AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_hinf_reg_300.orf -o02010_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 Input sequences: #1 HI0096 300 H. influenzae predicted coding region HI0096 #2 HI0097 272 iron(III) ABC transporter, periplasmic-binding protein (hitA) #3 HI0098 216 iron(III) ABC transporter, permease protein (hitB) #4 HI0126 43 ferric ABC transporter, ATP-binding protein (afuC) #5 HI0129 300 H. influenzae predicted coding region HI0129 #6 HI0131 165 afuA protein #7 HI0213 164 oligopeptide transporter, periplasmic-binding protein, putative #8 HI0213.1 119 H. influenzae predicted coding region HI0213.1 #9 HI0354 300 ABC transporter, ATP-binding protein #10 HI0357 21 thiamine biosynthesis protein, putative #11 HI0362 300 iron (chelated) ABC transporter, periplasmic-binding protein (yfeA) #12 HI0408 171 ABC transporter, ATP-binding protein (yebM) #13 HI0498 254 spermidine/putrescine ABC transporter, periplasmic-binding protein (potD) #14 HI0500 300 conserved hypothetical protein #15 HI0501 167 high affinity ribose transport protein (rbsD) #16 HI0621 175 ABC transporter, ATP-binding protein #17 HI0821 207 galactose operon repressor (galR) #18 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #19 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) #20 HI0851 300 molybdopterin-guanine dinucleotide biosynthesis protein B (mobB) #21 HI0853 140 heme-binding lipoprotein (dppA) #22 HI1019 300 thiamin ABC transporter, periplasmic-binding protein (tbpA) #23 HI1079 67 amino acid ABC transporter, permease protein #24 HI1080 300 amino acid ABC transporter, periplasmic-binding protein #25 HI1087 300 ABC transporter, ATP-binding protein #26 HI1110 50 D-xylose ABC transporter, ATP-binding protein (xylG) #27 HI1111 233 D-xylose ABC transporter, periplasmic-binding protein (xylF) #28 HI1123 80 oligopeptide ABC transporter, permease protein (oppB) #29 HI1124 295 oligopeptide ABC transporter, periplasmic-binding protein (oppA) #30 HI1180 126 arginine ABC transporter, ATP-binding protein (artP) #31 HI1181 206 phosphoheptose isomerase (gmhA) #32 HI1187 89 dipeptide ABC transporter, permease protein (dppB) #33 HI1188 300 DNA helicase II (uvrD) #34 HI1344 72 spermidine/putrescine ABC transporter, periplasmic-binding protein (potD) #35 HI1345 25 spermidine/putrescine ABC transporter, permease protein (potC) #36 HI1347 268 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #37 HI1382 90 phosphate ABC transporter, permease protein (pstC) #38 HI1383 300 phosphate ABC transporter, periplasmic-binding protein (pstS) #39 HI1472 67 iron chelatin ABC transporter, periplasmic-binding protein, putative #40 HI1475 227 H. influenzae predicted coding region HI1475 #41 HI1476 227 transcriptional regulatory protein #42 HI1618 95 ABC transporter, ATP-binding protein #43 HI1624 89 H. influenzae predicted coding region HI1624 #44 HI1638 69 peptide ABC transporter, periplasmic-binding protein (sapA) #45 HI1692 173 molybdenum ABC transporter, permease protein (modB) #46 HI1693 137 molybdenum ABC transporter, periplasmic-binding protein (modA) Motif number 1 GTTTCAACACAAAGTGCGGTCAATTCTGCG 1 236 0 AAAGTGCGGT 0.998174 -65 ATTATAAAGAAAAGTGCGGTGAATTTCACG 6 43 1 AAAGTGCGGT 0.998174 -123 GAAGCCGCAAAAAGTGCGGTGGTGGAAAGG 13 189 0 AAAGTGCGGT 0.998174 -66 AATTCTTGAGAAAGTGCGGTCAATTTTTCA 14 193 0 AAAGTGCGGT 0.998174 -108 TTTCTACAAGAAAGTGCGGTAGATTATTTT 24 148 1 AAAGTGCGGT 0.998174 -153 TACTCGTATTTAAGTGCGGTTAAAAATCGT 28 16 1 TAAGTGCGGT 0.98445 -65 AAATGGGCGAAAAGTGCGGTCAAAAAATAC 28 47 0 AAAGTGCGGT 0.998174 -34 ATTTCTTTGAAGAGTGCGGTGAATTTTTAC 32 42 1 AGAGTGCGGT 0.989455 -48 GTAGATAATAAAAGTGCGGTAAAAATTCAC 32 60 0 AAAGTGCGGT 0.998174 -30 AAATTCATCGAAAGTGCGGTTAAATTTCTC 36 104 1 AAAGTGCGGT 0.998174 -165 GGTTTTGTATAAAGTGCGGTATAAAATAAA 37 17 0 AAAGTGCGGT 0.998174 -74 TAACATTAATAAAGTGCGGTTATCTTAAAT 37 54 1 AAAGTGCGGT 0.998174 -37 ********** Masking position 3 Map Score: 49.6837 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 TCAACACAAAGTGCGGTCAATTCTGCGGAAG 1 232 0 GTGCGGTAAT 0.995005 -69 ATAAAGAAAAGTGCGGTGAATTTCACGTNTA 6 46 1 GTGCGGTAAT 0.995005 -120 TCTTGAGAAAGTGCGGTCAATTTTTCAGTCA 14 189 0 GTGCGGTAAT 0.995005 -112 CTACAAGAAAGTGCGGTAGATTATTTTCTTA 24 151 1 GTGCGGTGAT 0.98709 -150 AGCTTCTTTAGTGAGGTCAAAAAGAATGTTA 25 93 1 GTGAGGTAAA 0.934616 -208 TCGTATTTAAGTGCGGTTAAAAATCGTCGTA 28 19 1 GTGCGGTAAA 0.995005 -62 TGGGCGAAAAGTGCGGTCAAAAAATACGACG 28 43 0 GTGCGGTAAA 0.995005 -38 AGTGCGGTTGATTTCAATCAAG 30 2 1 GTGCGGTGAT 0.98709 -125 TCTTTGAAGAGTGCGGTGAATTTTTACCGCA 32 45 1 GTGCGGTAAT 0.995005 -45 GATAATAAAAGTGCGGTAAAAATTCACCGCA 32 56 0 GTGCGGTAAA 0.995005 -34 TTCATCGAAAGTGCGGTTAAATTTCTCGTTA 36 107 1 GTGCGGTAAA 0.995005 -162 TTTGTATAAAGTGCGGTATAAAATAAAGAGA 37 13 0 GTGCGGTTAA 0.965555 -78 ******* *** Masking position 10 Map Score: 33.3312 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 TTCCTATTATTTCTTCAATGCTTTTTTCAATTCAAGTAA 1 80 1 TTTTTTTTTA 0.916613 -221 CTGCGAGGCAAAGTTAAATCCTTTTAGGAATGTGAACTT 3 100 0 AATTTTTTTA 0.807905 -117 ACTTAACGAGTTAATTCATTTTTTTCGCT 4 1 0 TTATTTTTTT 0.686367 -43 TCCATAATGCATTCTGCTTATTTTTGGATTATTTTATCC 5 191 1 ATCTTTTTTT 0.645027 -110 TCAAAATAAAAATTTTGGTATTTTTCTTTAATGATCGAT 7 13 0 AATTTTTTTT 0.623149 -152 TACCAAAATTTTTATTTTGACTTTTGTTACCACAATGCT 7 32 1 TTATGTTTTA 0.678091 -133 ATGCAAACTATTATTACTGATTTTTTAGATTTTTCAACC 8 68 0 TTTTGTTTTA 0.806197 -52 GATAGAAACCTAATTGCTTGTTTTTTCTACCAAACAAGC 9 96 1 TATTTTTTTA 0.828386 -205 TTGTTTTGGTTTGTTCTGTCATTTTAGGTTTATCATCAC 11 43 1 TTTTTTTTTT 0.812093 -258 ACTAACCAAAATGTTTTGTTCTTTTTTCATACATTCAAT 11 111 1 ATTTTTTTTA 0.90546 -190 TAATTATAAATAAATCTATTATTTTGATAATCATTCCCA 11 165 1 TAATTTTTTA 0.709664 -136 ATAGTACTACTTTTTATATTGTTTTGGAATGGGAATGAT 11 194 0 TTTTTTTTTA 0.916613 -107 ATGGTTGGGGAAAATAACGCATTTTTATAGAATTCTCAA 12 122 0 AAATGTTTTA 0.446278 -50 CGCGCGCGCAAAATTTGCGTGTTTTATGATGAACGATAA 13 94 1 AATTGTTTTA 0.614142 -161 GCTGATTATAATCTTGAGTCGTTTTCGATAA 14 3 0 ATTTTTTTTT 0.790161 -298 AAATTTGAAATTTCTTAGTTGTTTTTCTATTTTTGTTAT 15 91 1 TTCTTTTTTA 0.841382 -77 ATAAGCCCTTTTTATTTATTGTTTTTAAATCTGTTTTGG 16 147 0 TTATTTTTTA 0.847705 -29 AAAATTTTGCTTATTTTCTTATTTTGTGACAAAGATCAC 17 78 0 TTTTTTTTTA 0.916613 -130 CAAAAAAATAATATTTCATCCTTTTAGGAAAAGCGGTTG 20 74 0 ATTTTTTTTA 0.90546 -227 ATTAACCCCGATCTTTCGGGGTTTTCCGTATCTAAAGTG 20 270 1 ATTTGTTTTT 0.587634 -31 GATATAAGCAAATTTCCCTTTTTTTAAATAAAAAAATTC 21 32 0 AATTTTTTTT 0.623149 -109 AAAATGTAGAAAGTTTATTTCTTTTTAAAAAGCCGTTGG 22 105 1 AATTTTTTTA 0.807906 -196 GTGCGGTAGATTATTTTCTTATTTTGATAGTAATCACTT 24 161 1 TTTTTTTTTA 0.916613 -140 CCATAAATAAATAATCTTTTTTTTTCATAAGTTTGGTTT 24 231 1 ATATTTTTTA 0.829055 -70 ATTTCTTCATTATTTATTGAATTTTAATAATACTTTGTT 25 50 0 TATTGTTTTA 0.646234 -251 AGTGATAAATTTTATTTCTATTTTTTATAGATTAAAATT 25 134 0 TTATTTTTTA 0.847705 -167 AGAAATAAAATTTATCACTATTTTTATGACCACATCAAA 25 154 1 TTATTTTTTA 0.847705 -147 AGGTGATGAAATTTTTCGTATTTTTGTGAAAAACTAACT 27 26 1 ATTTTTTTTA 0.90546 -208 TTCATCAATTATGTTATTTAATTTTTCTATGTTGATTAT 27 66 1 ATTTTTTTTA 0.90546 -168 ATCTTTCTCCATTATTACGTTTTTTCACAACTGTGATCC 27 120 0 ATATGTTTTA 0.647312 -114 AATCCCAAAATTTCTTGGGATTTTTTATTAATAGCACTT 30 40 1 TTCTGTTTTT 0.441103 -87 AGCCTAAATAAAAATTCATCTTTTTTCGATGAAATGATG 31 115 0 AAATTTTTTA 0.680481 -92 TATTATTGTCATCATGGGTATTTTTGGAAAAATGAGAAA 33 40 1 ATATTTTTTA 0.829055 -261 ATTCTCGCTCCTTTTAAAAATATCTTTTT 36 1 1 ATCTTTTTTA 0.82212 -268 CGATGAATTTTACTTCGTTAATTTTATAAATATTGTTAT 36 75 0 TATTTTTTTA 0.828386 -194 TGCGGTTAAATTTCTCGTTATTTTTATGAACGGCAGTTT 36 118 1 TTCTTTTTTA 0.841382 -151 AAGTGCGGTTATCTTAAATAATTTTGGAAAATACTT 37 65 1 ATTTTTTTTA 0.905364 -26 ATTCTTAGTTTTTCTGGTTCATTTTGACTAAATCAACCA 40 54 1 TTCTTTTTTT 0.675905 -174 AAAGATCTGATTTTTTCTTAGTTTTCTTTCCCTAAGAAT 40 92 1 TTTTTTTTTT 0.812093 -136 GCCAAATTCCTATTTCTTTTGTTTTCTTTGTTTTG 40 203 1 TATTTTTTTT 0.654913 -25 TGGCTATATTTTAATCTATTGTTTTACTATTTCGAATAA 41 103 1 TTATTTTTTA 0.847705 -125 TTGCTTACCCAATTTTTTTCATTTTTCAATCTGACGCCA 45 145 1 AATTTTTTTA 0.807906 -29 GTTATATATTTTACTAAATAATTTTTCTTTTGCTATATG 46 50 1 TTCTTTTTTT 0.675832 -88 ** ** * **** * Masking position 12 Map Score: 38.79 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 442 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 4 CGTCACATAAAAAAACAGTTTTCAAAAAAGGAACA 8 14 0 AAAAGTTTTA 0.918582 -106 ATGGAACAAGAAAAGCATTTTTAAATTTCTCTTGC 9 58 0 AAAATTTTTA 0.932211 -243 AATGAAAAGAAAATGGATTTTTTGGCATATTAGTT 9 220 0 AAAATTTTTG 0.897425 -81 CCCTAAAATAAAAAAGTTTTCAGCATTCAGACT 12 9 1 TAAAGTTTTG 0.658679 -163 TTGGGGAAAATAACGCATTTTTATAGAATTCTCAA 12 122 0 TAAATTTTTA 0.787128 -50 AGTGAGTGAGCAAAGAATTTTTTCAATTTATTGAC 13 142 0 CAAATTTTTA 0.853235 -113 ACAGAGAAAGAAAAATATTTTTCTGCACAACAACA 14 245 1 AAAATTTTTG 0.897424 -56 CTTTCTTTAGAAAGGCATTTTTTTACTGAAATTTT 24 76 1 AAAATTTTTA 0.932211 -225 CATTGTTTAGAAACGTATTTTTCTACAAGAAAGTG 24 129 1 AAAATTTTTA 0.932211 -172 TAATTGATGAAAAGTTAGTTTTTCACAAAAATACG 27 42 0 AAAAGTTTTA 0.918582 -192 ATTTGAAGAAAAATTGAGTTTTGTGAGTTGTGTCT 29 179 0 AAAAGTTTTG 0.877719 -117 ATTAGCTCAAAAATTCATTTTTGTAAAGATTTGTC 29 222 0 AAAATTTTTA 0.932211 -74 CGGTTGATTTCAATCAAGTTTTTTAAATCCCAAAA 30 15 1 CAAAGTTTTA 0.826682 -112 CCAACTACTCAAACTTATTTTTTCGATCTAAATCG 31 72 1 AAAATTTTTG 0.897425 -135 ATATGCTTTGAAAGCTATTTTTATACTATTTATAA 33 122 0 AAAATTTTTA 0.932211 -179 TTAAACTAAAAAAGATATTTTTAAAAGGAGCGAGA 36 13 0 AAAATTTTTA 0.932211 -256 TTACGGGTAATAATTTAGTTTTTAATCCCGTAATA 41 165 1 TAAAGTTTTA 0.752086 -63 ACTTTAGAATCAAGTCATTTTTTAAGGAAATTG 43 9 0 CAAATTTTTA 0.85325 -81 *** ****** * Masking position 9 Map Score: 18.613 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 88 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 TTATAATTGCAAGAATTTTCCTTACATCGAAAC 6 17 0 AAAATTTTTT 0.905184 -149 AGAAAAATACCAAAATTTTTATTTTGACTTTTG 7 25 1 CAAATTTTTT 0.719332 -140 ATGCCAAAAAATCCATTTTCTTTTCATTCCATT 9 227 1 ATCATTTTTT 0.894894 -74 AAAAAGAACAAAACATTTTGGTTAGTATTAAGT 11 104 0 AACATTTTTT 0.852263 -197 TTCCATAGGAATGAATTTTCTTTATAATCTGTA 12 43 0 ATAATTTTTT 0.933713 -129 CTAAATCATAAAAAATTTTGCTTATTTTCTTAT 17 95 0 AAAATTTTTT 0.905143 -113 TTTTTTATGTAATCATTTTCATTTTTGCAAATT 18 38 1 AACATTTTTT 0.852302 -53 TTTCCCATCAATTTTTGTTGTAATCTAAG 19 7 1 ATAATTTTTT 0.933712 -59 TTTATGGTTTATGAATTTTAGTTATAAAAAATT 24 205 0 ATAATTTTTT 0.933713 -96 AAAAATAGTGATAAATTTTATTTCTATTTTTTA 25 146 0 ATAATTTTTT 0.933713 -155 ACTCACAAAACTCAATTTTTCTTCAAATAATTT 29 186 1 CTAATTTTTT 0.790859 -110 TCGAAAAAAGATGAATTTTTATTTAGGCTAGCG 31 125 1 ATAATTTTTT 0.933712 -82 CGCACTTTCGATGAATTTTACTTCGTTAATTTT 36 89 0 ATAATTTTTT 0.933713 -180 TTAGATAAGGATTCATTTTGCTTACCCAATTTT 45 128 1 ATCATTTTTT 0.894893 -46 TATTTTACTAAATAATTTTTCTTTTGCTATATG 46 56 1 AAAATTTTTT 0.905114 -82 ** ****** ** Masking position 5 Map Score: 16.514 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 102 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 AAATGTCAGATCAAATAAATAAGGCGGAATAA 1 36 1 TAATAAATAA 0.778749 -265 GTGAATTACTTGAATTGAAAAAAGCATTGAAG 1 92 0 TAATGAAAAA 0.941743 -209 AAATTGATATTTAGATGAAAAACAAAACGGTA 2 41 0 TAGTGAAAAA 0.836257 -232 CAATTCAGGCTGAACTGAATAATTTGCACTCA 2 121 1 TAATGAATAA 0.849847 -152 TTTTTAAAATTCAAGTGAAAAAATAACGTGA 6 68 0 TAATGAAAAA 0.941743 -98 GAATTTGCCGTCACATAAAAAAACAGTTTTCA 8 25 0 TACTAAAAAA 0.822263 -95 CCCTAAAATAAAAAAGTTTTCAGCA 12 4 1 TAATAAAAAA 0.909527 -168 CGGAGGTCAATAAATTGAAAAAATTCTTTGCT 13 137 1 TAATGAAAAA 0.941743 -118 ATGAAAATGATTACATAAAAAATTATGAATTT 18 28 0 TACTAAAAAA 0.822262 -63 TTCCCTTTTTTTAAATAAAAAAATTCTATGGA 21 26 0 TAATAAAAAA 0.909526 -115 CAGTTTTATATGACCTGAAAAAGTTAGATTTG 25 248 0 TACTGAAAAA 0.881504 -53 CTATGCTTTATAAGATGAAAAAATATTACATT 30 96 0 TAGTGAAAAA 0.836257 -31 TTTTTCTCGTTAAACTAAAAAAGATATTTTTA 36 25 0 TAATAAAAAA 0.909527 -244 TGTTTATGCATAAAATGAAAAAAAATCTTATT 38 70 1 TAATGAAAAA 0.941743 -231 GATTATATATTGAAATAAATAACAATCATATA 46 83 0 TAATAAATAA 0.778749 -55 CAATATATAATCAAGTAAATAACGTTTAATCG 46 103 1 TAATAAATAA 0.778749 -35 * ** ******* Masking position 6 Map Score: 16.0941 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 121 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 TTATAGATAAAAATGATAACTATTAAAA 1 9 1 AAAAATGATA 0.544354 -292 AGCGAAAAAAATGAATTAACTCGTT 4 6 1 AAAAAATGAA 0.41131 -38 AATTCAAGTGAAAAAATAACGTGAAATTC 6 63 0 AAAAAATAA 0.757819 -103 TCCTACTTGAAAAATAGAAATAATACCGTG 6 113 0 AAAATAGAAA 0.802782 -53 AACAGTTTTCAAAAAAGGAACATTT 8 6 0 AAAAAAGGAA 0.784831 -114 TGTTCCTAATAAAAAAGGAAAATGCAAACT 8 98 0 AAAAAAGGAA 0.784831 -22 AGTGCGTAATAAAAAAGAAAGGATAAGAAA 9 258 0 AAAAAAGAAA 0.942316 -43 TGAATGTATGAAAAAAGAACAAAACATTTT 11 118 0 AAAAAAGAAC 0.556177 -183 GTCCTTATTTAAAAAAGATAGATTGAATGC 11 276 0 AAAAAAGATA 0.860803 -25 ATAGATAACAAAAATAGAAAAACAACTAAG 15 104 0 AAAATAGAAA 0.802782 -64 TAATCTGTCTAAAAAAGATAATCTGACATA 16 88 1 AAAAAAGATA 0.860803 -88 CTTTGTCACAAAATAAGAAAATAAGCAAAA 17 83 1 AAATAAGAAA 0.608192 -125 GCAAATTTGCAAAAATGAAAATGATTACAT 18 44 0 AAAAATGAAA 0.759376 -47 ACATTTTCTGAAAAAATAAAGGGGCTGACG 22 82 0 AAAAAATAAA 0.757819 -219 AACGGCTTTTTAAAAAGAAATAAACTTTCT 22 112 0 TAAAAAGAAA 0.458145 -189 ATTACTATCAAAATAAGAAAATAATCTACC 24 165 0 AAATAAGAAA 0.608192 -136 TAATCTATAAAAAATAGAAATAAAATTTAT 25 139 1 AAAATAGAAA 0.802782 -162 ATGTGTTGCGATAAAAGAAAAAACTTCATC 25 207 1 ATAAAAGAAA 0.458145 -94 ATCAACATAGAAAAATTAAATAACATAATT 27 72 0 AAAAATTAAA 0.376757 -162 ATTAATCGGTAAAAAATATAATACTCTTGA 32 14 0 AAAAAATATA 0.542244 -76 TCGTTAAACTAAAAAAGATATTTTTAAAAG 36 21 0 AAAAAAGATA 0.860803 -248 TTTAACGAGAAAAATAGAAAACATCTTGAT 36 43 1 AAAATAGAAA 0.802782 -226 GAATTTAAACAAAAAAGAAAACGCCCGTTT 40 28 0 AAAAAAGAAA 0.942316 -200 CAAAACAAAGAAAACAAAAGAAA 40 215 0 AACAAAGAAA 0.556177 -13 CGTCAGATTGAAAAATGAAAAAAATTGGGT 45 151 0 AAAAATGAAA 0.759376 -23 ATTATTTAGTAAAATATATAACGCTTAGGC 46 42 0 AAAATATATA 0.2279 -96 ********** Masking position 2 Map Score: 19.5408 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 301 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 8 ATTCTTGCAATTATAAAGAAAAGTGCGGTGA 6 34 1 TTATAAAAAA 0.918354 -132 TACGAAATAATTATAAATAAATCTATTATTT 11 158 1 TTATAAAAAA 0.918354 -143 AGACTACAGATTATAAAGAAAATTCATTCCT 12 39 1 TTATAAAAAA 0.918354 -133 GTCAAACCTTTTAGAAAAAAATGCTATACTG 13 63 1 TTAGAAAAAA 0.587874 -192 TACTAAATTATTGTAAATAAACCGTGATCTT 17 55 1 TTGTAAAAAA 0.838088 -153 AAATTTAAGATTATAAATAAACTTGTAATGT 24 35 0 TTATAAAAAA 0.918354 -266 AAAAATGCCTTTCTAAAGAAAGGCATTAATA 24 67 0 TTCTAAAAAA 0.780392 -234 AAAAATACGTTTCTAAACAATGCAATCAATC 24 120 0 TTCTAAAAAT 0.685027 -181 TGAATTTTAGTTATAAAAAATTAATATAAGT 24 196 0 TTATAAAAAT 0.873162 -105 TGATAAATGCTTATAAATAATAA 25 3 0 TTATAAAAAT 0.873162 -298 AATATCTCGTTTATAAATAAAAAGTTCAATC 25 279 0 TTATAAAAAA 0.918354 -22 ATTTTTCCTATTGTAAATATTTTCCTACATA 29 84 0 TTGTAAAATT 0.525881 -212 AAATTCATTTTTGTAAAGATTTGTCAGGAAA 29 216 0 TTGTAAAATT 0.525881 -80 AGAAGACTTTTTATAAAAATATCGCCTAATG 29 261 1 TTATAAAATA 0.797496 -35 TTTATACTATTTATAAACAAACTTTTAATTC 33 107 0 TTATAAAAAA 0.918354 -194 TTCGTTAATTTTATAAATATTGTTATATATC 36 70 0 TTATAAAATT 0.706768 -199 ******* *** Masking position 6 Map Score: 11.0726 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 75 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 AAAAATGATAACTATTAAAATGTCAGATCA 1 19 1 ACTATTAAAA 0.466974 -282 AAGGGGAACTACTATTACGATAATTAGCCG 5 45 0 ACTATTACGA 0.967014 -256 AAAGAATGTTACTATTACAAAAATTTTAAT 25 113 1 ACTATTACAA 0.835197 -188 GCAACATGCAACTATTACGGATAATATACA 41 43 0 ACTATTACGG 0.969476 -185 GCCAAATGAAACTATTACGGTGTATTTTAT 41 77 0 ACTATTACGG 0.969476 -151 CTATTGTTTTACTATTTCGAATAAAAACAA 41 118 1 ACTATTTCGA 0.804879 -110 CTTAATTAGTTCTATTACGGGTAATAATTT 41 151 1 TCTATTACGG 0.817154 -77 AATAATTACAACTATTACGGGATTAAAAAC 41 182 0 ACTATTACGG 0.969476 -46 TAATTATTCAACTATTACGACTAAAGAGGT 41 204 1 ACTATTACGA 0.967014 -24 GCCCTTCATGACTATTAAGATTCTATC 45 8 0 ACTATTAAGA 0.835197 -166 ********** Masking position 5 Map Score: 10.0344 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 10 TTTTTTCACTTGAATTTTAAAAACTGTGAACTTCATCACGGTATTAT 6 77 1 TAAAAAATAC 0.952933 -89 TACATACTCCTTATTGGATAAAATGTTTGAATCCTACTTGAAAAATA 6 127 0 TAAAAAATTC 0.791636 -39 AGAAAATTCATTCCTATGGAAAAAGCATTATTCAAACGCTTAAATAT 12 55 1 TCAAAAATAC 0.761527 -117 TATACATGTCAAATTGACAAAAATTATCTATTTAATCCAAGCAATTA 16 23 1 AAAAAAATAC 0.665853 -153 AACTTAGTGATGATGTGGCAAAAGTTGCTATTCTAGCAATGCCTGTT 20 12 1 TAAAAAATAC 0.952933 -289 GCATAAGCAATAATGAGCAAAAAAATAATATTTCATCCTTTTAGGAA 20 83 0 TAAAAAATAC 0.952933 -218 TACAAAAATTTTAATCTATAAAAAATAGAAATAAAATTTATCACTAT 25 128 1 TAAAAAATAT 0.55206 -173 CAAAGAGATGTGTTGCGATAAAAGAAAAAACTTCATCTTTAAATTAA 25 200 1 TTAAAAATAC 0.683 -101 AAGCCTTTTTTAAAGTGTGAAAACTAACAACTGGAGCAATAACTAGT 27 170 1 TAAAAAATAC 0.952933 -64 ACTTGCATAATTATGCATAAAAATGTAATATTTTTTCATCTTATAAA 30 75 1 TAAAAAATTC 0.791636 -52 TTTTTCGATCTAAATCGCAAAAAATCATCATTTCATCGAAAAAAGAT 31 90 1 TAAAAAATAC 0.952933 -117 ATCTATCTTGTGAAACAATAAGATTTGTGAGTATATCAAAAGTAGGG 33 221 0 TAAAGAATAC 0.747054 -80 TTAGTCAAAATGAACCAGAAAAACTAAGAATTTAAACAAAAAAGAAA 40 38 0 TAAAAAATAC 0.952933 -190 TTTCTTTCCCTAAGAATAAAAAAAGGGGCAATGCACCGCCAAAGCCC 40 114 1 TAAAAAATAC 0.952933 -114 * * **** * * * * Masking position 13 Map Score: 9.11222 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 28 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 AGTGATGATGCGCTCTCAACAAGCAGAAACC 1 179 0 CGCTCTCAAA 0.866781 -122 CTGAATAATTTGCACTCAACATAAGGAGCTT 2 135 1 TGCACTCAAA 0.777765 -138 TTCAAATACACGCACGCAATATTTGGA 3 7 0 CGCACGCAAA 0.987681 -210 TTTCAGTTCACGCACGCAAGCGGTTAATTTT 3 70 0 CGCACGCAAC 0.955148 -147 TTCTGTCGCACGCAAAATGACATACAG 3 200 0 CGCACGCAAA 0.987681 -17 CTATACTGCGCGCGCGCAAAATTTGCGTGTT 13 86 1 CGCGCGCAAA 0.961045 -169 TCTTTGCTCACTCACTCAAAAATCTTTTCCT 13 161 1 CTCACTCAAA 0.877575 -94 AATACATCATCTCACGCAAGAACGACAAAAT 14 157 1 CTCACGCAAA 0.94829 -144 ********* * Masking position 8 Map Score: 5.32006 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 31 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 AACTGTATAAACAAGCTGAAATGGAAAGCGA 1 141 0 ACAAGCTGAA 0.547431 -160 TGCGCTCTCAACAAGCAGAAACCGACAAAAA 1 171 0 ACAAGCAGAA 0.929644 -130 TAATCCAAAAATAAGCAGAATGCATTATGGA 5 191 0 ATAAGCAGAT 0.732899 -110 GCAAACGCTAACAAGGATAAAATAATCCAAA 5 213 0 ACAAGGATAA 0.607182 -88 ATTTTATCCAATAAGGAGTATGTATT 6 150 1 ATAAGGAGAT 0.802906 -16 GTTTATCATCACAAGCAGCCAAGACTATTGC 11 70 1 ACAAGCAGCA 0.780085 -231 AAATAAGAAAATAAGCAAAATTTTTTATGAT 17 93 1 ATAAGCAAAT 0.415655 -115 ATAGATTATAACAAGGAAAAAGTT 17 194 1 ACAAGGAAAA 0.835675 -14 CAAGGCAAGCATAAGCAATAATGAGCAAAAA 20 107 0 ATAAGCAAAA 0.447094 -194 CAAACACAACACAAGGAAGAAAAA 24 287 1 ACAAGGAAAA 0.835675 -14 ACAAGTCCATTCAAGGAGAATACA 29 4 0 TCAAGGAGAT 0.749683 -292 TCGCCTAATGACAAGGAGGCTCAA 29 282 1 ACAAGGAGCT 0.822463 -14 TTTATTCCCAACAAGGAGCAATCA 31 193 1 ACAAGGAGAA 0.951497 -14 TAAATAACACTCAAGGAGAATTTGTTATGTT 38 43 1 TCAAGGAGAT 0.749683 -258 TCTTAAACAAACAAGGAGTATCCAAA 43 74 1 ACAAGGAGAT 0.945225 -16 ******** ** Masking position 4 Map Score: 5.69149 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 138 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 13 TGAAGAAATAATAGGAAAAGGCGGAACAAT 1 67 0 ATAGGAAAAG 0.762806 -234 AAACAAGCTGAAATGGAAAGCGAATTGAAA 1 134 0 AAATGGAAAG 0.742986 -167 GCAGAATGCATTATGGAAAGTTTTTTTGCG 5 178 0 TTATGGAAAG 0.440768 -123 TGTTTCGATGTAAGGAAAATTCTTGCAATT 6 16 1 TAAGGAAAAT 0.700639 -150 TCCTAATAAAAAAGGAAAATGCAAACTATT 8 95 0 AAAGGAAAAT 0.761073 -25 AATAAAAAAGAAAGGATAAGAAATGGAATG 9 251 0 AAAGGATAAG 0.583165 -50 TTTTCTCCTTTAATGAAAAG 10 1 0 TAATGAAAAG 0.593576 -21 TCTTACCCCGAAAGGGAAATATGTCAAACC 13 41 1 AAAGGGAAAT 0.822462 -214 GCGGTGGTGGAAAGGAAAAGATTTTTGAGT 13 174 0 AAAGGAAAAG 0.896552 -81 AAATTTGCAAAAATGAAAATGATTACATAA 18 42 0 AAATGAAAAT 0.422157 -49 TGTTGTAATCTAAGGGGAAGTGGATCTTCC 19 26 1 TAAGGGGAAG 0.771081 -40 ACCTCTTTAAAAAGGGGAAGATCCACTTCC 19 41 0 AAAGGGGAAG 0.820929 -25 TTTCATCCTTTTAGGAAAAGCGGTTGCTCG 20 70 0 TTAGGAAAAG 0.702639 -231 TTATTTAAAAAAAGGGAAATTTGCTTATAT 21 40 1 AAAGGGAAAT 0.822462 -101 ATTAGCATTAAAAGGGTAATTTATGTAGGA 29 63 1 AAAGGGTAAT 0.427859 -233 GTTTAAGGATATAGGAGAATCCCGCTTAAT 33 171 1 ATAGGAGAAT 0.300654 -130 GAATTGTTAATAATGAAAAGGACTTAATGC 36 170 0 TAATGAAAAG 0.593576 -99 ATAAATTGGATAAGGGAAAGACGCTCCAGC 38 155 0 TAAGGGAAAG 0.902544 -146 TTTTTTATTCTTAGGGAAAGAAAACTAAGA 40 107 0 TTAGGGAAAG 0.774596 -121 ********** Masking position 3 Map Score: 10.9245 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 202 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 14 AGCACTGACGTAGGAAACTAATATGCCAAA 9 205 1 TAGGAAACTA 0.791107 -96 GTATTGAATGTATGAAAAAAGAACAAAACA 11 122 0 TATGAAAAAA 0.588597 -179 AAAAATCCCTTAGGAAAAAACTGGCAAAAT 13 12 1 TAGGAAAAAA 0.879018 -243 GTCAAACCTTTTAGAAAAAAATGCTATACT 13 63 1 TTAGAAAAAA 0.404149 -192 TGTCACAAAATAAGAAAATAAGCAAAATTT 17 86 1 TAAGAAAATA 0.88356 -122 AATACTGACGTAGGAAACTAGGAATATAAC 22 226 1 TAGGAAACTA 0.791107 -75 CACTTTCTTGTAGAAAAATACGTTTCTAAA 24 134 0 TAGAAAAATA 0.462 -167 ACTATCAAAATAAGAAAATAATCTACCGCA 24 162 0 TAAGAAAATA 0.88356 -139 AAACCAAACTTATGAAAAAAAAAGATTATT 24 240 0 TATGAAAAAA 0.588597 -61 GTAATTTATGTAGGAAAATATTTACAATAG 29 78 1 TAGGAAAATA 0.933806 -218 TTAAATAATTTTGGAAAATACTT 37 78 1 TTGGAAAATA 0.710007 -13 TTATTTTAAGTAAGAAAATATCATTATACA 39 39 0 TAAGAAAATA 0.88356 -29 GAAAGAAAACTAAGAAAAAATCAGATCTTT 40 92 0 TAAGAAAAAA 0.796256 -136 CTTGTTTGTTTAAGAAAATCTAGGCGTATG 43 59 0 TAAGAAAATC 0.507281 -31 AAAAATTATTTAGTAAAATATATAACGCTT 46 46 0 TAGTAAAATA 0.461991 -92 ********** Masking position 5 Map Score: 4.83863 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 106 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 15 ATAGTTATCATTTTTATCTATAA 1 4 0 TTTTTATCTA 0.755599 -297 CTCAAGCGGTTTATTATCCAGATACGAAAT 1 273 1 TTATTATCCA 0.662003 -28 ACCGTTTTGTTTTTCATCTAAATATCAATT 2 42 1 TTTTCATCTA 0.530614 -231 TTTCGGTTTTAATCCAAAATAAGAAG 7 149 0 TTTTAATCCA 0.690071 -16 CTAAAATTATTATCTAATATCAGTTG 9 7 1 TTATTATCTA 0.809745 -294 GGCAAGCTGATTATAATCTTGAGTCGTTTT 14 17 0 TTATAATCTT 0.555534 -284 TTTTCTATTTTTGTTATCTATATTTGTCTT 15 113 1 TTGTTATCTA 0.675366 -55 TTTTTCCTTGTTATAATCTATAAATCTTAT 17 185 0 TTATAATCTA 0.869463 -23 TCAATTTTTGTTGTAATCTAAGGGGAAGTG 19 18 1 TTGTAATCTA 0.765024 -48 ATTAATTTGTTATAATCCATAGAATTTTT 21 10 1 TTATAATCCA 0.754008 -131 ACAAGTTTATTTATAATCTTAAATTTCTAT 24 40 1 TTATAATCTT 0.555534 -261 ATTACAAAAATTTTAATCTATAAAAAATAG 25 126 1 TTTTAATCTA 0.828718 -175 TACCGCACTTTTATTATCTACGAGTGATGG 32 69 1 TTATTATCTA 0.809745 -21 TTTGGCTATATTTTAATCTATTGTTTTACT 41 101 1 TTTTAATCTA 0.828718 -127 ********** Masking position 6 Map Score: 7.08251 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 33 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405