAATTTTGGTTATAGAC 22 56 0 TTTGCCATTT 0.946989 -193 TTTCATTAACTTTGCTCCACCCATTTATGGGGG 25 102 0 TTTGCCACCA 0.830691 -37 ***** * *** * Masking position 3 Map Score: 7.24002 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 100 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 14 CTAAAAGAGCAGGTAAAATTGTCTG 3 6 0 AGGTAAAATT 0.896721 -295 TATTTCAGATACGTAAAATTAGGTAAAGGG 4 85 0 ACGTAAAATT 0.725621 -186 AAAGGCGATATGGTAAAAATTACTTCTCGT 10 43 1 TGGTAAAAAT 0.930722 -258 AAAACATTCTTGGTAAATATTGAAAAAGTT 10 268 1 TGGTAAATAT 0.875736 -33 AATCAACCTTGGAAAAAATTTGCCCTATT 11 10 1 TGGAAAAAAT 0.679268 -73 AAGAAAAAAAAGGTAAATTTGAGGAATAAA 20 91 1 AGGTAAATTT 0.819966 -174 TTTATTTAGTTGGTAAAATTCTTAAATCAT 20 120 0 TGGTAAAATT 0.943026 -145 GCATAGAAATTCGTAAAATTATTTTCCATT 20 204 0 TCGTAAAATT 0.834478 -61 ATGGAAATTTTGGTAAATATTCTAGCATAG 20 228 0 TGGTAAATAT 0.875736 -37 ********** Masking position 5 Map Score: 3.67383 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 110 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 15 CCGTTTTTGCCACGCTTCCCGCCACTCTTT 3 134 1 CACGCTTCCC 0.794561 -167 CCTTCAAGAACAAGGCCATCCCTTTACCTA 4 66 1 CAAGGCCATC 0.851716 -205 GCGCGCATTGCACGCCTGTCGGCAAATAAC 6 98 1 CACGCCTGTC 0.936855 -203 GACCCACATACGCGCCCGCCATGGCGGAGC 6 147 0 CGCGCCCGCC 0.933024 -154 TACCAAAGGTCGCGCCCATCACCAAAGGGC 6 228 0 CGCGCCCATC 0.911474 -73 GTTTTGTAACCACGGCGACCGCTTTAATAT 10 80 0 CACGGCGACC 0.939548 -221 TGGTGTACGACACGCCCATCAATTTCGAGA 10 120 0 CACGCCCATC 0.964063 -181 GTAGAGAATCCACGGTTACCTTTGCCATTT 10 186 0 CACGGTTACC 0.894579 -115 GGCTTGTGTACAAGGCTGCCCCGTGAATGC 14 135 1 CAAGGCTGCC 0.857992 -46 AAGCTATTTGCAAGCTGACCTGCATCAAAG 15 148 0 CAAGCTGACC 0.782609 -153 TGAGCTTGATCAAGCTTATCTTTTAAAATA 19 87 0 CAAGCTTATC 0.737727 -75 ********** Masking position 1 Map Score: 4.02134 Number of sites scoring better than the average of aligned sites = 1152 Number in coding regions = 1109 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775