AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_hinf_reg_100.orf -o00240_hinf_100.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: HI0206 22 5'-nucleotidase, putative Input sequences: #1 HI0011 105 DNA polymerase III, psi subunit (holD) #2 HI0075 280 anaerobic ribonucleoside-triphosphate reductase (nrdD) #3 HI0132 165 uridine kinase (udk) #4 HI0137 60 DNA polymerase III, epsilon subunit (dnaQ) #5 HI0205 292 H. influenzae predicted coding region HI0205 #6 HI0229 298 polynucleotide phosphorylase (pnp) #7 HI0272 23 orotate phosphoribosyltransferase (pyrE) #8 HI0273 300 ribonuclease PH (rph) #9 HI0280 214 uridine phosphorylase (udp) #10 HI0457 69 conserved hypothetical protein #11 HI0458 70 stationary phase survival protein SurA, putative #12 HI0459 131 pyrimidine operon regulatory protein (pyrR) #13 HI0514 241 DNA-directed RNA polymerase, beta' chain (rpoC) #14 HI0515 300 DNA-directed RNA polymerase, beta chain (rpoB) #15 HI0518 83 purine-nucleoside phosphorylase (deoD) #16 HI0519 98 transport protein, putative #17 HI0521 212 conserved hypothetical protein #18 HI0530 231 O-sialoglycoprotein endopeptidase (gcp) #19 HI0583 93 2',3'-cyclic-nucleotide 2'-phosphodiesterase (cpdB) #20 HI0584 71 hydrolase #21 HI0586 66 H. influenzae predicted coding region HI0586 #22 HI0587 99 peptidase E (pepE) #23 HI0739 300 DNA polymerase III, alpha subunit (dnaE) #24 HI0799 139 ribosomal protein S13 (rpS13) #25 HI0801 27 ribosomal protein S4 (rpS4) #26 HI0802 31 DNA-directed RNA polymerase, alpha chain (rpoA) #27 HI0856 148 DNA polymerase I (polA) #28 HI0876 300 nucleoside diphosphate kinase (ndk) #29 HI0900 100 glutamate 5-kinase (gamma-glutamyl kinase) (proB) #30 HI0901 80 conserved hypothetical protein #31 HI0921 248 leucyl-tRNA synthetase (leuS) #32 HI0922 49 rare lipoprotein B, putative #33 HI0953 124 DNA/pantothenate metabolism flavoprotein (dfp) #34 HI0954 47 deoxyuridinetriphosphatase (dut) #35 HI0993 191 chromosomal replication initiator protein (dnaA) #36 HI1077 300 CTP synthetase (pyrG) #37 HI1158 73 thioredoxin reductase (trxB) #38 HI1159 284 conserved hypothetical protein #39 HI1219 279 cytidylate kinase 1 (cmkA) #40 HI1221 122 integration host factor, beta-subunit (himD) #41 HI1222 74 conserved hypothetical protein #42 HI1224 23 orotidine 5'-phosphate decarboxylase (pyrF) #43 HI1228 123 uracil phosphoribosyltransferase (upp) #44 HI1230 147 adenine phosphoribosyltransferase (apt) #45 HI1243 90 16s pseudouridylate 516 synthase (rsuA) #46 HI1244 197 H. influenzae predicted coding region HI1244 #47 HI1350 273 cytidine deaminase (cdd) #48 HI1397 234 DNA polymerase III, chi subunit (holC) #49 HI1401 229 dihydroorotate dehydrogenase (pyrD) #50 HI1644 233 pseudouridylate synthase I (truA) #51 HI1646 300 cytidylate kinase 2 (cmkB) #52 HI1659 179 ribonucleoside-diphosphate reductase, alpha chain (nrdA) #53 HI1660 141 ribonucleoside diphosphate reductase, beta chain (nrdB) #54 HI1742 62 DNA-directed RNA polymerase, omega chain (rpoZ) #55 HI1743 249 guanylate kinase (gmk) Motif number 1 ATTATAAAGAAAAGTGCGGTGAATTTCACG 3 114 0 AAAGTGCGGT 0.99747 -52 TTAAACGCCCAAAGTGCGGTCATTTTTTCG 6 207 1 AAAGTGCGGT 0.99747 -92 AGTAAAAAAAGAAGTGCGGTCAAAAAGTTA 9 66 0 GAAGTGCGGT 0.98372 -149 TGAAATCGCCGAAGTGCGGTCAAAATTCTC 13 172 1 GAAGTGCGGT 0.98372 -70 TTAAAGGTTTAAAGTGCGGTTAAAAATTTC 13 203 0 AAAGTGCGGT 0.99747 -39 AGTAAGGTTCAGAGTGCGGTCATTTTAACG 14 221 1 AGAGTGCGGT 0.967989 -80 AATCAATTAAAAAGTGCGGTAAAAAATGAC 15 19 1 AAAGTGCGGT 0.99747 -65 AAAAATGAATAAAGTGCGGTCATTTTTTAC 15 37 0 AAAGTGCGGT 0.99747 -47 ACGTTTACAAAAAGTGCGGTGAAAATTCGC 16 11 1 AAAGTGCGGT 0.99747 -88 GCACTTAAATAAAGTGCGGTCAATTTTTTA 20 17 0 AAAGTGCGGT 0.99747 -55 GCACTTTATTTAAGTGCGGTCTGTTTTTAT 20 30 1 TAAGTGCGGT 0.95681 -42 GAAAATCCTTAAAGTGCGGTTAAATTTTGC 23 280 0 AAAGTGCGGT 0.99747 -21 AGAGAAATAAAAAGTGCGGTGGTTTTTTAG 31 137 0 AAAGTGCGGT 0.99747 -112 AAATGCTGCAAAAGTGCGGTTAAAATTTAA 31 220 1 AAAGTGCGGT 0.99747 -29 TTTTTAGGTAAAAGTACGGTTGGAA 34 6 0 AAAGTACGGT 0.926278 -42 GTAATAGAGAAAAGTGCGGTAAAAATTGTC 35 151 0 AAAGTGCGGT 0.99747 -41 AAATCAACCAAAAGTGCGGTCAAAAATCGA 36 225 0 AAAGTGCGGT 0.99747 -76 TGATTTTAGCAAAGTGCGGAAGATTTTAGA 38 32 0 AAAGTGCGGA 0.953277 -253 ATAATGCTCAAAAGTGCGGTAAAAAAAGAA 44 126 0 AAAGTGCGGT 0.99747 -22 ATAGATCATAAAAGCGCGGTGGATTTTCAG 48 114 1 AAAGCGCGGT 0.967989 -121 CCTTACCTTTAAAGTGCGGTGAAAATTGAC 49 169 1 AAAGTGCGGT 0.99747 -61 TTACTGTAAGAAAGTGCGGTCAATTTTCAC 49 187 0 AAAGTGCGGT 0.99747 -43 TTGGCTTAATAAAGTGCGGTTATGGTAGCC 50 204 0 AAAGTGCGGT 0.99747 -30 TCCTTCAAAGTGCGGTGAAAAATTCA 52 7 1 AAAGTGCGGT 0.99747 -173 AAAATAAGAAAAAGTGCGGTAAAAATTTGT 52 37 0 AAAGTGCGGT 0.99747 -143 AAAATCATCAAAAGTGCGGTGATTTTTTAC 55 176 0 AAAGTGCGGT 0.99747 -74 ********** Masking position 3 Map Score: 127.092 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 ATAAAGAAAAGTGCGGTGAATTTCACGTTA 3 110 0 GTGCGGTAAT 0.99436 -56 AACGCCCAAAGTGCGGTCATTTTTTCGAAAG 6 210 1 GTGCGGTATT 0.985551 -89 AAAAAAAGAAGTGCGGTCAAAAAGTTAAACG 9 62 0 GTGCGGTAAA 0.996471 -153 AATCGCCGAAGTGCGGTCAAAATTCTCCGAA 13 175 1 GTGCGGTAAA 0.996471 -67 AAGGTTTAAAGTGCGGTTAAAAATTTCGGAG 13 199 0 GTGCGGTAAA 0.996471 -43 AAGGTTCAGAGTGCGGTCATTTTAACGGTCA 14 224 1 GTGCGGTATT 0.985551 -77 CAATTAAAAAGTGCGGTAAAAAATGACCGCA 15 22 1 GTGCGGTAAA 0.996471 -62 AATGAATAAAGTGCGGTCATTTTTTACCGCA 15 33 0 GTGCGGTATT 0.985551 -51 TTTACAAAAAGTGCGGTGAAAATTCGCCGAC 16 14 1 GTGCGGTAAA 0.996471 -85 CTTAAATAAAGTGCGGTCAATTTTTTACTAT 20 13 0 GTGCGGTAAT 0.99436 -59 AATCCTTAAAGTGCGGTTAAATTTTGCCGTA 23 276 0 GTGCGGTAAA 0.996471 -25 GAAATAAAAAGTGCGGTGGTTTTTTAGTTGT 31 133 0 GTGCGGTGTT 0.861394 -116 TGCTGCAAAAGTGCGGTTAAAATTTAAGGTG 31 223 1 GTGCGGTAAA 0.996471 -26 ATAGAGAAAAGTGCGGTAAAAATTGTCGGAG 35 147 0 GTGCGGTAAA 0.996471 -45 TCAACCAAAAGTGCGGTCAAAAATCGAAGAT 36 221 0 GTGCGGTAAA 0.996471 -80 ATGCTCAAAAGTGCGGTAAAAAAAGAAACGT 44 122 0 GTGCGGTAAA 0.996471 -26 TACCTTTAAAGTGCGGTGAAAATTGACCGCA 49 172 1 GTGCGGTAAA 0.996471 -58 CTGTAAGAAAGTGCGGTCAATTTTCACCGCA 49 183 0 GTGCGGTAAT 0.99436 -47 GCTTAATAAAGTGCGGTTATGGTAGCCCAAG 50 200 0 GTGCGGTATG 0.940957 -34 TCCTTCAAAGTGCGGTGAAAAATTCAACAA 52 10 1 GTGCGGTAAA 0.996471 -170 ATAAGAAAAAGTGCGGTAAAAATTTGTTGAA 52 33 0 GTGCGGTAAA 0.996471 -147 ATCATCAAAAGTGCGGTGATTTTTTACGGTA 55 172 0 GTGCGGTATT 0.985551 -78 ******* *** Masking position 7 Map Score: 88.7807 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 360 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 3 TTCATCACGGTATTATTTCTATTTTTCAAGTAGGA 3 44 0 TATTTTATTT 0.805488 -122 GTTGTATTCCTTTTAATTATCATTCACAATTTATT 5 166 1 TTTTTTCTTC 0.783925 -127 AATGTTTTCCTTAAAATTTATATTAAAAA 6 280 0 TTTTTTATTT 0.91842 -19 TTAGTTTTTATTTTTGTTAAAATTCGCTAAGATAT 8 216 0 TTTTTTATTC 0.919153 -85 GCACTTCTTTTTTTACTTATTATTCGTTATCAGAA 9 79 1 TTTTTTTTTC 0.914325 -136 CATTTTCATTATTTCTTTTTTGTTTTTCTGATAAC 9 104 0 ATTTTTTTTT 0.853606 -111 ATTTTTAGAAAATTTTTTTCTCTTTCAAACATTTT 9 133 0 AATTTTTTTT 0.682018 -82 TTCTAAAAATATTTTATTTCTTTTCTTGAAAATAA 9 158 1 ATTTTTTTTC 0.85483 -57 TTTTGTTGTTTTTTATTTTCTCTTTCTTATAGCTT 10 45 1 TTTTTTTTTT 0.913552 -25 TTTAGGCGTATTTTCTTTATACTTTGTGCATTGAA 12 83 1 TTTTTTATTT 0.91842 -49 GACCGCACTTTATTCATTTTTATTCATTATTAAAA 15 46 1 TATTTTTTTC 0.796978 -38 AATGAGTTTAATTTAATTGCAATTTAAAATTTTAT 18 25 1 ATTTTTATTT 0.861337 -207 AAGTGCGGTCAATTTTTTACTATTT 20 1 0 AATTTTTTTT 0.682016 -71 TGATACGGTTTATTTTTTGATATTCGTCAAACAAT 22 21 1 TATTTTTTTC 0.796978 -79 AGCCGTTTTCATTTGTTAGATTTCCGCTAGTCTA 23 114 0 ATTTTTATTC 0.862507 -187 ATCGTTCACAAATTAATTCATCTTTTGCCGATATT 28 60 1 AATTTTTTTT 0.682018 -241 ATGCAACCAATTTTGTTTATAATTTTTTACAAAAT 28 156 0 TTTTTTATTT 0.91842 -145 TGCGGTGGTTTTTTAGTTGTTTTTTACAATAAATT 31 118 0 TTTTTTTTTT 0.913552 -131 AATTTCGTTATTTTACTTTAATTTTATTGAATGCC 33 72 0 TTTTTTATTT 0.91842 -53 AAATTTAACATTTTGNTTCCATTTCTTACATTTTT 39 108 1 TTTTTTATTC 0.919153 -172 ATTTCTTACATTTTTATTACTATTTGTGTTTAGTT 39 128 1 TTTTTTTTTT 0.913552 -152 ATCAAAAATATTTTAATTAAATTTTAATCAA 41 7 0 TTTTTTATTT 0.91842 -68 CAATTGGGGATTTTTATTTAAGTTTGAATTTACAA 44 32 0 TTTTTTATTT 0.91842 -116 TGATAGCTTCTATTTATTACAATTTCTTAACAAAC 47 132 0 TATTTTATTT 0.805488 -142 ATCACTTGCGTTTTAATTTTCATTCAATTCATAGG 48 19 0 TTTTTTCTTC 0.783925 -216 ATGCATATTTAATTATTTATTTTTTAGGGTTTTTT 48 156 1 AATTTTTTTT 0.682018 -79 TTTTAGGGTTTTTTCGTTAAAATTTTACCCTTTTT 48 177 1 TTTTTTATTT 0.91842 -58 TCCATTAATTATTTCTTTATTATTTGCACATCATT 49 109 1 ATTTTTTTTT 0.853606 -121 AATTTCCTTTTAGTTTTTCATAATAC 50 2 1 ATTTTTATTT 0.861337 -232 CCTTTCAAGCTTTTTCTTAAATTTCAGAAAATCTA 51 253 0 TTTTTTATTC 0.919153 -48 GTGCGGTAAAAATTTGTTGAATTTTTCACCGCACT 52 19 0 AATTTTATTT 0.695579 -161 TTTACCGCACTTTTTCTTATTTTTCTAAATAAAAA 52 44 1 TTTTTTTTTC 0.914325 -136 AAATAAAAAATTTTAATTTTTATTCTCACAAAAAC 52 70 1 TTTTTTTTTC 0.914325 -110 AGAACTTATCATTTATTTAGCTTTCCCTGTTTATC 53 99 0 ATTTTTCTTC 0.66687 -43 **** ** * *** Masking position 8 Map Score: 39.8864 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 267 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 4 AAAGATTGATTTTATTAGAAAAATATCAAATTA 2 139 0 TTTTTAAAAA 0.899914 -142 AACCTATCTCTTTCCATTAAAATACTTGCCATT 4 32 0 TTTCAAAAAT 0.740714 -29 ATTTTATACTTTTCAAGCAAAATTGCAAGTTTT 5 118 1 TTTAAAAAAT 0.795903 -175 AATTAGGTTCTTTTATATGAAATATAATGTAAT 6 19 0 TTTATGAAAT 0.688987 -280 TTCCTTAAAATTTATATTAAAAACAATGCCTTA 6 270 0 TTTTAAAAAA 0.836944 -29 TCTTAGCGAATTTTAACAAAAATAAAAACTAAA 8 219 1 TTTAAAAAAT 0.794976 -82 ATTTTATTTCTTTTCTTGAAAATAAGATTTTTC 9 168 1 TTTCTAAAAT 0.716109 -47 GTGGATGTGCTTTCTATCAAAAACACGGTTAAA 14 106 0 TTTTAAAAAA 0.910272 -195 TTCTACTTGTTTTCTTATGAAAAGTCGGCGAAT 16 35 0 TTTTTGAAAA 0.826899 -64 TGTCAGTTCATTTATATCAAAAACATATTTATT 17 73 1 TTTTAAAAAA 0.910272 -140 TTCTAATCTATTTTTAGGGAAAAAGTAAAGGAT 18 109 1 TTTTAGAAAA 0.81941 -123 AAAGGTTAATTTTCAACGAAAAATTATAATTGT 22 51 0 TTTAAAAAAA 0.833027 -49 AGCATAAGCATTTGTTTGAAAAATTCGCTATAA 23 228 1 TTTTTAAAAA 0.899914 -73 GAATGGCGGGTTTAATGTAAAATTTATGACGAA 27 67 0 TTTATAAAAT 0.775224 -82 AAAATCTCGTTTTAAACTGAAAAATGTGGGCAT 27 125 0 TTTAAGAAAA 0.762093 -24 TTGTTTATAATTTTTTACAAAATACGATAAAAA 28 146 0 TTTTTAAAAT 0.875803 -155 TTGAGCTATTTTTATAGGAAAAATTTAAGGTAA 30 51 1 TTTTAAAAAA 0.910272 -30 AAATTGAAAATTTATTGTAAAAAACAACTAAAA 31 110 1 TTTTTAAAAA 0.827497 -139 TTTTCACGCATTTATTGTAAAATCTCCGACAAT 35 124 1 TTTTTAAAAT 0.876523 -68 AAAATAAACTTTTTAATCAAAAATATTTTAATT 41 24 0 TTTAAAAAAA 0.831004 -51 TTCATTTCCTGTAAAATATTTGTAACC 41 58 0 TTTCTAAAAT 0.716488 -17 ATATCTGTTTTTTATTCAAAAAATTGTGACGAA 46 59 1 TTTTTAAAAA 0.834712 -139 CTTTTACAACTTTATAACAAAATTTTTTTGATG 46 99 1 TTTTAAAAAT 0.889953 -99 GACTTTTCATTTTTCAGCAAAAAAGGTAGGATT 46 146 1 TTTCAAAAAA 0.711898 -52 CCTTTATGCTTTTGTTGCGAAAATCCTACCTTT 46 167 0 TTTTTGAAAA 0.854282 -31 GTTTCTATAATTTGAAGTGAAATTGTTCTATTC 47 75 1 TTTAAGAAAT 0.714971 -199 CTTAGCCTTGTTTGTTAAGAAATTGTAATAAAT 47 123 1 TTTTTGAAAT 0.821237 -151 AAGGGTAAAATTTTAACGAAAAAACCCTAAAAA 48 176 0 TTTAAAAAAA 0.831004 -59 CACTCCAAAATTTATTCAAAAATAAGCGATAGT 50 140 0 TTTTTAAAAT 0.876619 -94 CTACACTTCGTTTATACAAAAAACTGAAATTAA 51 89 0 TTTTAAAAAA 0.844256 -212 ATTAAAATTTTTTATTTAGAAAAATAAGAAAAA 52 54 0 TTTTTGAAAA 0.829921 -126 TTGATGATTTTTTATAGAGAAATCTGCATAATA 55 195 1 TTTTAGAAAT 0.838533 -55 *** ** ***** Masking position 10 Map Score: 32.9584 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 214 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 5 TTTTTCAAGCAACGTTTTTAAAAATTCACTT 1 85 1 AGTTTTTAAA 0.911787 -21 ACCATAGACTATTTTTTCTCAAAACCTATAACC 2 41 1 ATTTTCTAAA 0.911787 -240 AGTTGTTGAGAGCTTTTCTCAAATATTTTTGAT 2 106 0 ATTTTCTAAA 0.911787 -175 TCCAATATATAGTGTTTTTGAAATGCGGATTGC 2 250 0 AGTTTTTAAA 0.911787 -31 GATGAAGTTCACAGTTTTTAAAATTCAAGTGAA 3 73 1 AGTTTTTAAA 0.911787 -93 AAAGAGAAAAAAATTTTCTAAAAATATTTTATT 9 143 1 ATTTTCTAAA 0.911787 -72 ACGTTTACAAAAAGTGCGGTGAA 16 1 1 ATTTACAAAA 0.484879 -98 CATTATGCAAACGGTTACTCAAAATAAATATGT 17 95 0 AGTTACTAAA 0.79706 -118 GAGGAAGATCACAGTTTTAGAAAATAAACATTA 17 123 0 AGTTTTAAAA 0.799954 -90 TTTTGTTTATAATTTTTTACAAAATACGATAAA 28 148 0 ATTTTTAAAA 0.712412 -153 ATAGCTCAAGATTGTTTCATAAATCAGTGCTTT 30 27 0 AGTTTCAAAA 0.865866 -54 GAAATGGTAAAACGTTTCTAAAATCTTCCGCAC 38 16 1 AGTTTCTAAA 0.943456 -269 GATATTGATCACATTTTCTTAAAATAGGTATAT 39 70 0 ATTTTCTAAA 0.911787 -210 TCAAGTCAGAATATTTTTATAAACCTCTACCAT 43 39 1 ATTTTTAAAA 0.712412 -85 AAAATAAGCGATAGTTTCTAAAAATTGCAGTAA 50 122 0 AGTTTCTAAA 0.943456 -112 AAACACTCCAAAATTTATTCAAAAATAAGCGAT 50 143 0 ATTTATTAAA 0.60115 -91 TAATATATACACATTTTTTCAAACTTGTTCTAA 51 34 0 ATTTTTTAAA 0.86492 -267 AAGTGCCACAATAGTTATTAAAAAAACCTTGAA 51 191 1 AGTTATTAAA 0.708713 -110 AAAACCTTGAAATGTTTTTAAAAACCTTTTTCT 51 213 1 AGTTTTTAAA 0.911787 -88 CTATGTGGTTAGATTTTCTGAAATTTAAGAAAA 51 244 1 ATTTTCTAAA 0.911787 -57 ATTACTTGCGATCTTTTCTCAAACACATTATCT 52 156 1 ATTTTCTAAA 0.911787 -24 AGTAGGGTTTATAGTTTTATAAAAATGCTCGTG 55 96 0 AGTTTTAAAA 0.799954 -154 * ****** *** Masking position 6 Map Score: 26.5354 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 = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 TGAAAAGTATAAAATTCGCAGGCTTTTTGTC 5 102 0 AAAATCGCAG 0.809453 -191 TATTTTTGTTAAAATTCGCTAAGATATTGAT 8 212 0 AAAATCGCTA 0.759349 -89 AAGTATAAAGAAAATACGCCTAAAAAGCGAC 12 76 0 AAAATCGCCT 0.909762 -56 AAGTGCGGTCAAAATTCTCCGAAATTTTTAA 13 183 1 AAAATCTCCG 0.858041 -59 GCATTCATTTAAAATTTACCGCCTTAAAATT 14 25 1 AAAATTACCG 0.840738 -276 TTACCGCCTTAAAATTAGCAAAGATTTAGAT 14 40 1 AAAATAGCAA 0.447319 -261 CACACAATGACAAATTCACCGTTATTTGTCG 14 136 1 CAAATCACCG 0.788769 -165 AAGTGCGGTGAAAATTCGCCGACTTTTCATA 16 22 1 AAAATCGCCG 0.983761 -77 AAATAGTAAAAAATTGACCGCACTTTATTT 20 10 1 AAAATGACCG 0.814004 -62 GTATTGATATCAAATGTGCCACATTCCATAT 21 13 0 CAAATTGCCA 0.510559 -54 CGAATATCAAAAAATAAACCGTATCAGGAGA 22 16 0 AAAATAACCG 0.899532 -84 TTTTTCGTTGAAAATTAACCTTTTCTAAGCG 22 61 1 AAAATAACCT 0.598403 -39 ATTTGTTTGAAAAATTCGCTATAATACCGCT 23 237 1 AAAATCGCTA 0.759349 -64 GCACAAGCAGAAAATGAACCTTTCTGGCGTT 28 11 1 AAAATAACCT 0.598403 -290 AAATCCCCCTAAAATTTGCCGTTACTATACC 29 11 1 AAAATTGCCG 0.929217 -90 ATTAAAATGCGCCAGATAGATTAA 35 4 1 AAAATCGCCA 0.969139 -188 AGAACAGAAAAAAATGCGCCAGTATTGTATA 35 47 0 AAAATCGCCA 0.969139 -145 TCCTACAGACAAAATCAACCAAAAGTGCGGT 36 235 0 AAAATAACCA 0.822734 -66 AAACGTTTCTAAAATCTTCCGCACTTTGCTA 38 25 1 AAAATTTCCG 0.567065 -260 GCACTTTGCTAAAATCAGCCATTATTTTTTT 38 45 1 AAAATAGCCA 0.920267 -240 CGATAAAAGGAAAATCAGCCATGTTTTATCC 38 81 0 AAAATAGCCA 0.920267 -204 GTAGTGCCAAAAAATCCGCCGATTCTTTATG 38 196 0 AAAATCGCCG 0.983761 -89 TTCTCTTATTAAAATTCGCTAGGCATTTTAC 45 64 0 AAAATCGCTA 0.759349 -27 CAAATGTCTGAAAATCCACCGCGCTTTTATG 48 120 0 AAAATCACCG 0.960568 -115 AAGTGCGGTGAAAATTGACCGCACTTTCTTA 49 180 1 AAAATGACCG 0.814004 -50 ***** ***** Masking position 5 Map Score: 24.3707 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 273 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 AAGTAAACATTGTGATATTGATCACAAAATCAAA 2 78 1 TGTGATATCA 0.98339 -203 TTTTAAAAACTGTGAACTTCATCACGGTATTATT 3 62 0 TGTGATATCA 0.984577 -104 ATTGTGTGGATGTGCTTTCTATCAAAAACACGGT 14 110 0 TGTGCTATCA 0.923069 -191 ACAAACTAACTGTGACGTGAATGACCGTTAAAAT 14 242 0 TGTGATATGA 0.881764 -59 TTTCTAAAACTGTGATCTTCCTCACGTTTTCAAA 17 133 1 TGTGATCTCA 0.923169 -80 GAATAAAAAATGTTAAGTAGATCAAAAAATTGAT 23 153 0 TGTTATATCA 0.834064 -148 TTAAATTTTATGAGATATTGATCACATTTTCTTA 39 82 0 TGAGATATCA 0.902473 -198 TCATTAAAACTGTGATCTTGATCACTTATTTGAT 47 163 0 TGTGATATCA 0.98455 -111 AAATCAGTTTTGTGACATAGATCATAAAAGCGCG 48 98 1 TGTGATATCA 0.98339 -137 ATTATCAGAATGAGATCTTTATCACAAAAAATTC 50 81 1 TGAGATATCA 0.934653 -153 ACTACTTTTTTGTGATCTATATCAAATCATCATT 55 126 1 TGTGATATCA 0.984408 -124 ***** * **** Masking position 14 Map Score: 13.7275 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 4 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 CGCACCATTTTAGCAAAGATTAATAAAAGAAAT 1 44 1 TCAAGATTAA 0.755857 -62 AGGAAAATTCTTGCAATTATAAAGAAAAGTGCG 3 126 0 TCAATATAAA 0.698235 -40 GCTGTTTTATTATCAATAATCAATATCTTAGCG 8 194 1 TCAAAATCAA 0.830184 -107 TAGCGAATTTTAACAAAAATAAAAACTAAAGCG 8 222 1 TCAAAATAAA 0.947945 -79 CAAAGTATCAAAAATAAAGGGGCTTAAT 10 6 1 TCAAAATAAA 0.947945 -64 ACAGGTGCTTTGGCAAAAATAAAATTTTAAATT 18 45 0 TCAAAATAAA 0.947945 -187 AAAGGTTAATTTTCAACGAAAAATTATAATTGT 22 51 0 TCAAGAAAAA 0.588947 -49 TATAGAGGTCTCTCAATAATAAAAATA 31 5 0 TCAAAATAAA 0.947945 -244 TACCGTAAAATGGCAAAAATTAATAGGGAGAGA 31 162 0 TCAAAATTAA 0.759644 -87 TGTGGATCCTTTCCAAGGATAAAAAGGATTAAG 36 122 1 TCAAGATAAA 0.946917 -179 ATTATTTTTTTCACAAGGATAAAACATGGCTGA 38 65 1 TCAAGATAAA 0.946917 -220 TGTTCGTTGATCTCAACGATAAAAGGAAAATCA 38 95 0 TCAAGATAAA 0.946917 -190 CAATTTACTTTTCCAAGAATAAATTGTCCTTGA 38 249 0 TCAAAATAAA 0.947945 -36 AAAAATGATGTGCAAATAATAAAGAAATAATTA 49 114 0 TAAAAATAAA 0.629263 -116 TTTCTAAAAATTGCAGTAATAAATGTGAATTTT 50 108 0 TCAGAATAAA 0.684325 -126 AGTTATCTATTGTCAAGAATCAAATCAAAAAAT 52 121 1 TCAAAATCAA 0.830184 -59 ATAAGTTCTATTTAAAGGATAAATAAA 53 125 1 TAAAGATAAA 0.624437 -17 * *** ****** Masking position 5 Map Score: 16.1124 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 38 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 9 GTGCGGTGAATTTCACGTTATTTTTTCACTTGAA 3 96 0 TTTACTATT 0.0102611 -70 TCAAGCAAAATTGCAAGTTTTGTATGCATAAAGTA 5 130 1 TTGAATTTTT 0.518606 -163 TTTAATTATCATTCACAATTTATTTTGTTTTACGA 5 177 1 ATTACTTTTT 0.645113 -116 ACTTTGGGCGTTTAAAAATTTCTTTTGATAGCCGC 6 187 0 TTTAATTTTT 0.884137 -112 TTTCAAACATTTTCATTATTTCTTTTTTGTTTTTC 9 111 0 TTTATTTTTT 0.630961 -104 GCGACGGCATTTGCACCATTTTTCTTGTTCGTTAT 12 46 0 TTGACTTTTT 0.721423 -86 TTAACCGCACTTTAAACCTTTAACTCCGACAGGAG 13 210 1 TTTAATTTAT 0.452712 -32 TATTGCTTAATTTAACCGTGTTTTTGATAGAAAGC 14 96 1 TTTACTGTTT 0.575135 -205 ATTTATTACCTTTTATATTCCGTTTTAT 17 4 1 TATACTTTTT 0.626055 -209 TTAATTGCAATTTAAAATTTTATTTTTGCCAAAGC 18 37 1 TTTAATTTTT 0.884137 -195 GCATTCTATCCTTTACTTTTTCCCTAAAAATAGAT 18 114 0 CTTACTTTCT 0.40715 -118 TTTTGATCTACTTAACATTTTTTATTCACGCAATC 23 160 1 CTTACTTTTT 0.737661 -141 GCGTTTACCATTTGAAGATTTTCATCGTTCACAAA 28 37 1 TTTAATTTCT 0.650809 -264 CATATTTTAATATTTGTCTCAACCAACAC 36 5 1 TTTAATTTTT 0.884138 -296 TTTAGAAACGTTTTACCATTTCTATTA 38 3 0 TTTACTTTTT 0.948303 -282 TCGCTCTTTTTCACAATTTACTTTTCCAAGAAT 38 262 0 TTTACTTTCT 0.817525 -23 TCTCATAAAATTTAACATTTTGNTTCCATTTCTTA 39 101 1 TTTACTTTNT 0.665377 -179 CTTACATTTTTATTACTATTTGTGTTTAGTTATAG 39 132 1 TATACTTTTT 0.626055 -148 TAATCTAGAATTTGTCAATTTGTTTTTTAAGAGTC 43 84 1 TTTTCTTTTT 0.477355 -40 CAAAACTGATTTTTAACGTTTTTGTTACGTTCCAC 48 75 0 TTTAATTTTT 0.884138 -160 ATAATGCATATTTAATTATTTATTTTTTAGGGTTT 48 153 1 TTTATTTTTT 0.630961 -82 TTCGTTAAAATTTTACCCTTTTTATAGGGTAAGAT 48 189 1 TTTACTTTTT 0.948303 -46 TTTTTACCTTTTGGCTTAATAAAGTG 50 218 0 TTTACTTTGT 0.625651 -16 TTTAAAAACATTTCAAGGTTTTTTTAATAACTATT 51 200 0 TTTAATTTTT 0.884138 -101 GTAAACTCCCTTTCAAGCTTTTTCTTAAATTTCAG 51 261 0 TTTAATTTTT 0.884138 -40 GAGAATAAAAATTAAAATTTTTTATTTAGAAAAAT 52 62 0 ATTAATTTTT 0.430164 -118 AGATTTTCACCTTTTATTTAAGTTAAACA 55 5 1 TTTACTTTTT 0.948303 -245 *** ** *** * * Masking position 9 Map Score: 15.5604 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 161 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 10 TGAGAAAAAATAGTCTATGGTAAAATAGATGAGTA 2 27 0 TAGTATGAAA 0.761242 -254 GAATGGCAAGTATTTTAATGGAAAGAGATAGGTTG 4 31 1 TATTAAGAAG 0.728294 -30 GGATGCCTCGTATTATATCGTAAAACAAAATAAAT 5 194 0 TATTATGAAA 0.935705 -99 TATTTAATCGGATAACAAACACATA 8 1 1 TATTATGAAA 0.935706 -300 ATGTTTTGGATAGTATAACGAACAAGAAAAATGGT 12 32 1 TAGTAAGAAA 0.831452 -100 TTATCAATAGTATTTCAATGCACAAAGTATAAAGA 12 96 0 TATTAAGAAA 0.956605 -36 AATTCTAATCTATTTTTAGGGAAAAAGTAAAGGAT 18 107 1 TATTTAGAAA 0.630187 -125 ATTTTTTATTTATTTCAACGAATAAGGATAACGCT 23 73 0 TATTAAGAAA 0.957477 -228 TGGCTGATATTATGCCATAGCAAAAAATATTCGTC 27 38 1 TATGATGAAA 0.634028 -111 AGACAATATTGTATTGAAAACTCCCGTTTCA 43 7 1 TATTATGAAC 0.634033 -117 CACTTCAAATTATAGAAACGTATAATACCCATATC 47 59 0 TATAAAGAAA 0.643945 -215 CTATCAATTATATTGAATAGAACAATTTCACTTCA 47 87 0 TATTATGAAA 0.935705 -187 AAAAGGGTAAAATTTTAACGAAAAAACCCTAAAAA 48 176 0 AATTAAGAAA 0.643945 -59 TTTATTGTAATGTAGAAAAGTCTTTAG 51 3 1 TATTAAGAAA 0.957477 -298 AATGTGTATATATTAAAAGGCATAATGTCTAGCGT 51 52 1 TATTAAGAAA 0.957478 -249 TTTTTTCTATTATTAAATTGGACAATCCTTCTGAC 51 125 0 TATTATGAAA 0.935692 -176 TGATAAGTTCTATTTAAAGGATAAATAAA 53 123 1 TATTAAGTAA 0.630188 -19 ATCAAATCATCATTAGAATGAAAAAGTACCGTAAA 55 146 1 CATTAAGAAA 0.728294 -104 **** ** * * ** Masking position 2 Map Score: 9.1454 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 45 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 TTTAACTGATATTTTATCAAGCTAAAATACCGCT 5 257 0 ATTTTCAATA 0.847819 -36 AGAGAAAAAAATTTTCTAAAAATATTTTATTTCT 9 145 1 ATTTTAAATA 0.583717 -70 CGCACTTTTTAATTGATTAAGATAAA 15 3 0 AATTTTAATA 0.766181 -81 AATAAGCCGAATTTTATTAACTTAACTAATCTAG 16 66 1 ATTTTTAATA 0.929461 -33 TGATTTTCTTAATTTATTACCTAAAA 18 216 0 ATTTTTAATA 0.929461 -16 CAGAATATCAAATTAATTAAAATATAGGAGTGCA 24 114 1 AATTTTAATA 0.766181 -26 TTGATTTCCTTAAATTAAATATTTGAA 27 4 1 ATTTTTAATA 0.929461 -145 CTTATCCACAATTTCGTTATTTTACTTTAATTTT 33 82 0 ATTTTTATTA 0.680207 -43 TATTGATCACATTTTCTTAAAATAGGTATATGCT 39 67 0 ATTTTTAATA 0.929461 -213 TTGCTAATATATTTGTGTAATTTATTATCAATAG 40 64 1 ATTTGTAATA 0.625611 -59 TTGATTAAAATTTAATTAAAATATTTTTGATTA 41 10 1 ATTTTTAATA 0.929461 -65 ACCATTTTGTATTTTTTTAATCTAGAATTTGTCA 43 67 1 ATTTTTAATA 0.929461 -57 CTCTCTTTCTATTTTTTTATGATAGAATGCCAAT 44 82 1 ATTTTTATTA 0.680207 -66 TTTAATGAATATTTAATCAAACTATCGCGGCTAA 47 189 1 ATTTTCAATA 0.847819 -85 GATTCCCTATAATTGATCAACGTATTATGAAAAA 50 24 0 AATTTCAATA 0.580792 -210 AAGCAAACAGATTTGTTTAACTTAAATAAAAGGT 55 19 0 ATTTTTAATA 0.929461 -231 **** **** ** Masking position 9 Map Score: 14.0556 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 20 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 AAGTAAACATTGTGATATTGATCACAAAATCAA 2 78 1 TGTGAATATC 0.939019 -203 TTTTAAAAACTGTGAACTTCATCACGGTATTAT 3 63 0 TGTGACTATC 0.975243 -103 TTTCTAAAACTGTGATCTTCCTCACGTTTTCAA 17 133 1 TGTGACTCTC 0.912765 -80 TTAAATTTTATGAGATATTGATCACATTTTCTT 39 83 0 TGAGAATATC 0.849335 -197 TCATTAAAACTGTGATCTTGATCACTTATTTGA 47 164 0 TGTGACTATC 0.975244 -110 AAATCAGTTTTGTGACATAGATCATAAAAGCGC 48 98 1 TGTGAATATC 0.939019 -137 ATTATCAGAATGAGATCTTTATCACAAAAAATT 50 81 1 TGAGACTATC 0.935156 -153 ACTACTTTTTTGTGATCTATATCAAATCATCAT 55 126 1 TGTGACTATC 0.975244 -124 ***** ** *** Masking position 5 Map Score: 6.41182 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 2 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ATATACAGAGAAAAAAGTAAGCTATATTCTCAA 5 66 0 AAAAAAAGCT 0.512157 -227 AAAGTATCAAAAATAAAGGGGCTTAATTGCCCC 10 12 1 AAATAAGGCT 0.876094 -58 AATAAAAAACAACAAAAGGGGCAATTAAGCCCC 10 29 0 AACAAAGGCA 0.875666 -41 AGTTAAGTTAATAAAATTCGGCTTATTCTACTT 16 60 0 ATAAAAGGCT 0.833027 -39 TTTTAAACTGAAAAATGTGGGCATTATAGCGTA 27 116 0 AAAAATGGCA 0.655315 -33 AAAAATTATAAACAAAATTGGTTGCATATTGAT 28 164 1 AACAAAGGTT 0.596781 -137 TCCTTGTGAAAAAAATAATGGCTGATTTTAGCA 38 51 0 AAAAATGGCT 0.876094 -234 TTTCACAAGGATAAAACATGGCTGATTTTCCTT 38 73 1 ATAAAAGGCT 0.833027 -212 AATAACTCCTAACAAATAAGGCTGGACATCAGC 40 33 0 AACAAAGGCT 0.963225 -90 TTTAGAACGAAACAAAAAAGGCTGCAATGCAGC 45 20 0 AACAAAGGCT 0.963225 -71 ACAATTTCTTAACAAACAAGGCTAAGACTATCA 47 116 0 AACAAAGGCT 0.963225 -158 TATTTAATCAAACTATCGCGGCTAACAATAAAT 47 198 1 AACTATGGCT 0.791828 -76 AAGATTGAGAAAATAACGGGGCTAAA 48 219 1 AAATAAGGCT 0.876094 -16 TTAATTATGTATAAAAAACGGCTAGTTTTATTT 49 35 0 ATAAAAGGCT 0.833027 -195 TTTTTTTAATAACTATTGTGGCACTTAAGGACG 51 184 0 AACTATGGCA 0.505628 -117 ****** **** Masking position 5 Map Score: 8.5689 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 139 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 AATCTTTGCTAAAATGGTGCGTAATTTTAA 1 35 0 AAAATGGTGC 0.970062 -71 TATATAGACAAAAAGCCTGCGAATTTTATA 5 96 1 AAAAGCCTGC 0.830165 -197 AAATAAAAACTAAAGCGTGCTAGAATAGTG 8 238 1 TAAAGCGTGC 0.742025 -63 ACGAACAAGAAAAATGGTGCAAATGCCGTC 12 49 1 AAAATGGTGC 0.970062 -83 CTGATTACTATAAATGGTGCTGATCCCTTG 13 14 1 TAAATGGTGC 0.928091 -228 TTTATTACCTAAAATGTTGCGCGATTTTAC 18 200 0 AAAATGTTGC 0.807801 -32 TTCTATTGTCAAAATGCTGCAAAAGTGCGG 31 209 1 AAAATGCTGC 0.956395 -40 ATACCTATAAAAAATGGTGCGTGAATTTTA 32 30 0 AAAATGGTGC 0.970062 -20 TAGATAAAGGCTGCATTGCAGCCT 45 5 1 TAAAGGCTGC 0.890952 -86 AACGAAACAAAAAAGGCTGCAATGCAGCCT 45 18 0 AAAAGGCTGC 0.953514 -73 CTGTTTCAAGAAAATGGAGCACTTATT 46 8 0 AAAATGGAGC 0.804578 -190 ********** Masking position 4 Map Score: 10.4878 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 37 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 ATAATTTTGTTAAAGATTGATTTTATTAGAAAAAT 2 148 0 TAAATTATTA 0.922626 -133 ATTTTCCTCCTAAAAATTGATTGTTCTCTCTGAAA 6 50 0 TAAATTATTT 0.871914 -249 GGCATTGTTTTTAATATAAATTTTAAGGAAAACAT 6 273 1 TAAATAATTA 0.611182 -26 CAATAAAAGGTCAAGATTGATTAAAAATCAATCTA 14 66 0 TAAATTATTA 0.922634 -235 TTACTCAAAATAAATATGTTTTTGATATAAATGAA 17 79 0 TAAATGTTTA 0.565592 -134 AATTGCAATTTAAAATTTTATTTTTGCCAAAGCAC 18 39 1 TAATTTATTT 0.502458 -193 ACTTTTTCCCTAAAAATAGATTAGAATTGCGTCCT 18 100 0 TAAATAATTA 0.614079 -132 TTTGATCTACTTAACATTTTTTATTCACGCAATCG 23 161 1 TAAATTTTTT 0.603078 -140 TAAAAATAGCTCAAGATTGTTTCATAAATCAGTGC 30 30 0 TAAATTTTTT 0.603078 -51 CTGCAAAAATTGAAAATTTATTGTAAAAAACAACT 31 104 1 TAAATTATTA 0.922626 -145 TACTTTTACCTAAAAATGAATTTCAAACGGAGTAT 34 20 1 TAAATGATTA 0.819174 -28 CGTTGGCGCGTAAAAATTGATGACAAGTGGTTTTT 38 161 0 TAAATTATGA 0.487826 -124 TAGAATATGATAAAGATTSSTTTAATGCCATATTA 39 183 1 TAAATTSTTA 0.922585 -97 ATTACTTAAATTAAGATCTATTGATAATAAATTAC 40 80 0 TAAATCATTT 0.432958 -43 CTATACTTCCTTAATATTACTTAAATTAAGATCTA 40 95 0 TAAATTCTTA 0.545265 -28 TTGATTAAAATTTAATTAAAATATTTTTGA 41 6 1 TAATTTATTA 0.637066 -69 AATTTACAATTTAAGATGAATTAAAACTTC 44 6 0 TAAATGATTA 0.853664 -142 ATAGTTTGATTAAATATTCATTAAAACTGTGATCT 47 179 0 TAAATTATTA 0.922634 -95 ACTTATTAAATCAAAATTTATTGTTAGCCGCGATA 47 211 0 TAAATTATTT 0.871914 -63 CACTTGCGTTTTAATTTTCATTCAATTCATAGGAG 48 17 0 TAATTTATTA 0.6389 -218 AATAAATAATTAAATATGCATTATTACAAATGTCT 48 142 0 TAAATGATTT 0.769056 -93 TTATACATAATTAAAATGTATTAATGATCGTGTAG 49 54 1 TAAATGATTT 0.769056 -176 TAAAAACACTCCAAAATTTATTCAAAAATAAGCGA 50 144 0 CAAATTATTA 0.487826 -90 AAAAGTGCGGTAAAAATTTGTTGAATTTTTCACCG 52 23 0 TAAATTGTTA 0.545265 -157 AGAATAAAAATTAAAATTTTTTATTTAGAAAAATA 52 61 0 TAAATTTTTT 0.603077 -119 * ** *** *** * Masking position 7 Map Score: 9.32734 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 84 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269