AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_hinf_reg_100.orf -a/home/amcguire/alignace/lib/ORF_hinf.txt -z/skink1/amcguire/genomes/hinf.fna -g0.38 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HI0250 153 single-stranded DNA binding protein (ssb) #2 HI0349 84 adenylate kinase (adk) #3 HI0350 141 permease, putative #4 HI0514 241 DNA-directed RNA polymerase, beta' chain (rpoC) #5 HI0515 300 DNA-directed RNA polymerase, beta chain (rpoB) #6 HI0517 172 ribosomal protein L11 (rpL11) #7 HI0546 28 primosomal replication protein N (priB) #8 HI0547 198 ribosomal protein S6 (rpS6) #9 HI0548 169 translation initiation factor 1 (infA) #10 HI0579 83 elongation factor G (fusA) #11 HI0580 156 ribosomal protein S7 (rpS7) #12 HI0581 181 ribosomal protein S12 (rps12) #13 HI0632 300 elongation factor Tu (tufB) #14 HI0640 271 ribosomal protein L10 (rpL10) #15 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #16 HI0716 237 preprotein translocase SecE subunit (secE) #17 HI0776 190 ribosomal protein S10 (rpS10) #18 HI0781 25 ribosomal protein S19 (rpS19) #19 HI0788 280 ribosomal protein L14 (rpL14) #20 HI0792 36 ribosomal protein S8 (rpS8) #21 HI0798.1 28 ribosomal protein L36 (rpL36) #22 HI0799 139 ribosomal protein S13 (rpS13) #23 HI0801 27 ribosomal protein S4 (rpS4) #24 HI0802 31 DNA-directed RNA polymerase, alpha chain (rpoA) #25 HI0803 40 ribosomal protein L17 (rplQ) #26 HI0861 191 virulence-associated protein (vacB) #27 HI1573 300 pyruvate kinase, type II (pykA) #28 HI1574 33 replicative DNA helicase (dnaB) #29 HI1618 95 ABC transporter, ATP-binding protein #30 HI1624 89 H. influenzae predicted coding region HI1624 #31 HI1644 233 pseudouridylate synthase I (truA) #32 HI1722 135 methionine aminopeptidase (map) Motif number 1 TCAGGCAAAATAACCGCACTTTTTTAGATAA 1 117 1 TACCGCACTT 0.998387 -37 TTTATAATTTTTACCGCACTT 2 1 0 TACCGCACTT 0.998387 -84 ATAAAAAATTTGACCGCACTATGCTTTATCA 2 27 1 TACCGCACTA 0.990778 -58 CAACTAAAATTAACCGCACTTT 3 130 1 TACCGCACTT 0.998387 -12 CGGAGAATTTTGACCGCACTTCGGCGATTTC 4 173 0 TACCGCACTT 0.998387 -69 CCGAAATTTTTAACCGCACTTTAAACCTTTA 4 201 1 TACCGCACTT 0.998387 -41 ATTTGAGTTGTCACCCCACTATAGAAGTAAG 5 196 1 TACCCCACTA 0.893803 -105 ACCGTTAAAATGACCGCACTCTGAACCTTAC 5 222 0 TACCGCACTC 0.989047 -79 GCTTGAAAAACAACCGCACTTTTTATATAAT 6 35 1 CACCGCACTT 0.993572 -138 ACCCCTATAATAACCGCACTTTTCTTATTAA 9 20 0 TACCGCACTT 0.998387 -150 AGATTAAAATTTACCGCACTTTTGTTTTTTT 12 21 0 TACCGCACTT 0.998387 -161 CTGGTGAAAACAACCGCACTTTTGCGATTAA 16 13 0 CACCGCACTT 0.993572 -225 CAGTTAAAATTTACCGCACTTTTGGAATTAT 19 103 0 TACCGCACTT 0.998387 -178 AATTTTTACCGCGCTTTTCATACTTT 26 6 1 TACCGCGCTT 0.987422 -186 AGTGTCAAACTCTCCGCACTTTTTAAAACTG 26 162 1 TTCCGCACTT 0.98147 -30 TGGGCTACCATAACCGCACTTTATTAAGCCA 31 202 1 TACCGCACTT 0.998387 -32 * ********* Masking position 10 Map Score: 64.2216 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 AATTTCAGGCAAAATAACCGCACTTTTTTAGAT 1 113 1 AATACCGCAC 0.996566 -41 ATTTTTTATAATTTTTACCGCACTT 2 3 0 ATTACCGCAC 0.993994 -82 AATTATAAAAAATTTGACCGCACTATGCTTTAT 2 23 1 ATTACCGCAC 0.993994 -62 AATACAACTAAAATTAACCGCACTTT 3 126 1 AATACCGCAC 0.996566 -16 ATTTCGGAGAATTTTGACCGCACTTCGGCGATT 4 175 0 ATTACCGCAC 0.993994 -67 TTCTCCGAAATTTTTAACCGCACTTTAAACCTT 4 197 1 TTTACCGCAC 0.938083 -45 AATGACCGTTAAAATGACCGCACTCTGAACCTT 5 224 0 AATACCGCAC 0.996566 -77 AAGTGCTTGAAAAACAACCGCACTTTTTATATA 6 31 1 AACACCGCAC 0.987325 -142 AACAACCCCTATAATAACCGCACTTTTCTTATT 9 22 0 AATACCGCAC 0.996566 -148 AACTAGATTAAAATTTACCGCACTTTTGTTTTT 12 23 0 AATACCGCAC 0.996566 -159 AAATCTGGTGAAAACAACCGCACTTTTGCGATT 16 15 0 AACACCGCAC 0.987325 -223 AATCCAGTTAAAATTTACCGCACTTTTGGAATT 19 105 0 AATACCGCAC 0.996566 -176 AATTTTTACCGCGCTTTTCATACT 26 2 1 ATTACCGCGC 0.957365 -190 TTACAGTGTCAAACTCTCCGCACTTTTTAAAAC 26 158 1 AATTCCGCAC 0.96372 -34 AACTTGGGCTACCATAACCGCACTTTATTAAGC 31 198 1 ACTACCGCAC 0.983744 -36 * * * ******* Masking position 8 Map Score: 51.376 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 386 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 3 AAATTTACATTTATTTCATACTTTTGAGTTATTTT 1 9 0 TTATATTTTA 0.761307 -145 TCCAGTTAAAATATATAGATCTTTTAAAAAATTTCAG 1 84 1 ATATTTTTTA 0.792022 -70 GTGCGGTCAAATTTTTTATAATTTTTACCGCACTT 2 9 0 ATTTATTTTA 0.904972 -76 TTTTTGTAAAAATTAGGGGATTTTTAATCATTCCCCT 3 61 0 AATTATTTTA 0.608156 -81 GTGCGGTTAATTTTAGTTGTATTTTAGAAATTTCGCC 3 112 0 TTTTTTTTTG 0.710957 -30 GCGGTTAAAAATTTCGGAGAATTTTGACCGCACTTCG 4 181 0 ATTTATTTTA 0.904972 -61 ATTAGCAAAGATTTAGATTGATTTTTAATCAATCTTG 5 53 1 ATTTGTTTTA 0.767468 -248 TTATTGCTTAATTTAACCGTGTTTTTGATAGAAAGCA 5 95 1 ATTTTTTTTG 0.728052 -206 GGGTTGCGGATTATACCGATTTTTTACGCTCCGCAA 8 86 0 TTATTTTTTA 0.777721 -113 TGCGAATTTCTCCGTATTTTAATCTTCAGGAT 11 135 0 ATTTTTTTTA 0.91264 -22 GTGCGGTAAATTTTAATCTAGTTTTAATCCTAGAGCA 12 33 1 TTTTATTTTA 0.897429 -149 GAATTTGGCTCTTTTTTCAACAATATTCT 14 3 1 ATTTTTTTTA 0.91264 -269 TCGCAGGTTCTTATGGCATTATTTTTACATTTCCATT 16 98 1 TTATTTTTTA 0.777721 -140 TCCAGTTAAAATTTACCGCACTTTTGGAATTATAAAA 19 99 0 ATTTATTTTG 0.709342 -182 AATTTTTACCGCGCTTTTCATACTTTAAAA 26 4 1 TTTTGTTTTA 0.752007 -188 AGTGATGACTTTTTATAGATATTTTTAAAGTATGAAA 26 26 0 TTTTTTTTTA 0.905645 -166 TCACTGTATATTTTAAGGATATTTTAAAATTGAAGAA 26 91 0 TTTTTTTTTA 0.905645 -101 TATTTTTTACAGTTTTAAAAAGTGCGGA 26 174 0 ATTTATTTTA 0.904972 -18 GCCGTTTTTGATTTCCAAAAGTTTTAAGCGTATAATG 27 193 1 ATTTATTTTA 0.904972 -108 ACTCCGTCAATAATTACAAAATTTTAAAGGTGTTATT 27 269 0 TAATATTTTA 0.342017 -32 AATTCACATTTATTACTGCAATTTTTAGAAACTATCG 31 110 1 TATTATTTTA 0.587792 -124 TTTTGAATAAATTTTGGAGTGTTTTTATGCATTTGCG 31 152 1 ATTTTTTTTA 0.91264 -82 TTTTATCTCACTTTTTTGAAAAAACTTTA 32 117 0 TTATTTTTTA 0.777721 -19 **** * **** * Masking position 12 Map Score: 20.7522 Number of sites scoring better than the average of aligned sites = 555 Number in coding regions = 319 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 4 TGCACAGATATTAAAATATGCGATAATGAT 1 50 0 TTAAAATATG 0.77413 -104 AAATATCCAGTTAAAATATATAGATCTTTT 1 79 1 TTAAAATATA 0.915599 -75 TAAAATACAACTAAAATTAACCGCACTTT 3 123 1 CTAAAATTAA 0.681651 -19 CTGCATTCATTTAAAATTTACCGCCTTAAA 5 23 1 TTAAAATTTA 0.903438 -278 ATTTACCGCCTTAAAATTAGCAAAGATTTA 5 38 1 TTAAAATTAG 0.681651 -263 TAAAACTAGATTAAAATTTACCGCACTTTT 12 29 0 TTAAAATTTA 0.903438 -153 CAATCAATTCCTAAAATAAATAAAGTTAGA 15 33 0 CTAAAATAAA 0.713417 -22 TTAAAATAAAAGCTTGCAAA 17 1 1 TTAAAATAAA 0.887316 -190 AATAATCCAGTTAAAATTTACCGCACTTTT 19 111 0 TTAAAATTTA 0.903438 -170 ATCAAATTAATTAAAATATAGGAGTGCATA 22 120 1 TTAAAATATA 0.915599 -20 TAAGGATATTTTAAAATTGAAGAACTTAAC 26 85 0 TTAAAATTGA 0.713179 -107 TAAAATATCCTTAAAATATACAGTGATAAT 26 102 1 TTAAAATATA 0.915599 -90 TCTAAATATGTTAAAATAAAAGAGCG 28 18 1 TTAAAATAAA 0.887316 -16 ********** Masking position 5 Map Score: 11.3595 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 80 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 AAAAAAACCTCATTTTTTATCTAAAAAAGTGCGGTT 1 128 0 CTTTTATAAA 0.923942 -26 TAATATTTGTTTTTCTTTTTTAGGAAGAAGAATGCTAAA 3 18 1 TTTTTAGAAA 0.893961 -124 CAATATCGACCTTCTTTTTTGTTCAAAAAGAACTCAAAC 8 44 1 CTTTTTTAAA 0.902193 -155 TTATGCCAAATTGAGTTTTTCATGAACAATATTATTTTT 9 79 1 TGTTTATAAA 0.727704 -91 TTACCGCACTTTTGTTTTTTTATAAAAAACT 12 3 0 TTTTTATAAA 0.948237 -179 TAGAATTCGCCGTCTATTTCTATATAGAAGTAGATTTTT 12 106 1 CTTTTATAAA 0.923942 -76 TGGCATTATTTTTACATTTCCATTTAAAACGGATTCAAT 16 111 1 TTTTTATAAA 0.948237 -127 TTCTTGCGTATTTTTCTTTTTATCAACAATTTCGGTTGC 16 156 0 TTTTTATAAA 0.948209 -82 TTTTCTGCAGTTTATTTTTCATTCGATAAATTTTTGAGA 19 48 1 TTTTTTTAAA 0.932936 -233 TCATTGCCTTTCTCTTTTTCTTTTGATAAAATCCGCCGC 19 174 1 TTTTTTTAAA 0.932937 -107 TGCTTATCCTTTTACTTTAAATGAACAA 21 1 0 TTTTTATAAA 0.946742 -28 TTATCATACGCCTAGATTTTCTTAAACAAACAAGGAGTA 30 55 1 CTTTTTTAAA 0.902193 -35 CAGTAATAAATGTGAATTTTTTGTGATAAAGATCTCATT 31 89 0 TTTTTTGAAA 0.864898 -145 TTTTATCTCACTTTTTTGAAAAAACTTTACGAGA 32 112 0 TTTTTTGAAA 0.864898 -24 * * *** ** * ** Masking position 16 Map Score: 11.9245 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 115 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 6 TCTCTAATATTTGTTTTTCTTTTTTAGGAAG 3 14 1 TTGTTTTTCT 0.794563 -128 AAATAACGGTGAATTTGTCATTGTGTGGATG 5 132 0 GAATTTGTCT 0.841196 -169 AAATTCACCGTTATTTGTCGTTGTTTTGCTC 5 147 1 TTATTTGTCT 0.705683 -154 TAGCCACATTGAATTTTTCGTTCCTTGCCTT 8 124 1 GAATTTTTCT 0.938591 -75 ATGCCAAATTGAGTTTTTCATGAACAATATT 9 81 1 GAGTTTTTCT 0.895229 -89 ATGAACAATATTATTTTTTCTTTCGTAGAAA 9 100 1 TTATTTTTTT 0.490117 -70 AACAGAATAAGAATTTTTCTTGCTTCTGGGC 14 176 1 GAATTTTTCT 0.938591 -96 CACTTCTTGCGTATTTTTCTTTTTATCAACA 16 167 0 GTATTTTTCT 0.938591 -71 TTTCTGCAGTTTATTTTTCATTCGATAAATT 19 49 1 TTATTTTTCT 0.87371 -232 TTGAACACAAGTATTTTTCTTAAAACCCGAT 27 120 1 GTATTTTTCT 0.938591 -181 AATTTCCTTTTAGTTTTTCATAATACGTTGA 31 11 1 TAGTTTTTCT 0.794563 -223 TAATAAATGTGAATTTTTTGTGATAAAGATC 31 94 0 GAATTTTTTT 0.679856 -140 ********* * Masking position 6 Map Score: 8.99142 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 204 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 ATTTTTGTAAAAATTAGGGGATTTTTAATCATTCCCC 3 62 0 AAAGGGTTTA 0.65721 -80 AGCTCCCCCGTAAACGGGTGGAGCCAAGGGATCAGCA 4 31 0 TAAGGGACAA 0.706483 -211 CTTCCCTCGCAAAGCAGGGGAAGGCAAGAGGAACAAC 4 124 1 AAAGGGACAA 0.957659 -118 AAAGTTAAGAAAAACGGGCGGATTATAGCCGTTTTTA 9 133 0 AAAGGGAATA 0.947413 -37 CTATATAGAAATAGACGGCGAATTCTAATAGTTTTAC 12 96 0 ATAGGGACTA 0.91912 -86 TCAACATAGAAAATCTGGTGAAAACAACCGCACTTTT 16 21 0 AAAGGGACAA 0.957659 -217 TCAAAATAGAAAAGGAGGTGCAAGTTACCTGTTATAT 17 147 0 AAAGGGATTA 0.947407 -44 AGAATGGCAGATAGGCGGCGGATTTTATCAAAAGAAA 19 190 0 ATAGGGATTA 0.852595 -91 GACGTATAGGATAGTTGGAGAAAGAAA 23 11 1 ATAGGGAAAA 0.78705 -17 AGCCAGATAAAAAATCGGTGCACATTATACGCTTAAA 27 215 0 AAAGGGATTA 0.947412 -86 TGTTTAAGAAAATCTAGGCGTATGATAAAATATGAAG 30 46 0 AATGGGAATA 0.65721 -44 TTTCTTAAACAAACAAGGAGTATCCAAA 30 72 1 AAAGGGACAA 0.957659 -18 CGCTCCAAATAAACTTGGGCTACCATAACCGCACTTT 31 187 1 AAAGGCAATA 0.637514 -47 *** ** * * *** Masking position 17 Map Score: 7.64664 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 106 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 TGTTGTTCCTCTTGCCTTCCCCTGCTTTGCGA 4 130 0 CTTGCTTCCC 0.67122 -112 TTTAATCAATCTTGACCTTTTATTGCTTAATT 5 76 1 CTTGCCTTTA 0.928553 -225 TTTTTCGTTCCTTGCCTTTGCAGATTGGTGGC 8 137 1 CTTGCTTTCA 0.821172 -62 GCCCGTTTTTCTTAACTTTTCCGCCTAAA 9 151 1 CTTACTTTCC 0.866059 -19 TTGATGAAGCCTTACCCTTATATAAACTGATA 10 40 1 CTTACCTTTA 0.940469 -44 TGGCTATTACCTTAGCCTTCCAAGCTAATGAT 13 68 1 CTTACCTTCA 0.961956 -233 AACCGCCGACCTCACCCTTACCAAGGGTGCGC 13 154 0 CTCACCTTCC 0.942446 -147 CTTATAATTCCTCATCCTTATATCAATCAGCA 13 209 1 CTCACCTTTA 0.89829 -92 CTGGTTGGTGCTTGACCTATTCAAGCCCCATC 14 100 1 CTTGCCTATC 0.679321 -172 TAAAAATATCCTCATCCTCTCAAAAATTTATC 19 72 0 CTCACCTCCA 0.844366 -209 TGCTTATCCTTTTACTTTAAATGA 21 15 0 CTTACCTTTA 0.940469 -14 GATCTTATCCTTCTCAGAAAAATCT 25 26 0 CTTACCTTTC 0.948188 -15 **** **** ** Masking position 8 Map Score: 6.90383 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 36 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 TAGATAAAAAATGAGGTTTTTTT 1 141 1 AGGTTTTTTT 0.903183 -13 TTTTGTATTAATGGAGATTTTTT 2 72 1 AGGATTTTTT 0.959051 -13 ACGACAAATAACGGTGAATTTGTCATTGTGTGG 5 135 0 AGGAATTTGT 0.690562 -166 GATTTGAGATAGGTCGATATTGTTACAATATCG 8 19 1 AGGATATTGT 0.909033 -180 ACAAAAAAGAAGGTCGATATTGTAACAATATCG 8 33 0 AGGATATTGT 0.909033 -166 GTTGCGGATTATACCGATTTTTTACGCTCCGC 8 88 0 AAGATTTTTT 0.626932 -111 TTCTATATAGAAGTAGATTTTTTGAACAACATT 12 123 1 AGGATTTTTT 0.95905 -59 TTTTGAGAGGATGAGGATATTTTTATAATTCCA 19 79 1 AGGATATTTT 0.923938 -202 TCGTCCCGAAAGGGTGTTTTTTTAATCTTAACG 19 248 1 AGGTTTTTTT 0.903183 -33 TCAGTTATTTAAGCTGGTTTTGTTTACTTTTTT 27 160 0 AGGGTTTTGT 0.818237 -141 CAAAATTTTAAAGGTGTTATTTTACTTCGCTAC 27 257 0 AGGTTATTTT 0.828719 -44 GCAGTAATAAATGTGAATTTTTTGTGATAAAGA 31 96 0 AGAATTTTTT 0.626932 -138 * * ******** Masking position 1 Map Score: 7.17141 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 136 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 TCTTCCTAAAAAAGAAAAACAAATATTAGAGA 3 14 0 AAAGAAAACA 0.53532 -128 AACGACAACTTGAGCAAAACAACGACAAATAA 5 157 0 TGAGAAAACA 0.76647 -144 AACAGTTAGCAGAGGAAAACCA 5 289 1 AGAGAAAACA 0.945918 -12 TTACCCAATTAGAGGAAAACTAAA 6 159 1 AGAGAAAACA 0.945918 -14 AACCGAAAAACTATTATCAATTT 7 16 0 ACCGAAAACA 0.783353 -13 CTGGTTGCGGAGCGTWAAAAAATCGGTATAAT 8 82 1 AGCGWAAAAA 0.692748 -117 TTTCGTAGAAAGCTAAAAACGGCTATAATCCG 9 120 1 AGCTAAAACG 0.752078 -50 GAAAATTTGCAGCGCAAAGCGCTTTTGACTGG 11 71 0 AGCGAAAGCC 0.85258 -86 TTGACAATAAAGCGTAAAACTATTAGAATTCG 12 83 1 AGCGAAAACA 0.973711 -99 GCAGGATTATAGAGAAAAGCTATGTTCTTGTA 14 41 0 AGAGAAAGCA 0.940858 -231 TGTATTCAGGAGCTAAAAGCCA 14 260 1 AGCTAAAGCA 0.897261 -12 CAAAAGAAAAAGAGAAAGGCAATGATAATTTA 19 167 0 AGAGAAGGCA 0.698851 -114 TAGTTAAGCTTAAAACCAAAGAGAGGAT 24 7 1 AGCTAAAACA 0.905677 -25 ATTCATGCCCTGCTGAAAGCTGAAACGGCGCA 29 57 1 TGCTAAAGCG 0.341133 -39 **** ***** * Masking position 6 Map Score: 6.64685 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 213 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 AAAATAACTCAAAAGTATGAA 1 1 1 AAAATACTCA 0.833632 -153 AAAAAAACCTCATTTTTTATCT 1 142 0 AAAAAACTCA 0.917123 -12 AAAAAATCTCCATTAATACAA 2 74 0 AAAAAACTCC 0.967866 -11 ATAACGCTATTAAATAGCTCCCCGATAATTT 6 129 0 TAAATACTCC 0.63409 -44 TTTTTGTTCAAAAAGAACTCAAACTGGTTGC 8 59 1 AAAAGACTCA 0.746142 -140 AGTTTTTTATAAAAAAACAAAAGTGCGGTAA 12 11 1 AAAAAACAAA 0.404429 -171 AATGTTGTTCAAAAAATCTACTTCTATATAG 12 125 0 AAAAAACTAC 0.822703 -57 TAAAAAAGCTCCAGTTTAAATG 12 170 0 AAAAAACTCC 0.967866 -12 CGTTAAGATTAAAAAAACACCCTTTCGGGAC 19 250 0 AAAAAACACC 0.92306 -31 GTAGCGAAGTAAAATAACACCTTTAAAATTT 27 257 1 AAAATACACC 0.844537 -44 GCAAATGCATAAAAACACTCCAAAATTTATT 31 157 0 AAAAACCTCC 0.850124 -77 ****** **** Masking position 4 Map Score: 5.68943 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 94 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 12 AATCCTTTAATTGAAAGGCGAAATTTCTAAAA 3 96 1 TTGAAGGCGA 0.898544 -46 GGGAAGGTGCCCGAAGGGCGGAAGGGGGCTTA 4 98 0 CCGAAGGCGA 0.973752 -144 ACCTTTAACTCCGACAGGAGAACATTT 4 225 1 CCGACGGAGA 0.922756 -17 GCTGATTAACCCGTAAGGAGCAGTA 8 184 1 CCGTAGGAGA 0.934266 -15 TTTGGCCTTACTTAACGGAGAACCA 11 4 0 CTTAAGGAGA 0.914801 -153 AAGACTGGTGCTGATAGGCGGATTTGAACCGC 13 180 0 CTGATGGCGA 0.889626 -121 TTTTTTTAATCTTAACGGAGCACTAAT 19 264 1 CTTAAGGAGA 0.914801 -17 GAGTTTGACACTGTAAGGAGGATAATGCAAGA 26 142 0 CTGTAGGAGA 0.945149 -50 TGGATTGCACTTGAATGGAGTAAAGGGTTATT 32 54 0 TTGAAGGAGA 0.914801 -82 ***** **** * Masking position 12 Map Score: 4.41801 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 36 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 GTGCCCATTATGAGCCGTTTGTGGCTCATA 6 68 1 TGAGCCGTTT 0.984537 -105 CGGGCGGATTATAGCCGTTTTTAGCTTTCT 9 126 0 ATAGCCGTTT 0.930608 -44 TTTTGCTAATTTAGACGTTTGGCCTTACTT 11 23 0 TTAGACGTTT 0.799947 -134 ACTATTAGAATTCGCCGTCTATTTCTATAT 12 101 1 TTCGCCGTCT 0.864554 -81 TCTCAATATGAGAGCCGTTTAATGTAATCA 17 61 1 AGAGCCGTTT 0.965155 -130 CTTAAATAACTGAGCCGTTTTTGATTTCCA 27 180 1 TGAGCCGTTT 0.984537 -121 TAACGCCATTTGCGCCGTTTCAGCTTTCAG 29 69 0 TGCGCCGTTT 0.977192 -27 ********** Masking position 8 Map Score: 6.24746 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 17 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 CATAAGATTTGAAATCGCCGAAGTGCGGTC 4 163 1 GAAATCGCCG 0.936623 -79 AAAACTATTAGAATTCGCCGTCTATTTCTA 12 98 1 GAATTCGCCG 0.973919 -84 TGGTAAGGGTGAGGTCGGCGGTTCAAATCC 13 163 1 GAGGTCGGCG 0.98014 -138 AGACTAGGATGACTTCGGCGCCCAGAAGCA 14 196 0 GACTTCGGCG 0.978595 -76 GTCACATAAAGAGTTCGGCGA 29 2 0 GAGTTCGGCG 0.988254 -94 ********** Masking position 5 Map Score: 1.58817 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 2 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 GCTGGCGCGAAGACTGAGGGGGGATTTATATCCTAA 4 65 1 AATGGGGATT 0.982819 -177 CAAACGGCTCATAATGGGCACGGATTATATAAAAAG 6 53 0 AATGCGGATT 0.962092 -120 TCAATGAGAAATATTGCTGATGGGTTTTGGATATCC 11 103 1 AATGGGGGTT 0.960932 -54 ATAATTAAACAATATGCTCTAGGATTAAAACTAGAT 12 48 0 ATTGCGGATT 0.781235 -134 TTCTATATAGAAATAGACGGCGAATTCTAATAGTTT 12 99 0 AAAGGGAATT 0.773408 -83 AGATTGACTAACACAGGCGCAGGATTATAGAGAAAA 14 55 0 AAAGGGGATT 0.975045 -217 ATAGAATGGCAGATAGGCGGCGGATTTTATCAAAAG 19 193 0 AAAGGGGATT 0.975044 -88 TTCTATCTGAATAGTGTGGATGGGTTCGTCCCGAAA 19 223 1 AATGGGGGTT 0.960932 -58 TTTTAAGCGTATAATGTGCACCGATTTTTTATCTGG 27 214 1 AATGCCGATT 0.766701 -87 AAGGGTTATTAGATAATGGCGGGATTGAAATTTTAG 32 28 0 AAAAGGGATT 0.773429 -108 * * ** * ***** Masking position 15 Map Score: 3.51293 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 60 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925