AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -inarL_ecoli_hinf_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 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A #2 narK 300 nitrite extrusion protein #3 narG 300 nitrate reductase 1, alpha subunit #4 fdnG 231 formate dehydrogenase-N, nitrate-inducible, alpha subunit #5 ccmC 41 heme exporter protein C #6 napF 300 ferredoxin-type protein: electron transfer #7 nirB 261 nitrite reductase (NAD(P)H) subunit #8 nirC 300 nitrite reductase activity #9 nrfA 300 periplasmic cytochrome c(552): plays a role in nitrite reduction #10 nrfB 38 formate-dependent nitrite reductase; a penta-haeme cytochrome c #11 nrfE 79 formate-dependent nitrite reductase; possible assembly function #12 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #13 HI0007 300 formate dehydrogenase, beta subunit (fdxH) #14 HI0342 205 ferredoxin-type protein (napF) #15 HI0343 180 napD protein (napD) #16 HI0345 300 ferredoxin-type protein (napG) #17 HI0833 22 fumarate reductase, 15 kDa hydrophobic protein (frdC) #18 HI0835 181 fumarate reductase, flavoprotein subunit (frdA) #19 HI0936 108 cytochrome C-type biogenesis #20 HI1047 253 anaerobic dimethyl sulfoxide reductase, chain A (dmsA) #21 HI1068 43 nitrite reductase, cytochrome C-type protein (nrfB) #22 HI1069 161 nitrite reductase, cytochrome C552 (nrfA) #23 HI1089 248 heme exporter ATP-binding protein A (ccmA) #24 HI1091 57 heme exporter protein C (ccmC) #25 HI1092 41 heme exporter protein D (ccmD) #26 HI1095 138 thiol:disulfide interchange protein (dsbE) Motif number 1 GGAGTAATTATTGTTCGGTATCAAAGGGAGACAA 1 30 0 TTGTGATCAA 0.94477 -271 TTATCTATCATTGATATTTATCATTACCCATAGT 2 190 0 TTGTTATCAT 0.908467 -111 ATCTTATCGTTTGATTTACATCAAATTGCCTTTA 2 228 1 TTGTTATCAA 0.499842 -73 CCCATCACTCTTGATCGTTATCAATTCCCACGCT 3 196 1 TTGTGATCAA 0.628065 -105 CCTTCGCAAATTGACCTACCTCAATAGCGGTAGA 4 99 0 TTGCTCTCAA 0.678643 -133 CTGAATCTTTTTGCGCGAAATCAAAAAGAACATC 4 154 0 TTGGGATCAA 0.742355 -78 TGCGGTTTATTTGGTCGCTCTCAATTTTCAGAGC 6 255 1 TTGTGCTCAA 0.778196 -46 AAAGGTGAATTTGATTTACATCAATAAGCGGGGT 7 190 1 TTGTTATCAA 0.499842 -72 ACTGTGAATGTTGTCTTTAATCAATTGTAAGTGC 9 160 0 TTGCTATCAA 0.958612 -141 TGAACTTTATTTGTTATAGATCAAAAAATCTAAG 14 82 0 TTGTTATCAA 0.663912 -124 TTTGTTTTAGATCATTCATTGTTAT 15 166 0 TTGTTATCAT 0.91249 -15 TATTTGCAAGCTGACCTGCATCAAAGAAAGTGGT 16 140 0 CTGCTATCAA 0.723679 -161 CTTAGCTTTTTTGAGGTAGATCACAAAATCCGAT 18 39 1 TTGGTATCAC 0.616505 -143 TAATGATTAATTGATTTGGCTCAAGTAAAACTTC 20 166 1 TTGTTCTCAA 0.713696 -88 AGGTATATTGTTGTTTTAAATAAATTAAGGCGGT 22 44 0 TTGTTATAAA 0.714113 -118 ATGCTAAAGTTTGAGCTTGATCAAGCTTATCTTT 22 94 0 TTGGTATCAA 0.745745 -68 AGCAAAAAAATTGATTTAGATCATTAAATGTTTT 23 83 1 TTGTTATCAT 0.627097 -166 TTATTAAATTTTGTTTTAAATCAATAAACCTATC 23 137 1 TTGTTATCAA 0.663912 -112 *** * * ***** Masking position 11 Map Score: 27.1294 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 54 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 ACAATTTTACCTGCTCTTTTAGTGTTAAAT 6 14 1 CTGCTCTTTT 0.731404 -287 ACGCTTCCCGCCACTCTTTTGATCCTGCTA 6 145 1 CCACTCTTTT 0.891668 -156 CTATCGTCGTCCGGCCTTTTCCTCTCTTCC 7 30 1 CCGGCCTTTT 0.829751 -232 TTCTATAAACCCGCTCATTTTGTCTATTTT 7 78 1 CCGCTCATTT 0.972742 -184 GCAGCGTTAGCCGCACACTTATTAATAGTG 8 70 0 CCGCACACTT 0.891782 -231 CCTTTTTCTGCCGCTAATTTTTCGC 13 6 0 CCGCTAATTT 0.701542 -295 TTGTGCTACGCCACCCATTTGTAATTTGAA 15 70 0 CCACCCATTT 0.895614 -111 TCCACTTTTACCGCACATTTTTTGAAGTCG 16 214 0 CCGCACATTT 0.98122 -87 TAAAAATCAACCGCACTTTATTTTCTCCCA 16 265 1 CCGCACTTTA 0.865612 -36 GAAAAATGCACCGCACTTTTTAGTGCAAAC 21 13 1 CCGCACTTTT 0.983747 -31 AGAAAAACCACCGCACTTTTATACGATGAA 24 16 0 CCGCACTTTT 0.983747 -42 TAACTTTGCTCCACCCATTTATGGGGGGAG 26 99 0 CCACCCATTT 0.895614 -40 TTTTTACCGCACTTTTTCATTAACTT 26 123 0 CCGCACTTTT 0.983747 -16 ********** Masking position 9 Map Score: 18.8408 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 193 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 3 GGGAGACAAAAAAAGCGCCCGCAGGCGC 1 6 0 AAAACCCGCA 0.961625 -295 TAGGATAATTAACAGCCACCACATAACAGACTG 3 128 0 AACAACCACA 0.926924 -173 TAGCGGTAGAAAAACGCACCACTGCCTGACAGG 4 76 0 AAAAACCACT 0.63397 -156 TGAGAGCGACCAAATAAACCGCATAATTAATAA 6 245 0 CAAAACCGCA 0.97203 -56 CGCCTGTCGGCAAATAACCCGCTCGGCTTTTGG 8 110 1 CAAACCCGCT 0.801518 -191 TCAGGATGATCCCAAGACCCACATACGCGCCCG 8 159 0 CCCACCCACA 0.801012 -142 TAGAATTGTGCAAATAAACGGCAGGGTAATTTT 9 22 1 CAAAACGGCA 0.824592 -279 CCTATGTGTAACAAATAACCACACTGTGAATGT 9 183 0 ACAAACCACA 0.806102 -118 TGTTTTTCACGACAGTAACCGCACCTACACTGT 9 232 0 GACAACCGCA 0.856446 -69 CAGCCTTGTACACAAGCCCCACAGCCATTACAA 15 120 0 CACACCCACA 0.922124 -61 CAGCCTTTTCCACTTTTACCGCACATTTTTTGA 16 219 0 CACTACCGCA 0.836209 -82 AAACCATGTAAAAATCAACCGCACTTTATTTTC 16 257 1 AAAAACCGCA 0.968297 -44 CGAAAAATGGCACAATGCCCACACAATATTACC 18 115 1 CACACCCACA 0.922124 -67 CATCAACGAAAAAAACGACGACATT 19 94 1 AAAAACGACA 0.62324 -15 ATGAAAAATGCACCGCACTTTTTAGTG 21 5 1 AAAAACCGCA 0.968297 -39 AATTAAAGAGAAAAACCACCGCACTTTTATACG 24 21 0 AAAAACCGCA 0.968297 -37 AAAATCGCTAAAAACTAACCGCACT 25 3 0 AAAAACCGCA 0.968297 -39 CCCTTCGGGCACCTTCCCCCGCAAGCAGGGGAA 26 24 0 ACCTCCCGCA 0.555841 -115 **** ****** Masking position 9 Map Score: 19.3136 Number of sites scoring better than the average of aligned sites = 674 Number in coding regions = 580 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 TCAGCAGCCAATACCGCATCAGGGATTTTC 1 232 0 ATACCGCATC 0.676625 -69 GCCACAAAATAATCCGCCTTCGCAAATTGA 4 119 0 AATCCGCCTT 0.971575 -113 ATGTAAATCAAATTCACCTTTATATACTCC 7 181 0 AATTCACCTT 0.594205 -81 GCGACCTTTGGTATCGCCTTAACGCTGGTG 8 245 1 GTATCGCCTT 0.740485 -56 AAAACAATAAAAACCGCCATTGCAACAATG 9 259 1 AAACCGCCAT 0.85878 -42 CCCCGTTCCGCCTCGCAAGGGGCG 10 5 1 GTTCCGCCTC 0.836413 -34 ATACGTCCAGAAACCACCTCTTTTCTGGC 11 10 0 AAACCACCTC 0.908187 -70 CAACGCCAGAAAACCGACTTCAGGAAGGAA 11 39 0 AAACCGACTT 0.876928 -41 AATTTTTACCATATCGCCTTTTTGGATGCC 13 34 0 ATATCGCCTT 0.914003 -267 ATAAGAAATCATTTCGCCTCGACGAGATGA 16 65 0 ATTTCGCCTC 0.81805 -236 CGGACGTAATAAACCACCTCGTGGCTTAGT 16 106 1 AAACCACCTC 0.908187 -195 ATTTCAAAAGAAACCGACTTCAAAAAATGT 16 200 1 AAACCGACTT 0.876928 -101 AGGCGGTATAAAACCGCCTTAATTTTGAGT 22 21 0 AAACCGCCTT 0.985163 -141 AGGCGGTTTTATACCGCCTTAATTTATTTA 22 32 1 ATACCGCCTT 0.978272 -130 GGGGATACGTAATCCCCCTTCCGCCCTTCG 26 50 0 AATCCCCCTT 0.784412 -89 ********** Masking position 5 Map Score: 11.5007 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 679 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 ATTTTCACTCGAAAGTAGTATTACGTGTAA 1 68 0 GAAAGTAGTA 0.521147 -233 TACCCCTGAAAAAAGAGGAAAGCA 4 218 1 AAAAGAGGAA 0.941485 -14 GTAGCGGGGGAAGAGAGGAAAAGGCCGGAC 7 38 0 AAGAGAGGAA 0.685833 -224 TCACGCAAAAGTAGAATTGTGCAAAT 9 7 1 AAAAGTAGAA 0.818852 -294 ATGCTGTTGAAAAAGAGGAAGATACTGACT 9 107 1 AAAAGAGGAA 0.941485 -194 GGCAGTGACTAAAAAAAGCACGATCTGATG 12 69 1 AAAAAAAGCA 0.640161 -226 ATTAGCGGCAGAAAAAGGCATCCAAAAAGG 13 18 1 GAAAAAGGCA 0.771004 -283 CTGCATCAAAGAAAGTGGTAAATACTAAGC 16 129 0 GAAAGTGGTA 0.773118 -172 AATGTGCGGTAAAAGTGGAAAAGGCTGCGT 16 225 1 AAAAGTGGAA 0.934008 -76 TCCCATCAATAAAAGAGGAAG 16 290 1 AAAAGAGGAA 0.941485 -11 ATTTGTAACGAAAAATGGCACAATGCCCAC 18 107 1 AAAAATGGCA 0.830505 -75 TAATAAAATTAAAAATAGCACCTTGATAGG 19 31 0 AAAAATAGCA 0.610128 -78 AAAATACTCAAAAAGAGGTATATTGTTGTT 22 63 0 AAAAGAGGTA 0.865024 -99 TTCACTTTTTAAAAAAGGAAAAACATTTAA 23 106 0 AAAAAAGGAA 0.871315 -143 ATTACAGAGGGAAAATAGAAAGTGACAGTA 23 228 0 GAAAATAGAA 0.534849 -21 ********** Masking position 4 Map Score: 9.85126 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 314 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 6 AAGAGATAGGTAGATTTTCACTCGAAAGTA 1 81 0 TAGATTTTCA 0.77174 -220 ACCTATCTCTTTGATTTTCAAATTATTCGA 1 100 1 TTGATTTTCA 0.947416 -201 ATCTTATCGTTTGATTTACATCAAATTGCC 2 228 1 TTGATTTACA 0.840585 -73 ATAAAACGTCTTAATTTACAGTCTGTTATG 3 110 1 TTAATTTACA 0.713463 -191 GGAATTTACTTTATTTTTCATCCCCATCAC 3 174 1 TTATTTTTCA 0.829134 -127 AAAATTCAGCTTAATTTTTAACGGCAAGAG 4 27 0 TTAATTTTTA 0.688033 -205 AAAGGTGAATTTGATTTACATCAATAAGCG 7 190 1 TTGATTTACA 0.840585 -72 TTTTTTGTTTTTATTTTTTAAAGGATAATC 8 27 1 TTATTTTTTA 0.557121 -274 TGGGATCATCCTGATTTTCACGCTCGGTAA 8 178 1 CTGATTTTCA 0.724384 -123 GCGGTTTTTATTGTTTTTCACGACAGTAAC 9 246 0 TTGTTTTTCA 0.911318 -55 CCAAAATAGGTAGTTTTTCAATTATTTGAA 14 112 0 TAGTTTTTCA 0.658511 -94 TAAAGTGCGGTTGATTTTTACATGGTTTTT 16 255 0 TTGATTTTTA 0.823655 -46 CTCGTTTTAGTTATTTTTCAATCTGACTGT 20 220 1 TTATTTTTCA 0.829134 -34 GTTTTTCTCTTTAATTTTTAAGGATTTTTT 24 38 1 TTAATTTTTA 0.688033 -20 ********** Masking position 10 Map Score: 9.49552 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 229 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 7 TTTTTACCAAACCACGGCGACTCACCTCAG 1 258 0 ACCACGGCGA 0.988179 -43 TTTGGTAAAAACGACAGCGATCGGCGGCCT 1 277 1 ACGACAGCGA 0.933432 -24 TACTCGCAACGCGACGGCGAGACAAATTTT 12 17 1 GCGACGGCGA 0.980305 -278 CTTTAATATAGCCACGACGAGAAGTAATTT 13 59 0 GCCACGACGA 0.96968 -242 ACGTTTTGTAACCACGGCGACCGCTTTAAT 13 82 0 ACCACGGCGA 0.988179 -219 AAATCATTTCGCCTCGACGAGATGAAATCT 16 60 0 GCCTCGACGA 0.951722 -241 GTGGTTTATTACGTCCGCGAGTATCTAAAT 16 93 0 ACGTCCGCGA 0.880149 -208 ATAGACCAAAACCTCAACGAAATCTGTTTT 23 32 0 ACCTCAACGA 0.847531 -217 ********** Masking position 10 Map Score: 7.85835 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 313 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 8 AATAAGGAGTAACTCTTTCCGGGTATGGGTATACT 2 65 0 AATCCGGGTA 0.849748 -236 TAGTCGCTTTACATCGGTAAGGGTAGGGATTTTAC 2 111 1 ACTCAGGGTA 0.97672 -190 GAAGTCACTGTACTCACTATGGGTAATGATAAATA 2 175 1 TATCAGGGTA 0.901261 -126 AAGGTGGCAGACATCGAAACGAGTATCAGAGGTGT 2 274 1 ACTCAGAGTA 0.750672 -27 TATTAAGGAGTATTCCCCATGGGTAACATATTAAT 3 33 0 TATCAGGGTA 0.934631 -268 GGCTGTTAATTATCCTAAAGGGGTATCTTAGGAAT 3 144 1 TACCAGGGTA 0.94484 -157 AAATTGACCTACCTCAATAGCGGTAGAAAAACGCA 4 91 0 ACTCACGGTA 0.830516 -141 TACAGGTTTTACCCCGATCGGGGTATGCATCTTTG 6 173 1 ACCCCGGGTA 0.947947 -128 ACCTTTATATACTCCTTAATGGGTATATTGCTGAT 7 161 0 ACCCAGGGTA 0.98289 -101 GATACTGACTAACTCTAAAGTGGTATTTTACATGC 9 127 1 AATCATGGTA 0.640072 -174 ATGACATTGCTCGCCCCTATGTGTAACAAATAACC 9 196 0 TCCCAGTGTA 0.726623 -105 GAATGAAAACAACCCAAAATAGGTAGTTTTTCAAT 14 120 0 AACCAAGGTA 0.710604 -86 TAAAAATAAATCCCCTAAAAGGGTAATATTGTGTG 18 134 0 TCCCAGGGTA 0.96164 -48 ** ** * ***** Masking position 15 Map Score: 9.29151 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 150 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 GTTTTTACCAAACCACGGCGACTCACCTCA 1 259 0 AACCACGGCG 0.976699 -42 TTAATATGTTACCCATGGGGAATACTCCTT 3 34 1 ACCCATGGGG 0.706114 -267 GGGTCAGCTCCGCCATGGCGGGCGCGTATG 8 141 1 CGCCATGGCG 0.499872 -160 CCGCCATTGCAACAATGGCGCAATTCGGAT 9 272 1 AACAATGGCG 0.645423 -29 CTACTCGCAACGCGACGGCGAGACAAATTT 12 16 1 CGCGACGGCG 0.920614 -279 GCTTTAATATAGCCACGACGAGAAGTAATT 13 60 0 AGCCACGACG 0.981981 -241 GACGTTTTGTAACCACGGCGACCGCTTTAA 13 83 0 AACCACGGCG 0.976699 -218 TTAATTTTATCGCCATGACGTAAACCACGT 16 31 0 CGCCATGACG 0.632331 -270 GAAATCATTTCGCCTCGACGAGATGAAATC 16 61 0 CGCCTCGACG 0.893912 -240 GTAAATACTAAGCCACGAGGTGGTTTATTA 16 112 0 AGCCACGAGG 0.93803 -189 ********** Masking position 3 Map Score: 8.7463 Number of sites scoring better than the average of aligned sites = 823 Number in coding regions = 799 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 TGAGCCATTATGAAAACGAAAATCCCTGATG 1 215 1 TAAAACGAAA 0.823686 -86 CGTGGTTTGGTAAAAACGACAGCGATCGGCG 1 272 1 TAAAACGACA 0.898841 -29 AAAACAAAAAATAAAACAAAAAGTTTA 8 7 0 AAAAACAAAA 0.607323 -294 CTTTAAAAAATAAAAACAAAAAATAAAACAA 8 19 0 TAAAACAAAA 0.924083 -282 TACAATTGATTAAAGACAACATTCACAGTGT 9 165 1 TAAGACAACA 0.813428 -136 TCTAAATTGAAAACAGCATAGTCAAAAT 14 8 1 TAAAACAGCA 0.828419 -198 TTGCAAGGGATTAAAACAAAACAGCATAGCA 14 39 0 TAAAACAAAA 0.924083 -167 GATGAATGAATGAAAACAACCCAAAATAGGT 14 131 0 TAAAACAACC 0.813428 -75 CCAAAGTTTATTAAAACATCAATCTACTAAA 20 111 1 TAAAACATCA 0.765126 -143 CTTAATTTATTTAAAACAACAATATACCTCT 22 49 1 TAAAACAACA 0.958594 -113 GTTTATTGATTTAAAACAAAATTTAATAAAT 23 135 0 TAAAACAAAA 0.924083 -114 * ********* Masking position 6 Map Score: 6.865 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 55 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 GCAGGATCAAAAGAGTGGCGGGAAGCGTGG 6 143 0 AAGAGTGGCG 0.676506 -158 CAGCTCCGCCATGGCGGGCGCGTATGTGGG 8 145 1 ATGGCGGGCG 0.847105 -156 ACGCCCTTTGGTGATGGGCGCGACCTTTGG 8 226 1 GTGATGGGCG 0.795171 -75 GATCTCGAAATTGATGGGCGTGTCGTACAC 13 118 1 TTGATGGGCG 0.92656 -183 TAACACCATCTTGGGGTGAGGCAATCACGC 13 224 1 TTGGGGTGAG 0.845834 -77 CAAATTACAAATGGGTGGCGTAGCACAACC 15 72 1 ATGGGTGGCG 0.954369 -109 TCCTCTTTTATTGATGGGAGAAAATAAAGT 16 279 0 TTGATGGGAG 0.887421 -22 AAAGCTAAGATTGAGTTGAGAGTAGCTCTC 18 18 0 TTGAGTTGAG 0.747421 -164 TTACTTTCTATTGATTGGAGGATATC 18 166 1 TTGATTGGAG 0.831223 -16 AGTTATGTGTTTGAGTTGCGAAAATTTCAT 23 186 1 TTGAGTTGCG 0.825671 -63 CCACCCATTTATGGGGGGAGCTGTCGCGAA 26 89 0 ATGGGGGGAG 0.954369 -50 CCCCCCATAAATGGGTGGAGCAAAGTTAAT 26 101 1 ATGGGTGGAG 0.928913 -38 ********** Masking position 3 Map Score: 6.10274 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 560 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 12 TCCTGTGGGAGCCTGTCGGCCCTCTGATAA 3 273 0 GCCTGTCGGC 0.981595 -28 TTTTTAACTGGCCTGTCAGGCAGTGGTGCG 4 65 1 GCCTGTCAGG 0.892444 -167 TTGCTCATGCCGGACGGCACTATCGTCG 7 9 1 GCCGGACGGC 0.809162 -253 AGAGGAAAAGGCCGGACGACGATAGTGCCG 7 25 0 GCCGGACGAC 0.90439 -237 CGCATTGCACGCCTGTCGGCAAATAACCCG 8 101 1 GCCTGTCGGC 0.981595 -200 GGTAATTTTTGAAGGTCAGCAACAAAAGTT 9 46 1 GAAGGTCAGC 0.759284 -255 TTTCTTTGATGCAGGTCAGCTTGCAAATAG 16 145 1 GCAGGTCAGC 0.960052 -156 ********** Masking position 5 Map Score: 4.64128 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 429 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 TTAACACTAAAAGAGCAGGTAAAATTGTCTG 6 9 0 AAGGCATAAA 0.796447 -292 TATTTCATGTTTGTGCAAAAAATAGACAAAATG 7 93 0 TTGGCAAAAT 0.855123 -169 AAAAGTAGAATTGTGCAAATAAACGGCAGGGTA 9 17 1 TTGGCATAAA 0.968834 -284 AATCAATTGTAAGTGCATGTAAAATACCACTTT 9 143 0 AAGGCATAAA 0.796452 -158 TTTAGCCCTCTTGCGCACTAAAAAAATCGATCT 12 133 1 TTGGCAAAAA 0.89628 -162 GCCAAGATAATTGTCCAGCTAATGCGATTCGTT 15 38 1 TTGCCATAAT 0.73307 -143 AACCACGTGCTTGTGCATCTAATGGGTG 16 6 0 TTGGCATAAT 0.955017 -295 ATAGGTGCTATTGTGCTTATAAAAA 19 3 0 TTGGCTTAAA 0.813922 -106 TTTTTCGTTGATGCGCAGATAAAGTCGCTAATC 19 74 0 ATGGCATAAA 0.933669 -35 ATAACCAAAATTGAGCAAATAATAGCAAAAAAA 23 60 1 TTGGCATAAT 0.955022 -189 *** *** **** Masking position 11 Map Score: 3.86186 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 77 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 GCTCTGAAACAGCGTGGGAATTGATAACGA 3 210 0 AGCGTGGGAA 0.958328 -91 CTACCTCAATAGCGGTAGAAAAACGCACCA 4 88 0 AGCGGTAGAA 0.840255 -144 AGTGGCGGGAAGCGTGGCAAAAACGGGCTT 6 130 0 AGCGTGGCAA 0.728675 -171 AGATGCACGTAGCGGGGGAAGAGAGGAAAA 7 46 0 AGCGGGGGAA 0.993345 -216 CCGCCTCGCAAGGGGCGGAAAACACAATGG 10 18 1 AGGGGCGGAA 0.95364 -21 CCTATAAAGGAGCAGTGGAATAGCGTTCGC 12 206 1 AGCAGTGGAA 0.840255 -89 GCGAAAAATTAGCGGCAGAAAAAGGCATCC 13 11 1 AGCGGCAGAA 0.922188 -290 TCAATCTGACTGTGGGGGAACGATATA 20 237 1 TGTGGGGGAA 0.784063 -17 TTCCCCCGCAAGCAGGGGAAGGCAAGAATA 26 14 0 AGCAGGGGAA 0.958328 -125 TTCCCCTGCTTGCGGGGGAAGGTGCCCGAA 26 24 1 TGCGGGGGAA 0.97371 -115 AAGGTGCCCGAAGGGCGGAAGGGGGATTAC 26 42 1 AAGGGCGGAA 0.618439 -97 ********** Masking position 9 Map Score: 9.20007 Number of sites scoring better than the average of aligned sites = 666 Number in coding regions = 605 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 15 CGGTATCAAAGGGAGACAAAAAAAGCGCCCG 1 18 0 GGGGACAAAA 0.810507 -283 TTAACGGCAAGAGAGACAAAACAGCGAGC 4 9 0 GAGGACAAAA 0.872272 -223 AAATTCTAATGAGAGAGCAAACCAGCAGAAA 6 40 1 GAGGAGCAAA 0.970667 -261 ACCATTTGAAATGTGAGCAAAAGCCCGTTTT 6 110 1 ATGGAGCAAA 0.785191 -191 TGAAAATTGAGAGCGACCAAATAAACCGCAT 6 254 0 GAGGACCAAA 0.937839 -47 GTAGCGGGGGAAGAGAGGAAAAGGCCGGACG 7 37 0 AAGGAGGAAA 0.685174 -225 TTGTGCAAAAAATAGACAAAATGAGCGGGTT 7 85 0 AATGACAAAA 0.438218 -177 GCAAATTACCGAGCGTGAAAATCAGGATGAT 8 182 0 GAGGTGAAAA 0.614491 -119 CGTACGGATGGATCGAGCAAATTACCGAGCG 8 198 0 GATGAGCAAA 0.904869 -103 TTACACATAGGGGCGAGCAATGTCATGACAG 9 205 1 GGGGAGCAAT 0.688043 -96 TCTTTTATTGATGGGAGAAAATAAAGTGCGG 16 275 0 ATGGAGAAAA 0.623289 -26 CTATAACCAAAATTGAGCAAATAATAGCAAA 23 58 1 AATGAGCAAA 0.790785 -191 CCCATAAATGGGTGGAGCAAAGTTAATGAAA 26 104 1 GGTGAGCAAA 0.856269 -35 *** ******* Masking position 9 Map Score: 3.37395 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 402 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644