AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ifnr_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 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 HI0007 300 formate dehydrogenase, beta subunit (fdxH) #16 HI0179 130 pyruvate formate-lyase activating enzyme (act) #17 HI0180 27 formate acetyltransferase (pfl) #18 HI0181 300 formate transporter #19 HI0745 225 L-asparaginase II (ansB) #20 HI0747 203 NADH dehydrogenase (ndh) #21 HI0936 108 cytochrome C-type biogenesis #22 HI1068 43 nitrite reductase, cytochrome C-type protein (nrfB) #23 HI1069 161 nitrite reductase, cytochrome C552 (nrfA) #24 HI1076 300 cytochrome D ubiquinol oxidase, subunit I (cydA) Motif number 1 TTCAGCCAATTTGATCGAGAACAATTTATCT 1 8 0 TTGATAACAA 0.632623 -293 ATCGATCGTATTTATTAAATACAAATTACCGATA 4 28 0 TTTATAACAA 0.813413 -273 CAGGCGAGATATGATCTATATCAATTTCTCATCT 4 227 1 ATGATATCAA 0.605341 -74 GCAACAAAACTTGATTAACATCAATTTTGGTATG 5 151 1 TTGATATCAA 0.643977 -150 ACTATGGGTAATGATAAATATCAATGATAGATAA 6 190 1 ATGATATCAA 0.881592 -111 TAAAGGCAATTTGATGTAAATCAAACGATAAGAT 6 228 0 TTGATATCAA 0.499845 -73 AGCGTGGGAATTGATAACGATCAAGAGTGATGGG 7 196 0 TTGATCTCAA 0.586666 -105 CCTTCGCAAATTGACCTACCTCAATAGCGGTAGA 8 99 0 TTGACATCAA 0.586666 -133 ACGTTGTAAATTGTTTAACGTCAAATTTCCCATA 9 105 1 TTGTTATCAA 0.847059 -71 ACCCCGCTTATTGATGTAAATCAAATTCACCTTT 10 190 0 TTGATATCAA 0.499845 -72 GCACTTACAATTGATTAAAGACAACATTCACAGT 12 160 1 TTGATAACAA 0.941958 -141 CAAGGTTTGTTTAATTAAAGACAAAATTCCCATA 18 118 0 TTAATAACAA 0.632954 -183 TTTCATCAACTTTTTCAATGTCAATAGTTGGAGT 18 271 1 TTTTTATCAA 0.599405 -30 ACCGCCTTAATTTATTTAAAACAACAATATACCT 23 44 1 TTTATAACAA 0.743852 -118 AAAGATAAGCTTGATCAAGCTCAAACTTTAGCAT 23 94 1 TTGATATCAA 0.960911 -68 GTCAATTTGATCTAAGTCAATTAAATAAAA 24 7 1 TTGATATCAA 0.527418 -294 ***** * **** Masking position 2 Map Score: 21.9845 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 20 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 2 CAATTTATAGCTAAATTACCGCCTTTCAGCCAATTT 1 30 0 CTAAATACTT 0.84635 -271 TTTATTAAATACAAATTACCGATATTTAACCTTATA 4 16 0 ACAAATACTT 0.89631 -285 GGATGCGGAAAAAATTCAACTCATTTGTTAATTTTT 4 113 1 AAAATTACTT 0.817959 -188 TCAAATAATAAACAATAAACTCTGTTTTTTGATCTC 5 89 1 AACAATACTT 0.874219 -212 GTGACTTCATAAAAATTATGAGATTTTTCACGGTGC 6 147 0 AAAAATAGTT 0.904259 -154 GATGGGGATGAAAAATAAAGTAAATTCCTAAGATAC 7 166 0 AAAAATAGTT 0.904399 -135 AAAATGCTATAAAATTCAGCTTAATTTTTAACGGCA 8 31 0 AAAATTACTT 0.817959 -201 CTGTTTGCCACAAAATAATCCGCCTTCGCAAATTGA 8 119 0 CAAAATACTT 0.953457 -113 AAAAAATAGACAAAATGAGCGGGTTTATAGAAATAG 10 74 0 CAAAATACTT 0.953457 -188 TTTGATTTACATCAATAAGCGGGGTTGCTGAATCGT 10 199 1 ATCAATACTT 0.651429 -63 AAGTGCGGTCAAAAATAAACATGTTT 16 1 0 AAAAATACTT 0.967379 -130 TTAGTCTATAAAAAATGAGCCTGATTTAAATCAGGC 16 60 0 AAAAATACTT 0.967508 -71 AGTAGTCTAACTAAATTAAGTTATTTATAAACAATG 19 166 0 CTAAATAGTT 0.636336 -60 AATAACTCAAAAAAATAACCGCACTTTGATATATAA 20 78 1 AAAAATACTT 0.967512 -126 AAACTTTCATAAAAATAACCGCACTTATATATCAAA 20 102 0 AAAAATACTT 0.967512 -102 TAATAATACTCAAAATTAAGGCGGTTTTATACCGCC 23 14 1 CAAAATAGTT 0.8668 -148 ATAAAATATAACAAATAAGCCCTATTTTTGTATTTA 24 35 1 ACAAATACTT 0.89631 -266 ****** * * ** Masking position 8 Map Score: 17.9597 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 74 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 3 CCACGAAAGTGGGGCCTTTTTTAGCGCGAGA 2 57 1 GGGGCTTTTT 0.954059 -135 TAACATGAATGGTGCATTGGTCATACCAAAA 5 175 0 GGTGCTTGGT 0.89929 -126 GTCAGGCAGTGGTGCGTTTTTCTACCGCTAT 8 79 1 GGTGCTTTTT 0.990058 -153 CGCCTTTTTGGATGCCTTTTTCTGCCGCTAA 15 19 0 GATGCTTTTT 0.896907 -282 TTCTATAATTGGTGCTATTTTACTCTCCTCC 18 204 0 GGTGCATTTT 0.985511 -97 CAACAAAAACGGTGCTATTTCAGCACCGTTC 20 30 0 GGTGCATTTC 0.934145 -174 CACCTTGATAGGTGCTATTGTGCTTATAAAA 21 12 0 GGTGCATTGT 0.966938 -97 CACCTATCAAGGTGCTATTTTTAATTTTATT 21 29 1 GGTGCATTTT 0.985511 -80 TAAAAAGTGCGGTGCATTTTTCAT 22 4 0 GGTGCTTTTT 0.990058 -40 TATAATAACTGGTGTTTTTTTAACCTTTAAA 24 157 1 GGTGTTTTTT 0.896907 -144 ***** ***** Masking position 8 Map Score: 12.2009 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 89 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 TGAGATTTTTCACGGTGCTGTAAAATCCCT 6 135 0 CACGGTGCTG 0.820432 -166 GGAAGAGAGGAAAAGGCCGGACGACGATAG 10 30 0 AAAAGGCCGG 0.781826 -232 CGCCCATCACCAAAGGGCGTACGGATGGAT 11 216 0 CAAAGGGCGT 0.818016 -85 AGACAACATTCACAGTGTGGTTATTTGTTA 12 178 1 CACAGTGTGG 0.779181 -123 TTCCGCCTCGCAAGGGGCGGAAAACACAAT 13 16 1 CAAGGGGCGG 0.980435 -23 ATGTTCCCGCCAAAGTGCGGTCAAAAATAA 16 19 0 CAAAGTGCGG 0.985288 -112 CTTTGCAATGAAAGGGGAGGAGAGTAAAAT 18 189 1 AAAGGGGAGG 0.659174 -112 GAAAGATAACCCAAGTGCGGTTATACTTGA 19 47 0 CCAAGTGCGG 0.919981 -179 GATAACAAAGAACGGTGCTGAAATAGCACC 20 21 1 AACGGTGCTG 0.71078 -183 ACTTATATATCAAAGTGCGGTTATTTTTTT 20 86 0 CAAAGTGCGG 0.985288 -118 ACTTTGATATATAAGTGCGGTTATTTTTAT 20 100 1 ATAAGTGCGG 0.80667 -104 ATAACAACGAAACAGGGCGGAAAACTTTCA 20 129 0 AACAGGGCGG 0.964228 -75 GTTTGCACTAAAAAGTGCGGTGCATTTTTC 22 13 0 AAAAGTGCGG 0.97299 -31 ********** Masking position 5 Map Score: 11.7063 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 581 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 5 AGATAAATTGTTCTCGATCAAATTGGCTGAA 1 10 1 GTTTCATCAA 0.756632 -291 TTTACTGTACGATTTCAGTCAAATCTAA 2 7 0 GATTCGTCAA 0.920896 -185 GGCGAGATATGATCTATATCAATTTCTCATCT 4 229 1 GATTAATCAA 0.971974 -72 AACAAAACTTGATTAACATCAATTTTGGTATG 5 153 1 GATAAATCAA 0.942138 -148 TATGGGTAATGATAAATATCAATGATAGATAA 6 192 1 GATAAATCAA 0.942138 -109 CTTATCGTTTGATTTACATCAAATTGCCTTTA 6 230 1 GATTAATCAA 0.971974 -71 CGTGGGAATTGATAACGATCAAGAGTGATGGG 7 196 0 GATACATCAA 0.900422 -105 TACCGCTATTGAGGTAGGTCAATTTGCGAAGG 8 101 1 GAGTAGTCAA 0.72666 -131 GTTGTAAATTGTTTAACGTCAAATTTCCCATA 9 107 1 GTTAAGTCAA 0.613711 -69 AGGTGAATTTGATTTACATCAATAAGCGGGGT 10 192 1 GATTAATCAA 0.971974 -70 AAATGAGCCTGATTTAAATCAGGCTCATACAT 16 52 0 GATTAATCAG 0.834957 -79 ACAAATTTATGATCTCGATCACATAATTTTTT 19 129 0 GATTCATCAC 0.837936 -97 AGATAAGCTTGATCAAGCTCAAACTTTAGCAT 23 96 1 GATAACTCAA 0.736509 -66 GTCAATTTGATCTAAGTCAATTAAATAAAA 24 9 1 GATTAGTCAA 0.954468 -292 CCTATTTTTGTATTTATATCAAAAATGTGATC 24 55 1 TATTAATCAA 0.775798 -246 TAAAAAATGCTATATAGATCACATTTTTGATA 24 71 0 TATTAATCAC 0.481536 -230 *** ** ***** Masking position 9 Map Score: 11.4001 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 159 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 ATTCAACTCATTTGTTAATTTTTAAAATTTATT 4 126 1 TTTGTTTTTT 0.790975 -175 TTGTTTATTATTTGAGCGAATTTGTGAGAGTGA 5 71 0 TTTGAAATTT 0.751065 -230 ACCCGCTCATTTTGTCTATTTTTTGCACAAACA 10 86 1 TTTGTTTTTT 0.790975 -176 ATATTGCTGATTTGTATAAATTTTCTTAAGTCA 10 139 0 TTTGTAATTT 0.894584 -123 TAAACTTTTTGTTTTATTTTTTGTTTTTA 11 7 1 TTTTGTATTT 0.831521 -294 TGTTTTATTTTTTGTTTTTATTTTTTAAAGGAT 11 20 1 TTTGTTATTT 0.915312 -281 CAATGGCGGTTTTTATTGTTTTTCACGACAGTA 12 248 0 TTTTATTTTT 0.455535 -53 CCTCCCCAACTTTTTCAATATTTACCAAGAATG 15 272 0 TTTTTTATTT 0.870488 -29 AGACTAAATCTTTGGTAAAATTTAGCTATATCT 16 89 1 TTTGGAATTT 0.861714 -42 CTATATCTAATTTTAGGAAATTTATGT 16 114 1 TTTTAAATTT 0.65233 -17 GTTAGACTACTTTGGAGAAATTTTTATTCATCT 19 191 1 TTTGGAATTT 0.861714 -35 GCGGTTATTTTTTTGAGTTATTTTAAGTTGATA 20 67 0 TTTTGTATTT 0.831521 -137 TAATGTAACATTTTTAACAATTTAAACTTTTAG 20 172 1 TTTTTAATTT 0.840699 -32 AATATACCTCTTTTTGAGTATTTTAAAAGATAA 23 69 1 TTTTTTATTT 0.870488 -93 ATAGGGCTTATTTGTTATATTTTATTTAATTGA 24 27 0 TTTGTATTTT 0.748187 -274 CTATATAGCATTTTTTACTATTTTTTATCCTTA 24 86 1 TTTTTTATTT 0.870488 -215 ***** ***** Masking position 3 Map Score: 9.17527 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 86 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 7 GTTGCAAACATGTTAATAAAAACTCAAATT 1 148 0 TGTTAATAAA 0.802888 -153 CCGCTAAAACAGTTAATTAAAAGGGAGCAT 4 82 0 AGTTAATTAA 0.713709 -219 CCAAAATTGATGTTAATCAAGTTTTGTTGC 5 151 0 TGTTAATCAA 0.955069 -150 TGTAACCTGTTGTTAATTAAGAGCTATGTT 5 235 1 TGTTAATTAA 0.951504 -66 ATTAACCAATTGTTAATTAATGGTTATTAA 5 263 0 TGTTAATTAA 0.951504 -38 GGCAATTTGATGTAAATCAAACGATAAGAT 6 228 0 TGTAAATCAA 0.894368 -73 CATAACAGACTGTAAATTAAGACGTTTTAT 7 110 0 TGTAAATTAA 0.886557 -191 ATGTGGTGGCTGTTAATTATCCTAAAGGGG 7 137 1 TGTTAATTAT 0.829588 -164 CGCTTATTGATGTAAATCAAATTCACCTTT 10 190 0 TGTAAATCAA 0.894368 -72 TTCCTTTGTTAATTAATAAATAAATC 17 12 0 TGTTAATTAA 0.951504 -16 GGCATCGCCTTGTTAATCATTGTTGGAACT 24 254 1 TGTTAATCAT 0.840617 -47 ********** Masking position 5 Map Score: 12.3039 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 19 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TGAATGCACACAAAAACGGCGTAAAGAAAGGTTG 1 174 0 CAAAAGGGTA 0.982511 -127 GAGCTGCGCACCAACACGGCCTCAGATGGGCCAC 2 150 1 CCAAAGGCTA 0.933837 -42 GGTTTTTATGCAAATACGGAGTAAATATTTGATT 4 170 0 CAAAAGGGTA 0.982511 -131 AACCACACGGCAAATAAGGAGTAACTCTTTCCGG 6 78 0 CAAAAGGGTA 0.982511 -223 ACCGCCATTGCAACAATGGCGCAATTCGGATGAA 12 271 1 CAACAGGGCA 0.881414 -30 AAAAAGGCATCCAAAAAGGCGATATGGTAAAAAT 15 29 1 CCAAAGGGAA 0.905839 -272 TTGCCTCACCCCAAGATGGTGTTAAGGTATTCGT 15 214 0 CCAAAGGGTA 0.978875 -87 TTAAGTACGTCAAAATAGGGCTCAAGTATAACCG 19 26 1 CAAATGGCTA 0.729544 -200 ATTAGAACAACAAAAACGGTGCTATTTCAGCACC 20 34 0 CAAAAGGGCA 0.969523 -170 **** * ** ** * Masking position 3 Map Score: 6.515 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 34 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ATAAACAGGTTTTTGTTGAAGCAAATTTGC 1 82 0 TTTTGTTGAA 0.869887 -219 ACTCGCATGGTTTTTATGCAAATACGGAGT 4 182 0 TTTTTATGCA 0.829641 -119 GTTAATCAAGTTTTGTTGCTGAAAAGATAG 5 140 0 TTTTGTTGCT 0.855464 -161 AATCTCATAATTTTTATGAAGTCACTGTAC 6 158 1 TTTTTATGAA 0.696937 -143 ACTATTAAGATTTTTATGCAGATGGGTATT 7 64 0 TTTTTATGCA 0.829641 -237 AGGCGGATTATTTTGTGGCAAACAGATGTT 8 130 1 TTTTGTGGCA 0.673767 -102 CATTTTGTCTATTTTTTGCACAAACATGAA 10 93 1 ATTTTTTGCA 0.534141 -169 TACCCTGCCGTTTATTTGCACAATTCTACT 12 20 0 TTTATTTGCA 0.574346 -281 ATTAATCAACTTTTGTTGCTGACCTTCAAA 12 53 0 TTTTGTTGCT 0.855464 -248 AATTTTTGCTTTTCTTTGCAATGAAAGGGG 18 176 1 TTTCTTTGCA 0.786344 -125 TTAAGCATAATTTTTTTGAAAGATAACCCA 19 64 0 TTTTTTTGAA 0.846179 -162 ACATAATTTTTTTTGTTGATTGTATAACCT 19 111 0 TTTTGTTGAT 0.736486 -115 AGTGCGGTTATTTTTATGAAAGTTTTCCGC 20 113 1 TTTTTATGAA 0.696937 -91 TCGTCGTTTTTTTCGTTGATGCGCAGATAA 21 85 0 TTTCGTTGAT 0.468927 -24 ********** Masking position 3 Map Score: 5.18542 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 282 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 10 AGAAAGGGTCACACGCATGCCCCAATAGAAA 1 236 0 ACCGCATGCC 0.748652 -65 TTTCTCCAGATGTGGCCCATCTGAGGCCGTG 2 164 0 TGGGCCCATC 0.716838 -28 ATAGATCATATCTCGCCTGGCTTATAGGCCC 4 215 0 TCCGCCTGGC 0.914792 -86 GCGCTTCTTATCAGGCCTACCGAACGCCCTG 5 20 1 TCGGCCTACC 0.91647 -281 CACCCGGTAAAGTCGCCTATCTTTTCAGCAA 5 124 1 AGCGCCTATC 0.874252 -177 CATTTTTTTAACTGGCCTGTCAGGCAGTGGT 8 61 1 ACGGCCTGTC 0.93146 -171 TCTTTTCTATTACCGCCTACCTTAACGATTC 10 228 0 TACGCCTACC 0.73415 -34 TGCGCGCATTGCACGCCTGTCGGCAAATAAC 11 97 1 GCCGCCTGTC 0.927315 -204 AGACCCACATACGCGCCCGCCATGGCGGAGC 11 147 0 ACCGCCCGCC 0.972491 -154 ATACCAAAGGTCGCGCCCATCACCAAAGGGC 11 228 0 TCCGCCCATC 0.960498 -73 ATGGTGTACGACACGCCCATCAATTTCGAGA 15 120 0 ACCGCCCATC 0.960498 -181 ** ******** Masking position 6 Map Score: 4.48528 Number of sites scoring better than the average of aligned sites = 982 Number in coding regions = 934 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 11 TAAGGATTTTGCGGCGTAATATATACGTGG 1 114 1 GCGGCGTAAT 0.882578 -187 GCACACAAAAACGGCGTAAAGAAAGGTTGC 1 173 0 ACGGCGTAAA 0.938619 -128 AAAGGCTCTCGCGCTAAAAAAGGCCCCACT 2 64 0 GCGCTAAAAA 0.337984 -128 TTGTCGAAGTACGCAGTAAATAAAAAATCC 3 14 1 ACGCAGTAAA 0.648733 -41 AGCGGAGGATGCGGAAAAAATTCAACTCAT 4 107 1 GCGGAAAAAA 0.63969 -194 TTATGCAAATACGGAGTAAATATTTGATTA 4 169 0 ACGGAGTAAA 0.83143 -132 TACCTCAATAGCGGTAGAAAAACGCACCAC 8 87 0 GCGGTAGAAA 0.833281 -145 TAGTTTCCTCGCGCAGTAATACCCCTGAAA 8 199 1 GCGCAGTAAT 0.475826 -33 CTATTTTAAGACGGCATAATACTTTTTTAT 9 15 1 ACGGCATAAT 0.744421 -161 GAAGAATTAAACGGCATAAAAAAGTATTAT 9 30 0 ACGGCATAAA 0.915486 -146 CGCCTCGCAAGGGGCGGAAAACACAATGGA 13 19 1 GGGGCGGAAA 0.825462 -20 CTTAACAACAACGCCAGAAAACCGACTTCA 14 47 0 ACGCCAGAAA 0.805188 -33 CGAAAAATTAGCGGCAGAAAAAGGCATCCA 15 12 1 GCGGCAGAAA 0.952781 -289 ACAACGAAACAGGGCGGAAAACTTTCATAA 20 126 0 AGGGCGGAAA 0.721232 -78 ATAAATTAAGGCGGTATAAAACCGCCTTAA 23 29 0 GCGGTATAAA 0.83065 -133 ********** Masking position 8 Map Score: 6.53516 Number of sites scoring better than the average of aligned sites = 2362 Number in coding regions = 2016 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 12 AAAAATCCACTTAAGAAGGTAGGTGTTAC 3 36 1 TTAAGAAGGT 0.77762 -19 TCTCTCTTTATTAAGTCGGCGACGAGATAC 4 275 0 TTAAGTCGGC 0.891693 -26 GTTAATAAATTTAAGGGGGTCACG 5 287 1 TTAAGGGGGT 0.910574 -14 AGACTGTAAATTAAGACGTTTTATACCTGT 7 104 0 TTAAGACGTT 0.873721 -197 TCCTCTATTTTAAGACGGCATAATACTTT 9 10 1 TTAAGACGGC 0.93888 -166 ATCACCAGCGTTAAGGCGATACCAAAGGTC 11 247 0 TTAAGGCGAT 0.885177 -54 TATTCCTTCCTGAAGTCGGTTTTCTGGCGT 14 37 1 TGAAGTCGGT 0.801577 -43 CGTGGCTATATTAAAGCGGTCGCCGTGGTT 15 73 1 TTAAAGCGGT 0.861034 -228 TTCGAGATCTTTAAGACGTTTTGTAACCAC 15 97 0 TTAAGACGTT 0.873721 -204 ATACTCAAAATTAAGGCGGTTTTATACCGC 23 19 1 TTAAGGCGGT 0.987443 -143 TTTAAATAAATTAAGGCGGTATAAAACCGC 23 34 0 TTAAGGCGGT 0.987443 -128 ********** Masking position 4 Map Score: 10.2274 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 172 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 TCGACATTGCTAATGTTTAAGGGCAAGGTAACGCTC 7 236 0 TTGTTTAGGA 0.942031 -65 AAATTCAGCTTAATTTTTAACGGCAAGAGAGACAAA 8 20 0 TTTTTTAGGA 0.977991 -212 TGCTTTCCTCTTTTTTCAGGGGTATTACTGCGCG 8 208 0 TTTTTTAGGA 0.977997 -24 TTTTTGTTTTTATTTTTTAAAGGATAATCAAATGTT 11 28 1 TTTTTTAGGA 0.977879 -273 AACGGCAGGGTAATTTTTGAAGGTCAGCAACAAAAG 12 38 1 TTTTTTAGGA 0.977991 -263 ATCTACATAATTATTTTTAAAGGTTAAAAAAACACC 24 167 0 TTTTTTAGGA 0.977879 -134 * ***** * ** * Masking position 8 Map Score: 2.97525 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 16 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 14 CGAAAAATGCAAATTTGCTTCAACAAAAAC 1 74 1 AAATTTGCTT 0.864682 -227 GCCCCAATAGAAATTTGTTTGAACACTTTC 1 219 0 AAATTTGTTT 0.854431 -82 TTAATTTTTAAAATTTATTTTTATTTGGAT 4 140 1 AAATTTATTT 0.530062 -161 TGATTTGTATAAATTTTCTTAAGTCACGGA 10 135 0 AAATTTTCTT 0.83233 -127 ACTTAATTTGAAACTTGTTTTATTCGCGTA 18 47 0 AAACTTGTTT 0.804655 -254 TAAAAGTATTAAATTTTCATCAACTTTTTC 18 257 1 AAATTTTCAT 0.692098 -44 TCGAGATCATAAATTTGTTTTTCCATTGTT 19 143 1 AAATTTGTTT 0.854431 -83 TACTTTGGAGAAATTTTTATTCATCTTAGG 19 198 1 AAATTTTTAT 0.674768 -28 ACAGGGCGGAAAACTTTCATAAAAATAACC 20 118 0 AAACTTTCAT 0.615448 -86 GCGAGTAGAAAAACTTTTTTCTTTTGGTAT 23 131 1 AAACTTTTTT 0.765216 -31 ********** Masking position 5 Map Score: 1.44998 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 34 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 ATACCCCTGAAAAAAGAGGAAAGCA 8 217 1 AAAAAGAGGA 0.961334 -15 TGCCGTCTTAAAATAGAGGA 9 1 0 AAATAGAGGA 0.859821 -175 CGTAGCGGGGGAAGAGAGGAAAAGGCCGGA 10 39 0 GAAGAGAGGA 0.916515 -223 CATGCTGTTGAAAAAGAGGAAGATACTGAC 12 106 1 AAAAAGAGGA 0.961334 -195 GCCAGAAAAGAGGTGGTTTCTGGA 14 5 1 GAAAAGAGGT 0.928883 -75 GAAAAGTGGATGATTATCTG 18 1 1 GAAAAGTGGA 0.861749 -300 TAAAATACTCAAAAAGAGGTATATTGTTGT 23 64 0 AAAAAGAGGT 0.915369 -98 ********** Masking position 5 Map Score: 4.20873 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 19 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493