AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_hinf_reg_300.orf -o00790_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -x5 -e 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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: HI0033 53 conserved hypothetical protein HI0910 64 mutator mutT protein (mutT) HI1336 111 dihydropteroate synthase (folP-1) Input sequences: #1 HI0028 55 conserved hypothetical protein #2 HI0030 51 lipoprotein, putative #3 HI0034 124 conserved hypothetical protein #4 HI0035 205 conserved hypothetical protein #5 HI0062 258 dnaK suppressor protein (dksA) #6 HI0063 247 poly(A) polymerase (pcnB) #7 HI0291 74 H. influenzae predicted coding region HI0291 #8 HI0292 76 mercuric ion scavenger protein (merP) #9 HI0316 21 datP pyrophosphohydrolase (ntpA) #10 HI0317 218 aspartyl-tRNA synthetase (aspS) #11 HI0652 62 3-deoxy-d-manno-octulosonic-acid transferase (kdtA) #12 HI0727.1 260 cyaY protein (cyaY) #13 HI0899_HI0900 100 HI0899: dihydrofolate reductase (folA), HI0900: glutamate 5-kinase (gamma-glutamyl kinase) (proB) #14 HI0901 80 conserved hypothetical protein #15 HI0908 79 H. influenzae predicted coding region HI0908 #16 HI0909 124 preprotein translocase SecA subunit (secA) #17 HI1188 300 DNA helicase II (uvrD) #18 HI1260 193 acetyl-CoA carboxylase carboxyl transferase subunit beta (accD) #19 HI1334 126 cell division protein (ftsJ) #20 HI1335 90 cell division protein (ftsH) #21 HI1447 137 GTP cyclohydrolase I (folE) #22 HI1464 111 dihydropteroate synthase (folP-2) #23 HI1465 137 cell division ftsH-related protein #24 HI1573 300 pyruvate kinase, type II (pykA) #25 HI1574 33 replicative DNA helicase (dnaB) #26 HI1741 260 guanosine-3',5'-bis(diphosphate) 3'- pyrophosphohydrolase (spoT) #27 HI1742 62 DNA-directed RNA polymerase, omega chain (rpoZ) #28 HI1743 249 guanylate kinase (gmk) Motif number 1 AATAAATCAAAAAGTGCGGTCAATTTTCAAATT 1 15 0 AAAGGCGGTA 0.998326 -41 TTAGACATAAAAAGCGCGGTTAATTTCGCGCTT 3 27 1 AAAGGCGGTA 0.998326 -98 ATCCGAGATAAAAGTGCGGTGAAAAATAACCGC 4 20 1 AAAGGCGGTA 0.998326 -186 CCTTTTACAAAAAGTGCGGTTATTTTTCACCGC 4 35 0 AAAGGCGGTT 0.991857 -171 GAAAAATACAAAAGTGCGGTTAAAATTAACCGC 6 22 1 AAAGGCGGTA 0.998326 -226 TAAATGCAAAAAAGTGCGGTTAATTTTAACCGC 6 37 0 AAAGGCGGTA 0.998326 -211 TAAATCTGATAAAATGCGGCAAATTATAAAGCC 12 224 0 AAAAGCGGCA 0.949306 -37 TCCTAATAAAAAAGAGCGGTTGATTTTCTCAAT 19 17 1 AAAGGCGGTA 0.998326 -110 AAAATGCGGTTAATTTTTAGAGT 22 99 0 AAAAGCGGTA 0.991648 -13 TAGCCAGATAAAAAATCGGTGCACATTATACGC 24 220 0 AAAATCGGTA 0.886622 -81 TCTTTTAAAAGTGCGGTAAAAAATAAAGGT 26 8 1 AAAGGCGGTA 0.998326 -253 TACTCTATTGAAAGGGCGTTATAATACTCAATT 27 16 0 AAAGGCGTTA 0.975173 -47 AAAATCATCAAAAGTGCGGTGATTTTTTACGGT 28 173 0 AAAGGCGGTT 0.991857 -77 **** ***** * Masking position 3 Map Score: 41.895 Number of sites scoring better than the average of aligned sites = 753 Number in coding regions = 457 Number in noncoding regions = 296 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 2 CCTAAAAATAAAATAAATCAAAAAGTGCGGTCA 1 26 0 AAAAATAAAA 0.956251 -30 CTTAAAGAAAGAATAAATGAAAAGCGTTAATAT 2 26 1 GAAAATAAAA 0.896752 -26 CACTTTTTGTAAAAGGGTCAAAAATTTTCGGTA 4 52 1 AAAGGTAAAA 0.863132 -154 TCATTCTATTGAAAAATACAAAAGTGCGGTTAA 6 12 1 GAAAAAAAAA 0.664264 -236 GCAAGAAGACAAAAAAATCAAAAGAGGTTGCCA 6 181 1 AAAAATAAAA 0.956251 -67 TTCATCAATAAAACAACTAACAAGGAGTAAAA 7 53 1 AAAAATACAA 0.908211 -22 ACCATCAATAAAACAACTAACAAGGAGTAAAA 8 55 1 AAAAATACAA 0.908211 -22 TTATGCTGACAAATCAATCAAAAAAGCAAAGAA 10 113 0 AAACATAAAA 0.848514 -106 GAGCATAATTAAAAGAGTACAAAGGATTTTGAA 10 196 1 AAAGATCAAA 0.719316 -23 TATAGCAAAAAAAGGATTGAAAAT 11 2 0 AAAGATAAAA 0.901118 -61 AAGTGAGAAAGAAAAAATGAAAAAATTACTATT 12 158 0 GAAAATAAAA 0.896752 -103 CGTTATCACTAAATCAATGAAAAATCACTTAAT 13 43 1 AAACATAAAA 0.848514 -58 TATTCTTCACAAAAAACAGAAAAA 16 2 0 AAAAAAAAAA 0.832751 -123 AATGAGAGGTAAACGAATTAAAAGTTTGTTTAT 17 93 1 AAAGATAAAA 0.901118 -208 GTTTGTTTATAAATAGTATAAAAATAGCTTTCA 17 116 1 AAAAGAAAAA 0.775057 -185 TCTGTAAGACAAAAAAATAAAAAAAATGTTCAA 18 43 1 AAAAATAAAA 0.956251 -151 TCTAGTCAATAAAAAGGTCAAAAA 18 180 1 AAAAGTAAAA 0.937986 -14 AAGCTAATTGAAATCAGTAAAAAACATTGAGAA 19 42 0 AAACATAAAA 0.848514 -85 AATATAGGCGAAACGACTACAAAAAATAGAAGA 19 102 1 AAAGATCAAA 0.719316 -25 TTTAGATATAGAATAGCTGACAAATTTTATCAA 21 24 0 GAAAGTACAA 0.731242 -114 GGTAAAATGAGAAAAATTGCAAATTTGAATGAA 21 63 0 GAAAATCAAA 0.70951 -75 TCTAGGTTAAAAAAAGGTTACAAGTATAAAAAA 23 33 1 AAAAGTACAA 0.872565 -105 TTACAAGTATAAAAAAAATACAACAAATTAAGA 23 50 1 AAAAAAACAA 0.692684 -88 TACAACAAATTAAGAAATGAAAATCATTATCAT 23 68 1 TAAAATAAAA 0.703206 -70 ATAACTGGCAAAAAAGTAAACAAAACCAGCTTA 24 151 1 AAAAGAACAA 0.60934 -150 TCAACAATCTAAATATGTTAAAATAAAAGAGCG 25 11 1 AAAATTAAAA 0.597232 -23 CTAAATCCGCAAACAGTTCCAAAGGAGACCTAC 26 179 0 AAAAGTCAAA 0.80965 -82 TTAACTTAAATAAAAGGTGAAAATCT 28 4 0 TAAAGTAAAA 0.621154 -246 *** ** * **** Masking position 3 Map Score: 31.0642 Number of sites scoring better than the average of aligned sites = 670 Number in coding regions = 471 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 3 AAATCAAAAAGTGCGGTCAATTTTCAAATTC 1 14 0 GTGCGGTAAT 0.995006 -42 GACATAAAAAGCGCGGTTAATTTCGCGCTTA 3 30 1 GCGCGGTAAT 0.985724 -95 CGAGATAAAAGTGCGGTGAAAAATAACCGCA 4 23 1 GTGCGGTAAA 0.993137 -183 TTTACAAAAAGTGCGGTTATTTTTCACCGCA 4 34 0 GTGCGGTATT 0.978088 -172 AAATACAAAAGTGCGGTTAAAATTAACCGCA 6 25 1 GTGCGGTAAA 0.993137 -223 ATGCAAAAAAGTGCGGTTAATTTTAACCGCA 6 36 0 GTGCGGTAAT 0.995006 -212 ATCTGATAAAATGCGGCAAATTATAAAGCCT 12 223 0 ATGCGGCAAT 0.866413 -38 AAAATGCGGTTAATTTTTAGAGTG 22 98 0 ATGCGGTAAT 0.971783 -14 TCTTTTAAAAGTGCGGTAAAAAATAAAGGTA 26 11 1 GTGCGGTAAA 0.993137 -250 GTATACCTACCCGCGGTAAAATACCTTTATT 26 32 0 CCGCGGTAAA 0.930611 -229 TCAATTTTATCTGCGGGCAAATACCCTTGAA 26 221 0 CTGCGGGAAA 0.879336 -40 ATCATCAAAAGTGCGGTGATTTTTTACGGTA 28 172 0 GTGCGGTATT 0.978088 -78 ******* *** Masking position 9 Map Score: 24.5844 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 490 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 4 TTTATTTTATTTTTAGGAAAGAAA 1 42 1 TTTTAGGAAA 0.981382 -14 TTTATTCTTTCTTTAAGAAAGAAAAAATGAAA 2 11 0 CTTTAAGAAA 0.794753 -41 AAGTTGTTTGTTTTAGCAAGTAAATTTTCCTG 5 117 0 TTTTAGCAAA 0.883627 -142 CTGACTGCTATTTTAGGAACCCAATTTTTGCG 5 166 0 TTTTAGGAAC 0.950444 -93 GTTTGAAATATTAGGAATGAA 9 9 1 TATTAGGAAA 0.944676 -13 GTTTTAGTTATTTTGGGAATGATATTAGATAA 12 22 1 TTTTGGGAAA 0.93402 -239 TGAGCTATTTTTATAGGAAAAATTTAAGGTAA 14 52 1 TTATAGGAAA 0.808736 -29 ATCATGGGTATTTTTGGAAAAATGAGAAACCT 17 50 1 TTTTTGGAAA 0.886141 -251 AAACCTTGCATTTTAGGAATGAGAGGTAAACG 17 76 1 TTTTAGGAAA 0.981389 -225 GGGTAGAACATTTTAAGAATAATATTAAGCGG 17 192 0 TTTTAAGAAA 0.882888 -109 CGCTCTTTTTTATTAGGAATCCTT 19 3 0 TATTAGGAAC 0.861315 -124 TACTACACATCATTAGCAATGAAAAGCTATCA 20 17 0 CATTAGCAAA 0.558392 -74 CCGATTATTTTTTTAGGAAAGACTATT 21 121 1 TTTTAGGAAA 0.981382 -17 AGAACAAAATCATTAGGAAAAAATAAAGCCTT 22 33 0 CATTAGGAAA 0.897643 -79 TAGATTTAACTTTTGGGAAGCAATTT 23 5 0 TTTTGGGAAA 0.93402 -133 TTATATCGGGTTTTAAGAAAAATACTTGTGTT 24 123 0 TTTTAAGAAA 0.882865 -178 ACGCTTAAAACTTTTGGAAATCAAAAACGGCT 24 192 0 CTTTTGGAAC 0.630949 -109 ********* * Masking position 8 Map Score: 20.3946 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 81 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 TATAATCCGAAGGAGTTAAATTTCATTTTT 4 175 1 AGGAGTTAAA 0.873392 -31 AACAACAAAACGGAGTAAATTATTCTTACT 6 132 1 CGGAGTAAAT 0.98138 -116 ACAACTAACAAGGAGTAAAA 7 65 1 AGGAGTAAAA 0.970784 -10 ACAACTAACAAGGAGTAAAA 8 67 1 AGGAGTAAAA 0.970784 -10 TAATATGTAGCGAAGTAAAATAACACCTTT 24 251 1 CGAAGTAAAA 0.899007 -50 TAATTATTGACGGAGTAAATA 24 290 1 CGGAGTAAAT 0.98138 -11 TTTGACAAATCGGAGTAAATT 27 52 1 CGGAGTAAAT 0.98138 -11 ********** Masking position 4 Map Score: 7.95106 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 10 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 AAAAGTGCGGTGAAAAATAACCGCACTTTTTG 4 29 1 TAAAAATAAC 0.642341 -177 TGTAAAAGGGTCAAAAATTTTCGGTATTGTAG 4 59 1 TAAAAATTTC 0.869229 -147 TTAACCAAACTCAAAAAATGATACGTTCGTCA 4 121 0 TAAAAAATGT 0.56595 -85 GTTAAGGTTTTCAAAAAACAACTTGGATATAA 4 148 1 TAAAAAACAC 0.775997 -58 TAAATTTTCCTGAAAAATTTATTTTTACGATA 5 97 0 TAAAAATTTT 0.833714 -162 CTTACTTATATCAAAAATTTGTTTGGCAAGAA 6 156 1 TAAAAATTTT 0.833714 -92 TTAATTATGCTCAAAAATCTGTCGCAATTATA 10 176 0 TAAAAATCTT 0.830834 -43 CGGTTATACTTAAAAAAATTTCGGCTAGTATA 11 31 0 TAAAAAATTC 0.845478 -32 AAAGAAAAAATGAAAAAATTACTATTAATTTT 12 152 0 TAAAAAATTC 0.845478 -109 ACTAAATCAATGAAAAATCACTTAATATCAGG 13 50 1 TAAAAATCAT 0.760443 -51 TAGCGATATTTTAAAAAATTATTGTGCATGAA 16 47 1 TAAAAAATTT 0.80496 -78 GACAAAAAAATAAAAAAAATGTTCAATAAGAG 18 50 1 TAAAAAAATT 0.63307 -144 CTTTCCTAAGTTAAAAAATTTCGTCACAAGAT 20 48 0 TAAAAAATTC 0.845478 -43 TAGTCTTTCCTAAAAAAATAATCGGCTATTCT 21 114 0 TAAAAAATAT 0.727335 -24 GTTACAAGTATAAAAAAAATACAACAAATTAA 23 49 1 TAAAAAAATC 0.695802 -89 TGTGTTCAAGTTAAAAATATCTATAATCACGA 24 97 0 TAAAAATATT 0.676997 -204 ATTAGCCAGATAAAAAATCGGTGCACATTATA 24 223 0 TAAAAATCGT 0.608096 -78 CTCCGATTTGTCAAAAATTACTCTATTGAAAG 27 35 0 TAAAAATTAT 0.764181 -28 AAAAGTACCGTAAAAAATCACCGCACTTTTGA 28 167 1 TAAAAATCAC 0.808003 -83 GATTTCTCTATAAAAAATCATCAAAAGTGCGG 28 187 0 TAAAAATCAC 0.808003 -63 * ******** * Masking position 1 Map Score: 17.633 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 389 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 7 AATTGGGTTCCTAAAATAGCAGTCAGGAAC 5 172 1 CTAAAATAGC 0.937494 -87 CAGGAACAAACTAAAATAACAAGACAGGAA 5 195 1 CTAAAATAAC 0.903344 -64 TGGTTTTCCGCTATAATTGCGACAGATTTT 10 165 1 CTATAATTGC 0.914002 -54 CCTTTTTTTGCTATACTAGCCGAAATTTTT 11 20 1 CTATACTAGC 0.787329 -43 AATATCATTCCCAAAATAACTAAAACAGGC 12 18 0 CCAAAATAAC 0.781991 -243 CCCATGATGACAATAATAGCATAGGAATGT 17 28 0 CAATAATAGC 0.892991 -273 ATAGATGGGACTATAATAACTGTAAATTTA 17 262 1 CTATAATAAC 0.936005 -39 TTATCCTTTGCTAGAATAGCCGATTATTTT 21 102 1 CTAGAATAGC 0.845776 -36 ATGTATTTCGCTATAATCGCCCACCAAAAT 22 68 1 CTATAATCGC 0.956429 -44 TAATCGCCCACCAAAATCACTCTAAAAATT 22 81 1 CCAAAATCAC 0.770354 -31 ACCAACTGAGCTATAGTCGCACTGTGTGAA 24 63 1 CTATAGTCGC 0.775895 -238 TTAAAAATATCTATAATCACGACTACTTCA 24 89 0 CTATAATCAC 0.931873 -212 TTTACTCCGTCAATAATTACAAAATTTTAA 24 279 0 CAATAATTAC 0.701903 -22 TCCGATTTGTCAAAAATTACTCTATTGAAA 27 36 0 CAAAAATTAC 0.60073 -27 ********** Masking position 5 Map Score: 8.84935 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 155 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 AAAATAAATCAAAAAGTGCGGTCAATTTTC 1 20 0 AAAAAGTGCG 0.929137 -36 ACCCTTTTACAAAAAGTGCGGTTATTTTTC 4 40 0 AAAAAGTGCG 0.929137 -166 AAAAGGGTCAAAAATTTTCGGTATTGTAGA 4 62 1 AAAATTTTCG 0.514733 -144 TACCGCCCGCAAAAATTGGGTTCCTAAAAT 5 159 1 AAAAATTGGG 0.79019 -100 TTTAAATGCAAAAAAGTGCGGTTAATTTTA 6 42 0 AAAAAGTGCG 0.929137 -206 TACTTATATCAAAAATTTGTTTGGCAAGAA 6 158 1 AAAAATTTGT 0.373621 -90 AAAAATTTCAATTCAGATTG 7 1 1 AAAAATTTCA 0.644846 -74 TTATACTTAAAAAAATTTCGGCTAGTATAG 11 30 0 AAAAATTTCG 0.939874 -33 GAAAAAATGAAAAAATTACTATTAATTTTA 12 151 0 AAAAATTACT 0.579636 -110 TTTTTCCTATAAAAATAGCTCAAGATTGTT 14 44 0 AAAAATAGCT 0.813996 -37 TGTTTATTATGAAAATTGCGTGTATTGTAA 15 51 0 GAAAATTGCG 0.865903 -29 AATAATTTTTTAAAATATCGCTATTTCAAT 16 40 0 TAAAATATCG 0.342869 -85 TAAATAGTATAAAAATAGCTTTCAAAGCAT 17 125 1 AAAAATAGCT 0.813996 -176 TTATTGACTAGAAAATTGCGCGTATTAGAA 18 162 0 GAAAATTGCG 0.865903 -32 ATTCCTAATAAAAAAGAGCGGTTGATTTTC 19 15 1 AAAAAGAGCG 0.852543 -112 TCCTAAGTTAAAAAATTTCGTCACAAGATA 20 47 0 AAAAATTTCG 0.939874 -44 GTAAAATGAGAAAAATTGCAAATTTGAATG 21 65 0 AAAAATTGCA 0.784168 -73 TGTTCAAGTTAAAAATATCTATAATCACGA 24 97 0 AAAAATATCT 0.686252 -204 CTTATCGTTGAAAAATATCGCCTAGGGTAA 26 150 0 AAAAATATCG 0.873329 -111 CCGATTTGTCAAAAATTACTCTATTGAAAG 27 35 0 AAAAATTACT 0.579636 -28 ********** Masking position 4 Map Score: 20.1926 Number of sites scoring better than the average of aligned sites = 907 Number in coding regions = 693 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 9 AAAATATTAACGCTTTTCATTTATTC 2 36 0 ATAACGCTTT 0.72005 -16 AATATTCAAAATAAAGGCTTTTTTGTGCCAT 10 74 0 AAAAGGCTTT 0.977712 -145 TTAAAAGAGTACAAAGGATTTTGAA 10 204 1 AAAAGGATTT 0.94929 -15 AGTATAGCAAAAAAAGGATTGAAAAT 11 6 0 AAAAGGATTG 0.796088 -57 CACAAGCTTGAGAAAGGCTTTATAATTTGCC 12 209 1 AAAAGGCTTT 0.977712 -52 TGTGCATGAAATAAAGTATTTCATAAGCATT 16 69 1 AAAAGTATTT 0.620534 -56 AATTTTATCAAATAAGGATTTTCT 21 4 0 ATAAGGATTT 0.894477 -134 AATTTGAATGAATTAGGCTTTAGATATAGAA 21 44 0 ATTAGGCTTT 0.736486 -94 GCCTTTCCGAAGAAAGGCTTTGATGAG 22 7 0 AAAAGGCTTT 0.977712 -105 GCCTTTCTTCGGAAAGGCTTTATTTTTTCCT 22 20 1 GAAAGGCTTT 0.901462 -92 * ********* Masking position 5 Map Score: 6.88301 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 101 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 TTTCTTTCCTAAAAATAAAATAAATCAAA 1 37 0 TTTTTATAAA 0.633875 -19 ATTTTTTCTTTCTTAAAGAAAGAATAAATGAAAAGCGT 2 15 1 TCTAAATAAA 0.586575 -37 TAAAAATAATTTCAATTTAGACATAAAAAGCGCGGTT 3 10 1 TTCAAATAAA 0.409889 -115 TTTGTTCTCACTTAGCAATAAAGGTGCGGAAT 3 103 0 TTTCAATAAA 0.920802 -22 GGCAAGTGGATTTTCCTGCATTTTTAAATGCAAAAAAG 6 56 0 TTTCCATAAA 0.847296 -192 TCCACTTGCCTTTTTCTTTACAAGAAAAGAGCCAAGTC 6 84 1 TTTTCAAAAA 0.401073 -164 GAGTAAATTATTCTTACTTATATCAAAAATTTGTTTGG 6 144 1 TTTTAAAAAA 0.659154 -104 CTTGTTAGTTGTTTTATTGATGGTTAAACTATAAACCT 8 41 0 GTTTAATAAA 0.506284 -36 TTGCGACAGATTTTTGAGCATAATTAAAAGAGTACAAA 10 181 1 TTTTGATAAA 0.592716 -38 AGCTTGATCTTTTTCAGGAAAATATAAAGAACCTTTTA 12 73 1 TTTCAATAAA 0.92047 -188 CATTTTTTCTTTCTCACTTATCGGTAAATCCGCCTTTC 12 172 1 TTTCAATAAA 0.920661 -89 ATTGCGTGTATTGTAACGGAAATCTAAACTAATGTCAT 15 29 0 TTTAAATAAA 0.879088 -51 TGAAAGCTATTTTTATACTATTTATAAACAAACTTTTA 17 111 0 TTTATATAAA 0.525205 -190 TTAAGCGGGATTCTCCTATATCCTTAAACTCAACATCA 17 162 0 TTTCCATAAA 0.84751 -139 TTTTTGACCTTTTTATTGACTAGAAAATTGCGCGTAT 18 167 0 TTTTAAAAAA 0.656553 -27 AAGAACAAAATCATTAGGAAAAAATAAAGCCTTTCCGA 22 28 0 TCTTAATAAA 0.676729 -84 TGTAACCTTTTTTTAACCTAGATTTAACTTTTGGGAAG 23 17 0 TTTAAATAAC 0.409262 -121 ACTCCGTCAATAATTACAAAATTTTAAAGGTGTTATTT 24 268 0 TATTAATAAA 0.434223 -33 TACCTTTATTTTTTACCGCACTTTTAAAAGA 26 4 0 TTTACATAAA 0.776226 -257 AGCACGAGCATTTTTATAAAACTATAAACCCTACTACT 28 94 1 TTTTAATAAA 0.914334 -156 TAGACTGAAATTGTCAGAGAAGGTTAAATATTCT 28 226 1 TTTCAATAAA 0.920864 -24 ** *** * **** Masking position 10 Map Score: 8.48824 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 166 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 11 TACCCTCTTGCGCAAAATCCACGCAAAAAATA 3 59 0 CGAAATCCAC 0.964228 -66 GTATTCAATGATAGAATTCCGCACCTTTATTG 3 88 1 ATAATTCCGC 0.854839 -37 GACAGGAAGTCGTGAAATCCACGCTTAATTCT 5 217 1 CGAAATCCAC 0.964228 -42 TTAAAAATGCAGGAAAATCCACTTGCCTTTTT 6 67 1 AGAAATCCAC 0.964912 -181 TCTCACTTATCGGTAAATCCGCCTTTCACAAG 12 183 1 CGAAATCCGC 0.985706 -78 TTTATTGACTAGAAAATTGCGCGTATTAGAAC 18 161 0 AGAATTGCGC 0.809981 -33 GAATAATTCGATCTAAATCCGCAAACAGTTCC 26 192 0 ATAAATCCGC 0.941491 -69 GATTTTTTATAGAGAAATCTGCATAATAGACT 28 200 1 AGAAATCTGC 0.887084 -50 ** ******** Masking position 6 Map Score: 2.70844 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 65 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 12 GAGAGGCTGGAATTAATCTTTTATAAAA 5 7 0 AATAACTTTT 0.826873 -252 CATATCGTAAAAATAAATTTTTCAGGAAAATT 5 95 1 AAAAATTTTT 0.871026 -164 TCTTCTTGCCAAACAAATTTTTGATATAAGTA 6 158 0 AAAAATTTTT 0.871026 -90 AGGTTAAGGTCAAGAAGTTTTTT 8 2 0 CAAAATTTTT 0.814868 -75 GATATGGCACAAAAAAGCCTTTATTTTGAATA 10 71 1 AAAAACCTTT 0.876627 -148 TTGTCAGCATAAATAACCTTTTTATCTCTCTT 10 134 1 AAAAACTTTT 0.950669 -85 TCAACAAACTCAATAATCTATTATCTAATATC 12 42 0 CAAAACTATT 0.606146 -219 AGGAAAATATAAAGAACCTTTTACGCCACATC 12 88 1 AAAAACTTTT 0.948898 -173 ATTTCATGCACAATAATTTTTTAAAATATCGC 16 49 0 CAAAATTTTT 0.811314 -76 TACTATTTATAAACAAACTTTTAATTCGTTTA 17 102 0 AAAAACTTTT 0.950669 -199 ATTAGGAAAAAATAAAGCCTTTCCGAAGAAAG 22 22 0 AATAACCTTT 0.647673 -90 *** ** ***** Masking position 6 Map Score: 6.67316 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 61 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 13 TCCTGTCTTGTTATTTTAGTTTGTTCCTGAC 5 193 0 TTATTTAGTT 0.677222 -66 GATAAAAAGGTTATTTATGCTGACAAATCAA 10 129 0 TTATTTTGCT 0.743507 -90 GATTATTGAGTTTGTTGAGCTTGATCTTTTT 12 56 1 TTTGTTAGCT 0.938077 -205 ATTTTAGTACTTAGTTCAGCTTGTATATTCG 12 126 0 TTAGTTAGCT 0.976405 -135 GTAAATGACATTAGTTTAGATTTCCGTTACA 15 25 1 TTAGTTAGAT 0.842953 -55 AACGGCTCAGTTATTTAAGCTGGTTTTGTTT 24 168 0 TTATTTAGCT 0.941777 -133 AGGGTAACATTTAGTTAAGCTAGGGTCTACT 26 120 1 TTAGTTAGCT 0.976405 -141 AGCAAACAGATTTGTTTAACTTAAATAAAAG 28 21 0 TTTGTTAACT 0.628485 -229 ****** **** Masking position 6 Map Score: 1.71752 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 59 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 AAGAAAGAATAAATGAAAAGCGTTAATATT 2 30 1 AAATGAAAAG 0.784255 -22 TTTATGTCTAAATTGAAATTATTTTTA 3 8 0 AATTGAAATT 0.838917 -117 GACCCCTTAAAAATGAAATTTAACTCCTTC 4 183 0 AAATGAAATT 0.943898 -23 CACCAATCTGAATTGAAATTTTT 7 4 0 AATTGAAATT 0.838917 -71 AAATGAAATTCGGTTATACT 11 53 0 AAATGAAATT 0.943898 -10 GAGAAAGAAAAAATGAAAAAATTACTATTA 12 157 0 AAATGAAAAA 0.710366 -104 TGCCCCCAGTAAATGACATTAGTTTAGATT 15 17 1 AAATGACATT 0.817466 -63 ACAAATTAAGAAATGAAAATCATTATCATT 23 72 1 AAATGAAAAT 0.931905 -66 AATAGACATTAAATGATAATGATTTTCATT 23 83 0 AAATGATAAT 0.710366 -55 ********** Masking position 6 Map Score: 4.1909 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 82 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 15 TGCGTGGATTTTGCGCAAGAGGGTATTCAA 3 66 1 TTGCGCAAGA 0.873548 -59 CTATGCTCAATTTCGCAAGAAAAAATGTGA 4 94 1 TTTCGCAAGA 0.962942 -112 CAAAAATTTGTTTGGCAAGAAGACAAAAAA 6 167 1 TTTGGCAAGA 0.941096 -81 GAGCACTTGTTTTGGCAACCTCTTTTGATT 6 196 0 TTTGGCAACC 0.807571 -52 TAAATCCGCCTTTCACAAGCTTGAGAAAGG 12 196 1 TTTCACAAGC 0.941609 -65 AAATAAAGTATTTCATAAGCATTTAACTAT 16 77 1 TTTCATAAGC 0.676552 -48 AATCTTATTGTTTCACAAGATAGATGGGAC 17 243 1 TTTCACAAGA 0.910444 -58 AGATTTAACTTTTGGGAAGCAATTT 23 6 0 TTTGGGAAGC 0.82978 -132 ********** Masking position 7 Map Score: 1.04949 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 203 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172