AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_hinf_reg_300.orf -o00530_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: HI0639 22 adenylosuccinate lyase (purB) HI1137 21 cell division protein (ftsW) Input sequences: #1 HI0059 72 conserved hypothetical protein #2 HI0060 40 ABC transporter, ATP-binding protein (msbA) #3 HI0061 258 recombination protein (rec2) #4 HI0140 272 N-acetylglucosamine-6-phosphate deacetylase (nagA) #5 HI0141 285 glucosamine-6-phosphate isomerase (nagB) #6 HI0144 45 glucose kinase, putative #7 HI0145 300 conserved hypothetical protein #8 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #9 HI0197 84 penicillin-insensitive murein endopeptidase (mepA) #10 HI0199 46 lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA acyltransferase (msbB) #11 HI0266 82 conserved hypothetical protein #12 HI0267 41 nitrate/nitrite sensor protein (narQ) #13 HI0301 300 hemolysin, putative #14 HI0413 300 ribonuclease E (rne) #15 HI0429 111 glucosamine--fructose-6-phosphate aminotransferase (glmS) #16 HI0431 35 conserved hypothetical protein #17 HI0432 66 conserved hypothetical protein #18 HI0433 75 orfG protein #19 HI0439 98 competence protein A (comA) #20 HI0448 71 PTS system, fructose-specific IIA/FPr component (fruB) #21 HI0449 86 H. influenzae predicted coding region HI0449 #22 HI0451 71 conserved hypothetical protein #23 HI0452 50 conserved hypothetical protein #24 HI0453 26 conserved hypothetical protein #25 HI0454 54 conserved hypothetical protein #26 HI0457 69 conserved hypothetical protein #27 HI0458 70 stationary phase survival protein SurA, putative #28 HI0459 131 pyrimidine operon regulatory protein (pyrR) #29 HI0638 128 conserved hypothetical protein #30 HI0640 271 ribosomal protein L10 (rpL10) #31 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #32 HI0642 159 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #33 HI0652 62 3-deoxy-d-manno-octulosonic-acid transferase (kdtA) #34 HI0759 176 A/G-specific adenine glycosylase (mutY) #35 HI0821 207 galactose operon repressor (galR) #36 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #37 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) #38 HI0825 145 H. influenzae predicted coding region HI0825 #39 HI0866 300 H. influenzae predicted coding region HI0866 #40 HI0867 237 lipopolysaccharide biosynthesis protein, putative #41 HI0870.1 300 H. influenzae predicted coding region HI0870.1 #42 HI0916 107 outer membrane protein, putative #43 HI0920 248 conserved hypothetical protein #44 HI1060 66 lipid-A-disaccharide synthetase (lpxB) #45 HI1062 85 (3R)-hydroxymyristol (acyl carrier protein) dehydrase (fabZ) #46 HI1064 56 conserved hypothetical protein #47 HI1084 29 conserved hypothetical protein #48 HI1087 300 ABC transporter, ATP-binding protein #49 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #50 HI1129 201 conserved hypothetical protein #51 HI1130 30 conserved hypothetical protein #52 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #53 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #54 HI1140 71 D-alanine--D-alanine ligase (ddlB) #55 HI1143 83 cell division protein (ftsZ) #56 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #57 HI1279 104 acylneuraminate cytidylyltransferase (neuA) #58 HI1334 126 cell division protein (ftsJ) #59 HI1335 90 cell division protein (ftsH) #60 HI1336 111 dihydropteroate synthase (folP-1) #61 HI1337 37 mrsA protein (mrsA) #62 HI1338 58 conserved hypothetical protein #63 HI1354 300 glutaminyl-tRNA synthetase (glnS) #64 HI1355 65 conserved hypothetical protein #65 HI1356 61 4-alpha-glucanotransferase (malQ) #66 HI1358 95 glycogen operon protein (glgX) #67 HI1527 84 lipid A biosynthesis lauroyl acyltransferase (htrB) #68 HI1578 300 glycosyl transferase, putative #69 HI1711 59 PTS system, glucose-specific IIA component (crr) #70 HI1712 79 phosphoenolpyruvate-protein phosphotransferase (ptsI) #71 HI1713 158 phosphocarrier protein HPr (ptsH) #72 HI1714 70 conserved hypothetical protein Motif number 1 CCTTTCTAATAAGTGCGGATAAAATAACGCG 1 45 0 AAGTGCGGAA 0.962172 -28 GGATCATTATAAGTGCGGCAATTTTCTATCT 5 189 0 AAGTGCGGCA 0.974159 -97 AAGCGCGCAAAAGTGCGGTTAAAATTAATTA 10 17 1 AAGTGCGGTA 0.997697 -30 AAATTTAGAAAAGTGCGGTAAAATTT 12 6 0 AAGTGCGGTA 0.997697 -36 TTTAAACCTAAAGTGCGGTTAAAAATACACA 13 173 0 AAGTGCGGTA 0.997697 -128 TTTAAACCCAATGTGCGGTTATTTTTTATTG 13 198 1 ATGTGCGGTA 0.960543 -103 GCACTTTCAAAAGTGCGGTCATTATAAATCT 17 25 0 AAGTGCGGTA 0.997697 -42 GCACTTTTGAAAGTGCGGTTATTTTTATGGA 17 40 1 AAGTGCGGTA 0.997697 -27 AAGTGCGGTAAATTTTTATCC 22 1 1 AAGTGCGGTA 0.997697 -71 AACGGTCGCAAAGTGCGGTCGTTTTCTTTTA 23 18 1 AAGTGCGGTG 0.995033 -33 AAAAAGAAAAGTGCGGTTAAAAATGCTGA 34 158 0 AAGTGCGGTA 0.997697 -19 AATGCTGCAAAAGTGCGGTTAAAATTTAAGG 43 18 0 AAGTGCGGTA 0.997697 -231 GAGAAATAAAAAGTGCGGTGGTTTTTTAGTT 43 104 1 AAGTGCGGTG 0.995033 -145 TTGGTGTGTAAAGTGCGGTTGAAAATGAAGA 44 18 0 AAGTGCGGTG 0.995033 -49 TTACACACCAAAGTGCGGTTATTTTTTAGGA 44 38 1 AAGTGCGGTA 0.997697 -29 ACTCAACTAAAAGTGCGGTTAAAATTCGCAA 53 89 0 AAGTGCGGTA 0.997697 -49 CCTAATAAAAAAGAGCGGTTGATTTTCTCAA 58 18 1 AAGAGCGGTG 0.918425 -109 AAAATGCGGTTAATTTTTAGAG 60 100 0 AAATGCGGTA 0.937492 -12 GCACTTTACTAAGTGCGGTCAAAAA 62 5 0 AAGTGCGGTA 0.997697 -54 GCACTTAGTAAAGTGCGGTTTATTTTTATAA 62 20 1 AAGTGCGGTT 0.968742 -39 TAAATGCACAAAGTGCGGTAAGTTTTTTGAA 63 122 0 AAGTGCGGTA 0.997697 -179 TTAATCAACCAAGTGCGGTCAAAACAAACGT 64 13 1 AAGTGCGGTA 0.997697 -53 TACAAATAAAAAGTGCGGTCAAAATCACGTT 64 39 0 AAGTGCGGTA 0.997697 -27 AAAAGTGCGGTCGTTTTTTCCCT 72 58 0 AAGTGCGGTG 0.995033 -13 ********* * Masking position 1 Map Score: 103.022 Number of sites scoring better than the average of aligned sites = 961 Number in coding regions = 606 Number in noncoding regions = 355 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 2 CTCGCGTTATTTTATCCGCACTTATTAGAAAG 1 43 1 TTTCCGCACT 0.906085 -30 CAAGATAGAAAATTGCCGCACTTATAATGATC 5 187 1 ATGCCGCACT 0.946764 -99 TGTAATTAATTTTAACCGCACTTTTGCGCGCT 10 18 0 TTACCGCACT 0.994664 -29 AAATTTTACCGCACTTTTCTAAATT 12 4 1 TTACCGCACT 0.994664 -38 ATTGTGTATTTTTAACCGCACTTTAGGTTTAA 13 171 1 TTACCGCACT 0.994664 -130 ATCAATAAAAAATAACCGCACATTGGGTTTAA 13 199 0 ATACCGCACA 0.954871 -102 GAAGATTTATAATGACCGCACTTTTGAAAGTG 17 23 1 ATACCGCACT 0.995705 -44 TCTCCATAAAAATAACCGCACTTTCAAAAGTG 17 41 0 ATACCGCACT 0.995705 -26 ATGGATAAAAATTTACCGCACTT 22 2 0 ATACCGCACT 0.995705 -70 TATAAAAGAAAACGACCGCACTTTGCGACCGT 23 19 0 ACACCGCACT 0.989261 -32 CATCAGCATTTTTAACCGCACTTTTCTTTTT 34 156 1 TTACCGCACT 0.994664 -21 TACTTATGAAAGTAACCGCTTTCAATTTATCG 35 132 1 ATACCGCTTT 0.639529 -76 CACCTTAAATTTTAACCGCACTTTTGCAGCAT 43 16 1 TTACCGCACT 0.994664 -233 ACAACTAAAAAACCACCGCACTTTTTATTTCT 43 105 0 ACACCGCACT 0.989261 -144 CTTCTTCATTTTCAACCGCACTTTACACACCA 44 16 1 TCACCGCACT 0.986679 -51 TATCCTAAAAAATAACCGCACTTTGGTGTGTA 44 39 0 ATACCGCACT 0.995705 -28 TATTCTATAAAATAACCGCTCAAGA 46 42 1 ATACCGCTCA 0.74233 -15 TAACATTCTTTTTGACCTCACTAAAGAAGCTT 48 92 0 TTACCTCACT 0.851069 -209 CGTTGCGAATTTTAACCGCACTTTTAGTTGAG 53 87 1 TTACCGCACT 0.994664 -51 CATTGAGAAAATCAACCGCTCTTTTTTATTAG 58 19 0 ACACCGCTCT 0.926162 -108 CACTCTAAAAATTAACCGCATTTT 60 98 1 ATACCGCATT 0.928724 -14 TTTTTGACCGCACTTAGTAAAGTG 62 3 1 TTACCGCACT 0.994664 -56 CTTTATAAAAATAAACCGCACTTTACTAAGTG 62 21 0 AAACCGCACT 0.934432 -38 CATTCAAAAAACTTACCGCACTTTGTGCATTT 63 120 1 ATACCGCACT 0.995705 -181 TCACGTTTGTTTTGACCGCACTTGGTTGATTA 64 14 0 TTACCGCACT 0.994664 -52 CAAACGTGATTTTGACCGCACTTTTTATTTGT 64 37 1 TTACCGCACT 0.994664 -29 CAAGGGAAAAAACGACCGCACTTTT 72 56 1 ACACCGCACT 0.989261 -15 * * ******** Masking position 6 Map Score: 86.7934 Number of sites scoring better than the average of aligned sites = 1114 Number in coding regions = 707 Number in noncoding regions = 407 Number of orfs with sites within 600 bp upstream = 277 Fraction of orfs with sites within 600 bp upstream = 0.0444908 Motif number 3 AGAAAATCCTTTCTAATAAGTGCGGATAAAATAACGCGAG 1 43 0 TAATAAAAAA 0.867344 -30 AAAGAATTTCTTTTTAAAAACAAGATAGAAAATTGCCGCAC 5 167 1 TAAAAAAAAA 0.941097 -119 TGATCACATTTATGAAAAAACACTTCAAAAATATTCTTTAA 7 138 1 TAAAAAAAAA 0.94111 -163 TATCCATTTCTCTACAAAATTATGTTATAAAACCATAAAAA 22 27 1 TAAAATAAAA 0.867341 -45 TACTCAAAAATATAAAAGAAAACGACCGCAC 23 30 0 TAAAAAAAAA 0.94111 -21 GCACAAAGTATAAAGAAAATACGCCTAAAAAGCGACGGCAT 28 71 0 TAAAATAAAA 0.867351 -61 TATGTTCTTGTAAAGAATATTGTTGAAAAAAGAGCCAAATT 30 12 0 TAATATAAAA 0.727918 -260 TTGCGAATTATACTGAAAAAATGCAGATAAACAAGCTCTAT 34 102 1 TAAAAAAAAA 0.94111 -75 TCACGGTTTATTTACAATAATTTAGTATAAATTAATGTAAT 35 41 0 TAATAAAAAA 0.850613 -167 CTTTCATAAGTATGAACTAAATCATAAAAAATTTTGCTTAT 35 103 0 TACTAAAAAA 0.647736 -105 TATATTTTGATCATAAATAATTTACGATAAATTGAAAGCGG 35 147 0 TAATAAAAAA 0.867351 -61 AAATTTGCAAAAATGAAAATGATTACATAAAAAATTATGAA 36 31 0 AAAAATAAAA 0.691642 -60 AATATCCCTTATCTTAAAATCAAAAAAGAAAGTAATAAGCA 41 85 0 AAAAATAAAA 0.691642 -216 CCTCCAGAATATTGGACAAAATAATAATAAACCCTACCAAA 41 224 0 AACAAAAAAA 0.606547 -77 TGAAAATTTATTGTAAAAAACAACTAAAAAACCACCGCACT 43 115 0 TAAAAAAAAA 0.94111 -134 GTTGATACCTTACAAAAAATAAACAAATAAAATCTATCGGA 45 55 0 TAAAATAAAA 0.867351 -31 ACTTTGTTTATGGAAAATAAACATTGATAAATGCTTATAAA 48 17 0 TAATAAAAAA 0.867351 -284 AAAATTTTAATCTATAAAAAATAGAAATAAAATTTATCACT 48 132 1 TAAAAAAAAA 0.94111 -169 AATGTGATACAAGTCACAAATCTTATAAAAATCTTTAAATT 49 76 1 AACAAAAAAA 0.606547 -106 TCAATAAAATTTTATGAAAAAAGCCGTTTGA 50 1 1 TAAAATAAAA 0.867344 -201 ATCATCAGTAAGAAGAAAAACAGGATAGAAA 54 51 1 AAAAAAAAAA 0.845725 -21 CTAATTGAAATCAGTAAAAAACATTGAGAAAATCAACCGCT 58 31 0 TAAAAAAAAA 0.94111 -96 TTTGCTTTCCTAAAAACTTTATAAAAATAAACCGCAC 62 32 0 TAAAAAAAAA 0.93902 -27 TAAATAAAAGATTGTAAAAACTTGCCATAAAAAACCGCCAC 63 173 0 AAAAAAAAAA 0.845725 -128 AAATGTAATTTGCCTACAAAATCGATAAAAAT 66 74 1 TACAAAAAAA 0.817985 -22 CCTTTTTCAAAGCAAAATAATCAAGAATAAACACTAAAAAG 71 70 0 AAATAAAAAA 0.691642 -89 TAATCAATAATTAAAAATATAAAACCAGAAAATTGCCCTAG 71 114 0 TAATATAAAA 0.727918 -45 TTTTTTCATTTTACCAAAAACAAGGGAAAAAACGACCGCAC 72 36 1 TAAAAAAAAA 0.94111 -35 * ***** * *** Masking position 9 Map Score: 38.1697 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 222 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 4 GCGAGTTGAAAAACTCGCGTTATTTTATCCGCACTTA 1 30 1 AAACTTTTTA 0.696271 -43 AATTCAGTAAAATATTTCACGGTTTTCACTTTTAGCT 4 70 0 AATATTTTTC 0.598597 -203 TTATTGGAGCAAAAGAATTTCTTTTTAAAAACAAGAT 5 156 1 AAAAGTTTTA 0.770676 -130 TAAAAAAACAAATTTAAAATAGTTTTACGAGTTTTAT 7 85 1 AATTTTTTTA 0.811277 -216 TATAAGTTGTAATATGCTTATATTTTCATCATTTAAC 7 206 0 AATATTTTTC 0.598597 -95 AGTGCGGTTAAAATTAATTACATTTTATT 10 28 1 AAATTTTTTA 0.870855 -19 AGTGCGGTTAAAAATACACAATTTTTACGGAGAGGGG 13 156 0 AAAATTTTTA 0.854277 -145 TTGACGGCGAAAAATTATCATATTTTAGAAAAAATCG 13 251 0 AAAATTTTTA 0.854277 -50 TTCACCAACAAAACTTATCCTTTTTTACGCAAATTCT 14 76 0 AAACTTTTTA 0.696271 -225 ACGCGTGCGGAATATCGCGTTGTTTTATCAAGCAAAT 14 183 1 AATATTTTTA 0.788905 -118 TTTAACCTCAAATTTTTTATGGTTTTATAACATAATT 22 44 0 AATTTTTTTA 0.811277 -28 GAATTTGGCTCTTTTTTCAACAATATTC 30 2 1 AATTTTTTTC 0.631723 -270 GTGCGGTTAAAAATGCTGATGATTTTACACGAAAATA 34 140 0 AAATGTTTTA 0.794476 -37 AAATCATAAAAAATTTTGCTTATTTTCTTATTTTGTG 35 89 0 AAATTTTTTC 0.729053 -119 CATGGATCACAAATTCATAATTTTTTATGTAATCATT 36 18 1 AAATTTTTTA 0.870855 -73 AAAAGTGGACAAATTTGCCCACTTTTCATTCATTTTA 38 28 0 AAATTTTTTC 0.729053 -118 TACAGATCATAAAAGCATTTAGTTTTCCTTTTATTCT 40 200 0 AAAAGTTTTC 0.572832 -38 AGTGCGGTTGAAAATGAAGAAGTTTTA 44 1 0 AAAATTTTTA 0.854277 -66 TGGTCATAAAAATAGTGATAAATTTTATTTCTATTTT 48 149 0 AATAGTTTTA 0.68177 -152 ACGCCTTAAAAATTGAACTTATTTTTAGAAAATCTCT 50 172 0 AATTGTTTTA 0.711342 -30 CTTTCTTCTTAATTGCTATAAATTTTAAAATTATATC 52 93 0 AATTGTTTTA 0.711342 -30 TTAGAAATAAAAACGTTGCGAATTTTAACCGCACTTT 53 74 1 AAACGTTTTA 0.567874 -64 AAGATTCTAGAATAGTCAGCGCTTTTATCACAGAGG 57 79 1 AATAGTTTTA 0.68177 -26 TAACGATAAAAAATTAAAGGAATTTTATT 61 19 1 AAATTTTTTA 0.870855 -19 AGAATAGCCGAATATTTTTTTATTTTAACGAGAGAAA 63 274 1 AATATTTTTA 0.788905 -27 TGAATAACCAAAATTGTGGCGATTTTACCACAACTCA 67 28 1 AAATTTTTTA 0.870855 -57 TTTGAAATAGAAATTTGAGTTTTTTTAAATCACTGTG 68 171 0 AAATTTTTTA 0.870855 -130 CAAAACAATTAATTTAGGAGAGTTTTAATTGGTTATC 68 204 1 AATTTTTTTA 0.811277 -97 ACAAAATTATTTGATTTTACGTTAAAATA 69 3 1 AAAATTTTTA 0.854277 -57 ACTTAGCCATAAAATTGTGAAATTTTATGGCTATTGT 70 16 1 AAAATTTTTA 0.854277 -64 TCCTATGCAAAAATTTTTTTCATTTTACCAAAAACAA 72 22 1 AAATTTTTTA 0.870855 -49 ***** ***** Masking position 13 Map Score: 37.336 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 258 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 5 AGCAAGTAAATTTTCCTGAAAAATTTATTTTT 3 145 1 TTTTCCTAAA 0.644533 -114 GCGAATGTAATTCGCCCCTACATAAAGATGAA 4 21 0 TTCGCCCTAA 0.869682 -252 GCGAATTACATTCGCCCTATAATCTCAACAAG 4 38 1 TTCGCCCATA 0.933044 -235 GCGAATGTAATTCGCCCCTACATAAAGATGAA 4 157 0 TTCGCCCTAA 0.869682 -116 GCGAATTACATTCGCCCTATAATCACAAACAA 4 174 1 TTCGCCCATA 0.933044 -99 GTAAGGACAATTTGCCCTATGATTGTTTGTGA 4 196 0 TTTGCCCATA 0.93552 -77 AAGAAATTCTTTTGCTCCAATAATTTACGACA 5 147 0 TTTGCTCAAA 0.885806 -139 AGCATAAATATTTGCTTGATAAAACAACGCGA 14 197 0 TTTGCTTATA 0.751637 -104 TTTGCTTCATTATCGACCTCGT 14 289 0 TTTGCTTATA 0.751637 -12 TTTTTCTCCATAAAAATAACCGC 17 54 0 TTTTCTCATA 0.827344 -13 AGTGCGGTCGTTTTCTTTTATATTTTTGAGTA 23 29 1 TTTTCTTTAA 0.418563 -22 AGAACATAGCTTTTCTCTATAATCCTGCGCCT 30 45 1 TTTTCTCATA 0.827344 -227 ACCATCGGTTTTTTCTTATATAAAAGTTTGTT 32 53 1 TTTTCTTTAA 0.418563 -107 TTTTTGCAAATTTGCTCATAGATTAATTACGA 36 59 1 TTTGCTCTAA 0.822069 -32 TTTTTTCTCTCTATGAAAATGGTGGC 38 130 0 TTCTCTCATA 0.821507 -16 AATTGAACTTTTTTCTTCATCAGAACTCAAAA 42 13 1 TTTTCTTATA 0.60051 -95 TAATATTTTCTCTGCCCAATTAAATTAGGCAG 42 55 0 TCTGCCCATA 0.517067 -53 ATTTGCTTTTATACCTATTCAAT 49 2 1 TTTGCTTTAA 0.591724 -180 TATAGCTAGGTTCGCTCTTTCACTTTTGAAAG 52 15 1 TTCGCTCTTA 0.846602 -108 ATTTTTCCTTTTCTCCCAATGACAAAACTCAA 53 114 0 TTCTCCCATA 0.873762 -24 AGGCTTTATTTTTTCCTAATGATTTTGTTCTT 60 34 1 TTTTCCTATA 0.693309 -78 TGAACCTTTATTTTCCCTTAGATTTGTATAGA 63 245 1 TTTTCCCTAA 0.775338 -56 TTTCTCTCGTTAAAATAAAAAAA 63 288 0 TTCTCTCTTA 0.732711 -13 GCGAATGTAATTCGCCCCTACAATTTATCTAT 66 16 0 TTCGCCCTAA 0.869682 -80 GCGAATTACATTCGCCTGATAAACCACCGATG 66 33 1 TTCGCCTATA 0.813829 -63 GCAAATTACATTTGCCCAAAAACATCGGTGGT 66 55 0 TTTGCCCAAA 0.921046 -41 ACCTTGTTTATTTTCTCGAATAATCGGTAACA 68 62 0 TTTTCTCAAA 0.793929 -239 ******* ** * Masking position 1 Map Score: 19.8512 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 311 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 ACGCGAGTTGAAAAACTCGCGTTATTTTATCCGCAC 1 28 1 AAAAACGATT 0.814004 -45 TCTTAGGCGCAAAAAGAGGCTCTATTATCCATAGAA 14 43 0 AAAAACTATT 0.873087 -258 ATTAAAGTTAATAAAACGCCGCCATTATACTGTCTA 21 56 0 ATAAACGATT 0.939566 -31 AGTATCAAAAATAAAGGGGCTTAATTGCCCCTTTTG 26 14 1 ATAAACTATT 0.960687 -56 AAATACGCCTAAAAAGCGACGGCATTTGCACCATTT 28 60 0 AAAAACGATT 0.814013 -72 AAAAGCTAGGTTAAAAATGCTATATTTAACGGAAAC 29 84 1 TTAAACTATT 0.786649 -45 AAAAATGCAGATAAACAAGCTCTATTTTCGTGTAAA 34 118 1 ATAAACTATT 0.960687 -59 AAATAAATTATCGTAATTAATCTATGAG 36 73 0 ATAAACGATT 0.939566 -18 CGATTATTGCATAAATATCCTTAATTCAGAATTGAA 38 75 0 ATAAACTATT 0.960687 -71 TTGATAAATATCCTTAATTAAATGATGGG 42 89 0 ATAAACTATT 0.960687 -19 AAATTTAAGATAAAAGTACTACATTATTTT 51 6 0 ATAAACTATT 0.960687 -25 TGATGGAAATATAAATTTCCTTTACTAACGTAAAAA 52 55 0 ATAAACTACT 0.732691 -68 TATATAAAATATAAATTCCCTTTATTGTAGATGAAA 55 22 0 ATAAACTATT 0.960687 -62 AATAAAATTCCTTTAATTTTTTATCGT 61 21 0 ATAAACTAAT 0.649042 -17 TGTTCTTGCCATAGAAATACTAGATTTAAATAAAAG 63 204 0 ATAGACTATT 0.721549 -97 CAAGTGCGGTCAAAACAAACGTGATTTTGACCGCAC 64 22 1 CAAAACGATT 0.505311 -44 TTTAAAATCTCTCTATTTGAATAACCA 67 2 1 TTAAACTATT 0.786649 -83 AACAATAGCCATAAAATTTCACAATTTTATGGCTAA 70 18 0 ATAAACAATT 0.706328 -62 AGAATAAACACTAAAAAGCCTGAATTAAATCATAAA 71 52 0 CTAAACTATT 0.85082 -107 ***** ** *** Masking position 16 Map Score: 16.5109 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 52 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ACGCGTTTACACAATAAAAAACCCCTGCGCA 15 44 0 AAATAAAAAA 0.826998 -68 AATAGAATAAATAAGGAAAACTT 15 99 1 AAAGGAAAAC 0.880578 -13 CACAGTTCTAACAAGGGAAAAGT 24 14 1 AAAGGGAAAA 0.842207 -13 AGCCTTAGGCATAAGGAAAAATAATT 25 39 1 AAAGGAAAAA 0.954187 -16 TAAGAAAGAGAAAATAAAAAACAACAAAAGG 26 43 0 AAATAAAAAA 0.826998 -27 AAACTTTTATATAAGAAAAAACCGATGGTTT 32 51 0 AAAGAAAAAA 0.90891 -109 ATAGATTATAACAAGGAAAAAGTT 35 194 1 AAAGGAAAAA 0.954187 -14 AGATGACAGAAGAATAAAGACATATTTATAT 39 213 1 AAATAAAGAC 0.374667 -88 TGGTGAGAATAAAAGGAAAACTAAATGCTTT 40 195 1 AAAGGAAAAC 0.880578 -43 AAGCACTAGAACAATGAAAAAGATAAGATAA 41 40 0 AAATGAAAAA 0.90891 -261 CAGCATTTTGACAATAGAAAATGTGGCATAG 43 42 1 AAATAGAAAA 0.550566 -207 AGTGCGGTTGAAAATGAAGAAGTTTTA 44 7 0 AAATGAAGAA 0.779374 -60 TTTTTAAGCCAGAAGGAAAAAACA 46 4 0 AAAGGAAAAA 0.954187 -53 AATTCAATAAATAATGAAGAAATGTAAAGCT 48 66 1 AAATGAAGAA 0.779374 -235 GTGTTGCGATAAAAGAAAAAACTTCATCTTT 48 209 1 AAAGAAAAAA 0.90891 -92 GATTTTTATCAAAATAAAAAAGCCGTTTGAA 50 50 0 AAATAAAAAA 0.826998 -152 ATAGCAATTAAGAAGAAAGAAA 52 111 1 AAAGAAAGAA 0.779374 -12 TCATTGGGAGAAAAGGAAAAATAA 53 124 1 AAAGGAAAAA 0.954187 -14 ATCATCAGTAAGAAGAAAAACAGGATAGAAA 54 51 1 AAAGAAAAAC 0.779374 -21 GAACAAAATCATTAGGAAAAAATAAAGCCTT 60 33 0 ATAGGAAAAA 0.550151 -79 TTCTCTCGTTAAAATAAAAAAATATTCGGCT 63 279 0 AAATAAAAAA 0.826998 -22 TGTTTTTGGTAAAATGAAAAAAATTTTTGCA 72 27 0 AAATGAAAAA 0.90891 -44 TTTACCAAAAACAAGGGAAAAAACGACCGCA 72 45 1 AAAGGGAAAA 0.842207 -26 * ********* Masking position 4 Map Score: 27.3981 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 213 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 8 TTTTATAAAAGATTAATTCCAGCC 3 245 0 ATAAAAGATT 0.911107 -14 TAAAAACAAGATAGAAAATTGCCGCACTTA 5 181 1 ATAGAAAATT 0.732757 -105 ATTACAACTTATAAAAGATTGTTTTGTGTG 7 230 1 ATAAAAGATT 0.911107 -71 TGAGTTATAAAAGAAGATTTATAATGACC 17 10 1 AAAGAAGATT 0.579556 -57 GCTGTTAAGTATAAAAGATTCAGCCTTTAA 19 64 1 ATAAAAGATT 0.911107 -35 AGAGAAATGGATAAAAATTTACCGCACTT 22 10 0 ATAAAAATTT 0.680484 -62 TTATAAAACCATAAAAAATTTGAGGTTAAA 22 51 1 ATAAAAAATT 0.85162 -21 TTTTTCTTATATAAAAGTTTGTTATAGTTT 32 62 1 ATAAAAGTTT 0.791809 -98 GGTTATACTTAAAAAAATTTCGGCTAGTAT 33 32 0 AAAAAAATTT 0.374825 -31 GAACTAAATCATAAAAAATTTTGCTTATTT 35 101 0 ATAAAAAATT 0.85162 -107 TATGATCAAAATATAAGATTTATAGATTAT 35 173 1 ATATAAGATT 0.48408 -35 AAATGATTACATAAAAAATTATGAATTTGT 36 26 0 ATAAAAAATT 0.85162 -65 TGATCCGAAGAAAAAAGATTTAACTGAG 39 283 1 AAAAAAGATT 0.742626 -18 GTGGTGCCATATTAAAGATTAGTTTTTGCT 57 38 1 ATTAAAGATT 0.423068 -67 ACTACAAAAAATAGAAGATT 58 117 1 ATAGAAGATT 0.830408 -10 TTTTATAACGATAAAAAATTAAAGGAATTT 61 14 1 ATAAAAAATT 0.85162 -24 CTAGATTTAAATAAAAGATTGTAAAAACTT 63 191 0 ATAAAAGATT 0.911107 -110 TTGTTTTGAAATAGAAATTTGAGTTTTTTT 68 182 0 ATAGAAATTT 0.504322 -119 TGGTAAAATGAAAAAAATTTTTGCATAGGA 72 22 0 AAAAAAATTT 0.374825 -49 ********** Masking position 9 Map Score: 15.6929 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 82 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 9 TCCTGTACCTAGGGTAGTATACTCTAGGTTAGTTCT 9 10 1 TGTAGATATA 0.791492 -75 AGTTTTGCTGTAGGTAAGTATATCCTAGGTTCAGTCC 9 53 0 TGAAGATACA 0.957257 -32 GCTATCAATTTTGGGTAGAATAACGAACAGTTTTTCT 11 42 1 TGTAGATACA 0.979974 -41 ATGGAATGTTTTGGATAGTATAACGAACAAGAAAAAT 28 27 1 TGTAGATACA 0.979974 -105 TAAAAAAATTTCGGCTAGTATAGCAAAAAAAGGATTG 33 16 0 TGTAGATACA 0.977932 -47 AGCCGAAATTTTTTTAAGTATAACCGAATTTCATTT 33 37 1 TTAAGATACA 0.666741 -26 ATAGAAAATGTGGCATAGAATACCGTAAAATGGCAAA 43 55 1 TGTAGATACA 0.980598 -194 ATAAATTTGGTGGTAAACTATATCATAAGTTATATTG 43 198 0 TGAACATACA 0.747818 -51 TCCCTTAGATTTGTATAGAATAGCCGAATATTTTTTT 63 258 1 TGTAGATACA 0.979974 -43 AAAAAAATTTTTGCATAGGATACCTGATATT 72 5 0 TGTAGATACA 0.980598 -66 * * *** *** * * Masking position 10 Map Score: 8.30489 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 AAGTGCGGTTATTTTTATGGAGAAAAA 17 50 1 ATTTTTATGG 0.893959 -17 TAACCTCAAATTTTTTATGGTTTTATAACA 22 49 0 TTTTTTATGG 0.824665 -23 TTGACTCCTGTTTTTTATCAATGTAAACGA 35 12 1 TTTTTTATCA 0.780639 -196 ATAAGCAAAATTTTTTATGATTTAGTTCAT 35 103 1 TTTTTTATGA 0.805206 -105 GAAAAAGGCTATTTTTATCAGTACGGGAGC 40 12 1 ATTTTTATCA 0.864473 -226 GGTATAGAGTATTTGTATGAAAATTACTCT 41 179 1 ATTTGTATGA 0.729348 -122 TTTATTTCTATTTTTTATAGATTAAAATTT 48 133 0 TTTTTTATAG 0.633434 -168 ATTTATCACTATTTTTATGACCACATCAAA 48 163 1 ATTTTTATGA 0.881081 -138 GAATTTAAAGATTTTTATAAGATTTGTGAC 49 88 0 ATTTTTATAA 0.731334 -94 AAAGCAACTGATTTTTATCAAAATAAAAAA 50 60 0 ATTTTTATCA 0.864473 -142 ATTCCTTTAATTTTTTATCGTTATAAAACC 61 12 0 TTTTTTATCG 0.801949 -26 AGTGCGGTTTATTTTTATAAAGTTTTTAGG 62 31 1 ATTTTTATAA 0.731334 -28 TTCGTGGCGGTTTTTTATGGCAAGTTTTTA 63 170 1 TTTTTTATGG 0.824665 -131 TTTCCCTTAGATTTGTATAGAATAGCCGAA 63 256 1 ATTTGTATAG 0.529749 -45 CGCACTTTTTATTTGTATCAACT 64 53 1 ATTTGTATCA 0.698793 -13 ATTTTTATCGATTTTGTAGG 66 86 0 ATTTTTATCG 0.878902 -10 TATTTAGCTTATTTTTATGATTTAATTCAG 71 39 1 ATTTTTATGA 0.881081 -120 ********** Masking position 6 Map Score: 11.7281 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 142 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 11 ACTCGTAAAACTATTTTAAATTTGTTTTTTTAC 7 84 0 CTATAAATTT 0.55197 -217 TTTGTGTGGATTAAATTAATTTTAAAGTGATTT 7 252 1 TTATAATTTT 0.917592 -49 TAGCATACGCCTACAATAATTTTAGAGGAAACC 11 13 0 CTATAATTTT 0.722122 -70 TTTTTCTAAAATATGATAATTTTTCGCCGTCAA 13 255 1 ATATAATTTT 0.62687 -46 TTATGGTTTTATAACATAATTTTGTAGAGAAAT 22 32 0 ATATAATTTT 0.62687 -40 ATGTAAACGATTACATTAATTTATACTAAATTA 35 32 1 TTATAATTTA 0.758139 -176 CACGGTTTATTTACAATAATTTAGTATAAATTA 35 48 0 TTATAATTTA 0.758139 -160 CGCTTTCAATTTATCGTAAATTATTTATGATCA 35 148 1 TTATAAATTA 0.597756 -60 CATAGATTAATTACGATAATTTATTT 36 75 1 TTATAATTTA 0.758139 -16 TGTCATCTCCTTAGTATAATTTTCACCCATACA 39 188 0 TTATAATTTT 0.917592 -113 ATAGCTAACATTAGAGTAATTTTCATACAAATA 41 188 0 TTATAATTTT 0.917592 -113 TTGGTAGGGTTTATTATTATTTTGTCCAATATT 41 225 1 TTATTATTTT 0.472109 -76 CGGTTAAAATTTAAGGTGATTTT 43 1 0 TTATGATTTT 0.709249 -248 TAGTTGTTTTTTACAATAAATTTTCAATTTTTG 43 130 1 TTATAAATTT 0.840733 -119 CGGTTATTTTTTAGGATAAATTTG 44 53 1 TTATAAATTT 0.840733 -14 TGTAGTACTTTTATCTTAAATTT 51 18 1 TTATAAATTT 0.840733 -13 TTATTTTAATTTTTCATCTACAA 55 1 1 TTATAATTTT 0.917591 -83 CGGTTAATTTTTAGAGTGATTTTGGTGGGCGAT 60 83 0 TTATGATTTT 0.709249 -29 GGGGCGTAGTTTATCGTAAATTTGAGTTGTGGT 67 54 0 TTATAAATTT 0.840733 -31 *** ******* Masking position 7 Map Score: 13.5094 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 50 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 TCATTTTGGAAATAAAACTCGTAAAACTAT 7 103 0 AATAAAACTC 0.865432 -198 AAGTATCGGGAATAATACGCTTATCGCGCT 18 31 0 AATAATACGC 0.823176 -45 GATTAAAGTTAATAAAACGCCGCCATTATA 21 63 0 AATAAAACGC 0.961253 -24 CGCGTGAGTGAATAATACGCCATAATTGGC 34 62 1 AATAATACGC 0.823176 -115 TTTCTAGAGATTTAAAACGCCAGTTCTTAA 39 151 1 TTTAAAACGC 0.779489 -150 TATAGCTAAAAATAAAACGCACTCAATATA 45 13 0 AATAAAACGC 0.961253 -73 ACAAAGTATTATTAAAATTCAATAAATAAT 48 51 1 ATTAAAATTC 0.492958 -250 TAAAACATCCATTAAAATGCTAATAAATAA 49 37 0 ATTAAAATGC 0.789489 -145 TGAGGCTATTTATAAAACGCCACAACCC 53 9 0 TATAAAACGC 0.823176 -129 AATAAAATTCCTTTAATTTT 61 28 0 AATAAAATTC 0.561476 -10 ACTTTATAAAAATAAACCGCACTTTACTAA 62 24 0 AATAAACCGC 0.783497 -35 ACTACATCACATTAAAAAGCGGTATCGCCG 63 25 1 ATTAAAAAGC 0.597468 -276 AATCACTGTGATTAAAACGCCATTCATATT 68 151 0 ATTAAAACGC 0.949591 -150 TAGATAACCAATTAAAACTCTCCTAAATTA 68 213 0 ATTAAAACTC 0.83003 -88 ********** Masking position 5 Map Score: 8.69135 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 62 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 CGAATGTAATTCGCCCCTACATAAAGATGAA 4 21 0 TCGCCCCTAA 0.950202 -252 CGAATTACATTCGCCCTATAATCTCAACAAG 4 39 1 TCGCCCTATA 0.908777 -234 CGAATGTAATTCGCCCCTACATAAAGATGAA 4 157 0 TCGCCCCTAA 0.950202 -116 CGAATTACATTCGCCCTATAATCACAAACAA 4 175 1 TCGCCCTATA 0.908777 -98 TAAGGACAATTTGCCCTATGATTGTTTGTGA 4 196 0 TTGCCCTATA 0.785413 -77 AGCAACTATATTGCTCTTAAACGTAAGGACA 4 219 0 TTGCTCTTAA 0.733092 -54 AGAAATTCTTTTGCTCCAATAATTTACGACA 5 147 0 TTGCTCCAAA 0.684862 -139 TCTTGCTCCTTAATAATTTAAAA 20 59 0 TTGCTCCTTA 0.814127 -13 ATAGCTAGGTTCGCTCTTTCACTTTTGAAAG 52 16 1 TCGCTCTTTA 0.898823 -107 GTAAAAAAGGTCGCTCTTTCAAAAGTGAAAG 52 31 0 TCGCTCTTTA 0.898823 -92 CGAATGTAATTCGCCCCTACAATTTATCTAT 66 16 0 TCGCCCCTAA 0.950202 -80 ********* * Masking position 11 Map Score: 5.96529 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 47 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 14 CGAATGTAATTCGCCCCTACATAAAGATGA 4 22 0 TCGCCCCTAC 0.992868 -251 CGAATGTAATTCGCCCCTACATAAAGATGA 4 158 0 TCGCCCCTAC 0.992868 -115 AATTAAGATTACTCCCCTACGGTCTTGGAT 30 129 0 ACTCCCCTAC 0.949021 -143 CGAATGTAATTCGCCCCTACAATTTATCTA 66 17 0 TCGCCCCTAC 0.992868 -79 ACGATAAACTACGCCCCTAACTTAC 67 70 1 ACGCCCCTAA 0.949021 -15 ********** Masking position 8 Map Score: 4.63039 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 3 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 15 GACGTGTGAGAMAAMGACTTTACACTATAAGG 6 17 1 AMAMGACTTA 0.596118 -29 TTGGGGGAGAAAACATACATTTTTGGCCTAAA 7 26 0 AAAATACTTT 0.627941 -275 AAAAGAGGGCAAAGATCCTTATCACATCAAAC 13 18 0 AAAATCCTAT 0.795813 -283 ATTCACAATCAAAAATCCATTATTCACAAGTT 13 60 1 AAAATCCTTA 0.924684 -241 ATTATTGCATAAATATCCTTAATTCAGAATTG 38 77 0 AAAATCCTAA 0.836948 -69 GTACTGATAAAAATAGCCTTTTTCT 40 4 0 AAAAGCCTTT 0.858981 -234 GATAAAATCAAAATATCCCTTATCTTAAAATC 41 105 0 AAAATCCTTA 0.924684 -196 TTGATAAATATCCTTAATTAAATGATG 42 91 0 AAAATCCTAA 0.836948 -17 GTAAAATCTAAAACATCCATTAAAATGCTAAT 49 43 0 AAAATCCTTA 0.924684 -139 AATTTTATGAAAAAAGCCGTTTGAATTGTTTA 50 18 1 AAAAGCCTTT 0.858981 -184 TATCAAAATAAAAAAGCCGTTTGAATAAACAA 50 43 0 AAAAGCCTTT 0.858981 -159 ATGGAAATATAAATTTCCTTTACTAACGTAAA 52 57 0 AAATTCCTTA 0.697343 -66 TTTGGATATAAAAAATACTTATGACTGAGGCT 53 32 0 AAAATACTAT 0.414044 -106 AATAAAATTCCTTTAATTTTTTATC 61 23 0 AAATTCCTTA 0.697343 -15 *** **** *** Masking position 3 Map Score: 7.32547 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 127 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405