AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_hinf_reg_300.orf -o00330_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: HI0052 26 conserved hypothetical protein HI0812 21 glucosephosphate uridylyltransferase (galU) HI0819 37 galactokinase (galK) Input sequences: #1 HI0050 74 conserved hypothetical transmembrane protein #2 HI0051 38 conserved hypothetical transmembrane protein #3 HI0053 109 zinc-type alcohol dehydrogenase #4 HI0307 65 pyrroline-5-carboxylate reductase (proC) #5 HI0591 250 ornithine decarboxylase (speF) #6 HI0592 300 H. influenzae predicted coding region HI0592 #7 HI0596 300 ornithine carbamoyltransferase (arcB) #8 HI0675 110 aminoacyl-histidine dipeptidase (pepD) #9 HI0727.1 260 cyaY protein (cyaY) #10 HI0729 84 prolyl-tRNA synthetase (proS) #11 HI0811 134 argininosuccinate lyase (argH) #12 HI0813 77 carbon storage regulator (csrA) #13 HI0814 187 alanyl-tRNA synthetase (alaS) #14 HI0815 101 universal stress protein A (uspA) #15 HI0817 170 conserved hypothetical protein #16 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #17 HI1126.1 181 H. influenzae predicted coding region HI1126.1 #18 HI1129 201 conserved hypothetical protein #19 HI1130 30 conserved hypothetical protein #20 HI1136 122 UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD) #21 HI1137 21 cell division protein (ftsW) #22 HI1139 137 UDP-N-acetylmuramate--alanine ligase (murC) #23 HI1140 71 D-alanine--D-alanine ligase (ddlB) #24 HI1143 83 cell division protein (ftsZ) #25 HI1144 38 UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase (lpxC) #26 HI1213 300 thiol:disulfide interchange protein (dsbC) #27 HI1214 288 single-stranded-DNA-specific exonuclease (recJ) #28 HI1583 79 arginyl-tRNA synthetase (argS) #29 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #30 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #31 HI1617 138 aspartate aminotransferase (aspC) #32 HI1723 135 conserved hypothetical protein #33 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) #34 HI1727 155 argininosuccinate synthetase (argG) Motif number 1 GGGCTATAATACCGCACATTCTACCCTATA 4 28 0 ACCGCACATT 0.984647 -38 GTCATTTTTAACCGCACTTTTAACAC 10 7 0 ACCGCACTTT 0.998343 -78 GTTAAAAATGACCGCACTTTTTGTTATACT 10 25 1 ACCGCACTTT 0.998343 -60 TTAAATTTTAACCGCACTTCTCAAATAGCG 13 48 1 ACCGCACTTC 0.996724 -140 CCAAAATAAAACCGCACTTCACGACGCTAT 13 72 0 ACCGCACTTC 0.996724 -116 GCGAATTTTAACCGCACTTTTAGTTGAGTT 22 91 1 ACCGCACTTT 0.998343 -47 GATTTATCTGACCGCACTTCAGTGCTTCGG 26 113 0 ACCGCACTTC 0.996724 -188 AGCATATAATTCCACACTTTATCACACAGT 26 188 0 TCCACACTTT 0.890287 -113 TTTAGATCTGACCGCACTTTTAAAGTGCGG 30 18 1 ACCGCACTTT 0.998343 -52 GAAAAAAACAACCGCACTTTAAAAGTGCGG 30 29 0 ACCGCACTTT 0.998343 -41 GTAAAAAATGACCGCACTTTTTGATGAATA 31 12 1 ACCGCACTTT 0.998343 -127 ATAAAAATTAACCACGCTTTGATATTTTTA 31 44 0 ACCACGCTTT 0.923236 -95 ATAGAGTATAACCGCACTTTTCCTCTTTGT 34 75 0 ACCGCACTTT 0.998343 -81 ********** Masking position 9 Map Score: 46.7265 Number of sites scoring better than the average of aligned sites = 1218 Number in coding regions = 781 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 292 Fraction of orfs with sites within 600 bp upstream = 0.0469001 Motif number 2 CGGTCATTTTTAACCGCACTTTTAACAC 10 9 0 TAACCGCACT 0.998098 -76 CGGTTAAAAATGACCGCACTTTTTGTTATA 10 23 1 TGACCGCACT 0.998244 -62 ACTTAAATTTTAACCGCACTTCTCAAATAG 13 46 1 TAACCGCACT 0.998098 -142 CTCCAAAATAAAACCGCACTTCACGACGCT 13 74 0 AAACCGCACT 0.988058 -114 TTGCGAATTTTAACCGCACTTTTAGTTGAG 22 89 1 TAACCGCACT 0.998098 -49 TCGATTTATCTGACCGCACTTCAGTGCTTC 26 115 0 TGACCGCACT 0.998244 -186 TCTTTAGATCTGACCGCACTTTTAAAGTGC 30 16 1 TGACCGCACT 0.998244 -54 ACGAAAAAAACAACCGCACTTTAAAAGTGC 30 31 0 CAACCGCACT 0.991911 -39 TGTAAAAAATGACCGCACTTTTTGATGAA 31 10 1 TGACCGCACT 0.998244 -129 CTATAGAGTATAACCGCACTTTTCCTCTTT 34 77 0 TAACCGCACT 0.998098 -79 ********** Masking position 3 Map Score: 36.3391 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 409 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 185 Fraction of orfs with sites within 600 bp upstream = 0.0297141 Motif number 3 CAAAAAGAGTTTTTATGTTTCATAATCATATCAT 3 32 1 TTTTATCATA 0.678894 -78 TTTTTCCTACTTTTATGGGCTATAATACCGCACA 4 40 0 TTTTATTATA 0.821248 -26 GTAAGAAATGTTTTATGAAATTAACTTGATCTTA 5 83 1 TTTTATTTAA 0.675358 -168 GTAAGAATATATTTATTTTAAATTAAATAAGATC 5 110 0 ATTTATAATT 0.698171 -141 CGATCTAGTTTTTTATTATAAAAACTAAAGTAAG 5 139 0 TTTTATAAAA 0.931312 -112 GATCGTGTTATTTTATTCTAAATAAATCTATTGC 5 168 1 TTTTATAATA 0.93301 -83 TTGGTTTAAGATTTATATAAAATAGCTTTATTTC 6 95 1 ATTTATAATA 0.805426 -206 GTTTTGTATTTTTTATGTAAAATTTAAAATTGTT 6 170 1 TTTTATAATT 0.882202 -131 TAAGATCACATTTTTTAAAAAATATTATTGACAT 6 210 1 TTTTTTAATA 0.506454 -91 TTTTATTAAGTATAGATAGACACA 7 1 1 TTTTATTATA 0.821225 -300 CTTAGTTTAAATTTATCGAGAAATAAAAAATTGC 8 19 1 ATTTATAAAT 0.652956 -92 CGAAATGGCGTTTTATGCTATTATTTCGTCAATA 8 65 1 TTTTATTTAT 0.532527 -46 ATTTGCCGCATTTTATCAGATTTAAACAGGAAAA 9 233 1 TTTTATTTTA 0.657088 -28 ATTTTGTCCATTTTATTTGTATTAGTGCTAT 11 8 0 TTTTATATTA 0.853218 -127 TCCATTTTTGTTTTATTATTAATATAGAATATTG 11 53 1 TTTTATAATA 0.932473 -82 TATTGTGCATATTTATTCATAAAGCAATATTCTA 11 77 0 ATTTATAAAG 0.728952 -58 CTTTTATCTCCTTAGTTTGCATTTA 12 63 0 TTTTATTTAG 0.60977 -15 GCGACTTAGTTTTTATTTTTATTATGGGTAACAA 13 152 1 TTTTATATTA 0.853218 -36 GTACACAGTTTTTTATTGCTCAAAATGTTAGCAT 14 35 1 TTTTATCAAA 0.696138 -67 GTAATGACATTTTTATTATAAATAATGGC 15 6 0 TTTTATAATA 0.93301 -165 GCGATGGCTTTTTTATTTACAAAGGTTTACACTA 15 120 1 TTTTATAAAG 0.918322 -51 AAAATATAAGATTTATAGATTATAACAAGGAAAA 16 15 0 ATTTATTATA 0.581865 -193 ATCGTAAATTATTTATGATCAAAATATAAGATTT 16 35 0 ATTTATAAAA 0.820721 -173 ACCGCTTTCAATTTATCGTAAATTATTTATGATC 16 49 0 ATTTATAATT 0.698171 -159 GATTACATTAATTTATACTAAATTATTGTAAATA 16 155 0 ATTTATAATT 0.698171 -53 TCAATTACTTATTTATTAGCATTTTAATGGATGT 17 29 1 ATTTATATTT 0.491038 -153 ATTTAAAGATTTTTATAAGATTTGTGACTTGTAT 17 82 0 TTTTATTTTG 0.590015 -100 TCAATAAAATTTTATGAAAAAAGCCGTTTGAAT 18 10 1 TTTTATAAAG 0.910662 -192 AGCAACTGATTTTTATCAAAATAAAAAAGCCGTT 18 54 0 TTTTATATAA 0.857068 -148 AATGTAGTACTTTTATCTTAAATTT 19 16 1 TTTTATAATT 0.884124 -15 TAATTTTAAAATTTATAGCAATTAAGAAGAAAGA 20 97 1 ATTTATATTA 0.63796 -26 CATAAGTATTTTTTATATCCAAAAGTGCTAATAT 22 41 1 TTTTATAAAA 0.93738 -97 TTCGCAACGTTTTTATTTCTAATATTAGCACTTT 22 62 0 TTTTATAATA 0.932473 -76 GGAATTTATATTTTATATATTTAGTCAGCTTATC 24 39 1 TTTTATTTAG 0.609766 -45 TTTTATAATGAAAAACAAGGGGCA 27 1 1 TTTTATAAAA 0.934059 -288 TAAATTATGTATTTATATCATAATTTTGGGTTG 27 101 0 ATTTATTAAT 0.452935 -188 AACCGATTATTTTTATTATTCAATTTGAACATAG 28 48 1 TTTTATCAAT 0.55681 -32 TAAGCACAATTTTTATAAGAATAGGTCAAATT 29 9 0 TTTTATATAG 0.825792 -152 TAGGATAAAATTTTATCCTTAAAGTTGCAATGGT 29 41 1 TTTTATAAAG 0.918389 -120 GCTAAATGGCTTTTATAGGAAAATACCATTGCAA 29 65 0 TTTTATAAAT 0.890353 -96 ATTTTCTCAATTTTCTAATTAAAAACGTGGCGTA 29 134 0 TTTTCTAAAA 0.369836 -27 AGTGCGGTTGTTTTTTTCGTAAATTTAACGAGAA 30 41 1 TTTTTTAAAT 0.372141 -29 TCAAGAAAGATTTTATAAAAATTAACCACGCTTT 31 54 0 TTTTATATTA 0.853182 -85 AGTCATTTTATTTTATCAAGAAAGATTTTATAAA 31 69 0 TTTTATAAAG 0.914123 -70 TCTCGTAAAGTTTTTTCAAAAAAGTGAGATAAAA 32 11 0 TTTTTTAAAG 0.454981 -125 TTCAGAGGATTTTTATTTCTTTTTAAAAAATAGC 33 75 1 TTTTATTTTT 0.511991 -50 AATTAGGATTTTTTATGCACAAAGCTAAATAAAG 34 12 1 TTTTATAAAG 0.918322 -144 TCTATAGAATTTTTATTCACAAAAATCGATTATT 34 100 1 TTTTATAAAA 0.856529 -56 ****** **** Masking position 6 Map Score: 48.3794 Number of sites scoring better than the average of aligned sites = 819 Number in coding regions = 477 Number in noncoding regions = 342 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 4 TTAACTATGATATGATTATGAAACATAAAAACTCTTTTTGG 3 31 0 TATTAACAAA 0.532906 -79 ATATTCTTACTTTAGTTTTTATAATAAAAAACTAGATCGTG 5 134 1 TGTTAAAAAA 0.595049 -117 ACGCAATAGATTTATTTAGAATAAAATAACACGATCTAGTT 5 163 0 TTTTAAAACA 0.471499 -88 TAATGCTGGGTAACTTTACGTCAAAAATAAATAAAGGAGTT 5 216 1 TTTTTAAAAA 0.410574 -35 CCAATGAACATTGCATTTGAACAAGCAGAAAACCGTATGCA 6 26 1 TATTAAAAAA 0.948457 -275 GGTAGCAAGTTTGGTTTAAGATTTATATAAAATAGCTTTAT 6 85 1 TTTTATTAAA 0.371841 -216 AATAAAGTTATTAAATTTTTAGAATTAGAAATAAAGCTATT 6 115 0 TATTAAAAAA 0.948315 -186 TGGTTTTGTATTTTTTATGTAAAATTTAAAATTGTTTTTGA 6 168 1 TTTAAAAAAA 0.690276 -133 GATTATTTTATTAAATTCTAATAATACTAAAAATCTCGCAA 7 121 1 TATTAAAAAA 0.948432 -180 GTTCGAACAGTTGCATTATAAGAGAGGTAAAATGAAATTTG 7 203 0 TATTAAGAAA 0.677419 -98 ACGCAATTTTTTATTTCTCGATAAATTTAAACTAAGGTGCA 8 14 0 TTTCAAAAAA 0.501177 -97 TATTATCTAATATCATTCCCAAAATAACTAAAACAGGCACA 9 15 0 TATTAAATAA 0.368501 -246 TTGAGCTTGATCTTTTTCAGGAAAATATAAAGAACCTTTTA 9 70 1 TTTTGAAAAA 0.81827 -191 TGTTTAACCTTAAATTCTAAGAACTGAAAAAATTGGCGCA 10 55 0 TATTAAAAAA 0.948457 -30 AGCAATATTCTATATTAATAATAAAACAAAAATGGACAAAA 11 48 0 TTTAAAAAAA 0.69035 -87 AACAAGAAATTGTTTTTTGAATAATCTGAAATAACTTAAAT 13 13 1 TTTTAAAAAA 0.950748 -175 TTATAAAAAGGCTTTTTGCCAAAACTCCAAAATAAAACCGC 13 87 0 GTTTAAAAAA 0.729245 -101 AGCCTTTTTATAAATTTCAAAAATATGCAAAAATAGGGCGA 13 115 1 TTTTAATAAA 0.836718 -73 GCTCCAATGCTAACATTTTGAGCAATAAAAAACTGTGTACT 14 34 0 TATTACAAAA 0.489163 -68 ATAATAAAAATGTCATTACAAGATCTATAAATCAGGTTCAT 15 21 1 TATTAATAAA 0.830045 -150 ATTTCCTGAGTAAATTTGAAATTAGTGTAAACCTTTGTAAA 15 135 0 TTTTATAAAA 0.690437 -36 TATAAGATTTATAGATTATAACAAGGAAAAAGTT 16 4 0 AATTAAAAAA 0.532557 -204 TTGATCATAAATAATTTACGATAAATTGAAAGCGGTTACTT 16 47 1 ATTTAAAAAA 0.544501 -161 TAAACCGTGATCTTTGTCACAAAATAAGAAAATAAGCAAAA 16 116 0 TTGTAAAAAA 0.488126 -92 AAATAAGTAATTGAATAGGTATAAAAGCAAAT 17 2 0 TATAAAAAAA 0.680072 -180 GTGACTTGTATCACATTTGTAAAATCTAAAACATCCATTAA 17 52 0 TATTAAAAAA 0.948457 -130 AAATTCAATTTTGATTTGACGTAATTTGAAATAGAATACAG 17 112 1 TTTTGAAAAA 0.818271 -70 TAAAGCAACTGATTTTTATCAAAATAAAAAAGCCGTTTGAA 18 50 0 GTTTAAAAAA 0.729244 -152 AAATTGAACTTATTTTTAGAAAATCTCTAAAAATCTCCACA 18 159 0 TTTTAATAAA 0.836718 -43 TTTAAAATTATATCATTGATGGAAATATAAATTTCCTTTAC 20 66 0 TATTGAAAAA 0.811014 -57 TATCCAAAAGTGCTAATATTAGAAATAAAAACGTTGCGAAT 22 56 1 TAATAAAAAA 0.519537 -82 AGTTGAGTTTTGTCATTGGGAGAAAAGGAAAAATAA 22 112 1 TATTAAAAAA 0.948456 -26 AAATATAAATTCCCTTTATTGTAGATGAAAAATTAAAATAA 24 11 0 TTTTGAGAAA 0.339436 -73 TAGAGAGATTGCTAATTTCTGCAAGGTCAAACTATCCAAAA 26 228 0 GATTGAAAAA 0.374472 -73 TTTGTCCCTTTGAGAAATATACAAAGAACGGTATC 28 5 1 TTTTAATAAA 0.836718 -75 ATTTTTATTATTCAATTTGAACATAGGAAAAAAC 28 56 1 TATTAATAAA 0.830045 -24 ACGCCACGTTTTTAATTAGAAAATTGAGAAAATAGC 29 135 1 TATTAATAAA 0.830038 -26 CACTTTTTGATGAATATTTAAAAATATCAAAGCGTGGTTAA 31 26 1 TTATAAAAAA 0.531462 -113 GGAAAATGTTTATTATTGGAAATTTAGTAAATCCTACGGCT 33 14 0 TATTATTAAA 0.360689 -111 GGATTTTTATTTCTTTTTAAAAAATAGCAAACGTTTGCTTT 33 81 1 TTTTAAAAAA 0.950756 -44 AAATTAGGATTTTTTATGCACAAAGCTAAATAAAGATTTT 34 10 1 TTTAAAAAAA 0.690419 -146 TTTATTCAATTCTAATTATTAGTAAGGAAAATAT 34 132 1 TATTATAAAA 0.680072 -24 * *** * ** *** Masking position 21 Map Score: 34.6882 Number of sites scoring better than the average of aligned sites = 458 Number in coding regions = 311 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 5 GCTTATAATGTTACTATTATTTTGTGTAGTTTA 1 13 1 TATATATTTT 0.707444 -62 TAAGATCCCCTATGTTCAATTTTATAAATTGCT 2 15 1 TTTTAATTTT 0.859261 -24 AAATATATTCTTACTTTAGTTTTTATAATAAAA 5 130 1 TATTAGTTTT 0.836488 -121 AATAAACTCCTTTATTTATTTTTGACGTAAAGT 5 228 0 TTTTATTTTT 0.773051 -23 AATAATAAAGTTATTAAATTTTTAGAATTAGAA 6 126 0 TATAATTTTT 0.83621 -175 TTTAATAACTTTATTATTTTTTTGTTTTGGTTT 6 141 1 TATATTTTTT 0.574309 -160 AAGGATCATGTCAATAATATTTTTTAAAAAATG 6 218 0 TATATATTTT 0.707438 -83 AAAATATGTTTTAGTTTATTTTTGATGAAGAGG 7 37 0 TATTATTTTT 0.861152 -264 GTAATGCCAGTATGTAGAATTTTATTGCGAGAT 7 153 0 TTTAAATTTT 0.834045 -148 TTAATAGTAATTTTTTCATTTTTTCTTTCTCAC 9 156 1 TTTTATTTTT 0.773051 -105 TAATCTGAAATAACTTAAATTTTAACCGCACTT 13 34 1 TATTAATTTT 0.917433 -154 TAAAAATCTTTAAATTCAATTTTGATTTGACGT 17 101 1 TATTAATTTT 0.915106 -81 TCAATAAAATTTTATGAAAAAAG 18 1 1 TATAAATTTT 0.901477 -201 TTTCTAAAAATAAGTTCAATTTTTAAGGCGTAA 18 178 1 TATTAATTTT 0.917433 -24 AACCGCACTTTTAGTTGAGTTTTGTCATTGGGA 22 100 1 TATTAGTTTT 0.836488 -38 TTATTTTAATTTTTCATCTACAA 24 1 1 TATTAATTTT 0.917468 -83 GATAAATCGATGATTTTATTTTTTACAGGATTG 26 135 1 TATTATTTTT 0.861152 -166 ATTAGCAATCTCTCTATAATTTTAAACTTTCTC 26 253 1 TTTAAATTTT 0.834045 -48 TTTTCCTCTTTGTCTAGTGTTTTGTGCATTAAA 34 55 0 TTTATGTTTT 0.379332 -101 GCGGTTATACTCTATAGAATTTTTATTCACAAA 34 90 1 TTTAAATTTT 0.834045 -66 * * ** ****** Masking position 5 Map Score: 18.4402 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 245 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 6 CACGATCTAGTTTTTTATTATAAAAACTAAAGTAAGAATA 5 135 0 TTATATAAAA 0.498382 -116 TTACCCAGCATTATTAATTTTAATAACGCAATAGATTTAT 5 189 0 TTATTTTAAA 0.724138 -62 GCATACGGTTTTCTGCTTGTTCAAATGCAATGTTCATTGG 6 26 0 TTTTTTAATA 0.877913 -275 ATAGCTTTATTTCTAATTCTAAAAATTTAATAACTTTATT 6 116 1 TTTTTAAATA 0.445614 -185 TGCGAGATTTTTAGTATTATTAGAATTTAATAAAATAATC 7 121 0 TTTTTTAATA 0.877929 -180 AAATTTCATTTTACCTCTCTTATAATGCAACTGTTCGAAC 7 204 1 TTCTTTAATA 0.713707 -97 GCGCCAATTTTTTCAGTTCTTAGAATTTAAGGTTAAACA 10 56 1 TTTTTTAATA 0.87793 -29 TTTGTCCATTTTTGTTTTATTATTAATATAGAATATTGCT 11 49 1 TTTTTTTAAA 0.670319 -86 TTTAAGTTATTTCAGATTATTCAAAAAACAATTTCTTGTT 13 13 0 TTTTTTAAAA 0.886071 -175 CGCCCTATTTTTGCATATTTTTGAAATTTATAAAAAGGCT 13 115 0 TTATTTAAAA 0.90942 -73 AGAATCCTTGTTACCCATAATAAAAATAAAAACTAAGTCG 13 153 0 TTATATAAAA 0.598286 -35 TGAACCTGATTTATAGATCTTGTAATGACATTTTTATTAT 15 21 0 TTATTTAATA 0.902782 -150 TTATCGTAAATTATTTATGATCAAAATATAAGATTTATAG 16 31 0 TTATATAAAA 0.596148 -177 TAATGGATGTTTTAGATTTTACAAATGTGATACAAGTCAC 17 53 1 TTTTTAAATA 0.449981 -129 GTGGAGATTTTTAGAGATTTTCTAAAAATAAGTTCAATTT 18 160 1 TTATTTAAAA 0.909424 -42 TTATTTTTCCTTTTCTCCCAATGACAAAACTCAACT 22 112 0 TTTTTCAATA 0.6483 -26 GATGGATTGATTGAAAATCTTAGTATTAGAAAAGTATCAT 23 16 1 TTATTTTATA 0.708271 -56 ACACAGTGAATTTATTATGTTTGAAATCAATCCTGTAAAA 26 155 0 TTATTTAAAA 0.909043 -146 ATACCGTTCTTTGTATATTTCTCAAAGGGACAAA 28 5 0 TTATTCAAAA 0.720125 -75 GTTTTTTCCTATGTTCAAATTGAATAATAAAAAT 28 56 0 TTATTTAATA 0.902062 -24 AATTTGACCTATTCTTATAAAAATTGTGCTTA 29 3 1 TTCTTTTATA 0.394589 -158 GCTATTTTCTCAATTTTCTAATTAAAAACGTGGCGT 29 135 0 TTATTTAATA 0.902782 -26 TAAAGTGCGGTTGTTTTTTTCGTAAATTTAACGAGAAATA 30 38 1 TTTTTCAAAA 0.665895 -32 AAAGCAAACGTTTGCTATTTTTTAAAAAGAAATAAAAATC 33 82 0 TTATTTAAAA 0.909424 -43 ATTTATTCAATTCTAATTATTAGTAAGGAAAATAT 34 131 1 TTTTTTTAAA 0.67032 -25 ** ** ** *** * Masking position 8 Map Score: 20.3726 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 235 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 7 AGGAAAAATCCCTCTTTCTATCT 6 288 0 AAAAATCCCT 0.789556 -13 GCGGCAAATTATAAAGCCTTTCTCAAGCTT 9 212 0 ATAAAGCCTT 0.633761 -49 GAGTTTTGGCAAAAAGCCTTTTTATAAATT 13 101 1 AAAAAGCCTT 0.952883 -87 TTTCTAGCGTTAAAAGCTGTGACGCACCAC 15 61 1 TAAAAGCTGT 0.835464 -110 TTTGTAAATAAAAAAGCCATCGCTTGACCA 15 113 0 AAAAAGCCAT 0.864698 -58 CAAATCTTATAAAAATCTTTAAATTCAATT 17 92 1 AAAAATCTTT 0.730611 -90 AATTTTATGAAAAAAGCCGTTTGAATTGTT 18 18 1 AAAAAGCCGT 0.959062 -184 TATCAAAATAAAAAAGCCGTTTGAATAAAC 18 45 0 AAAAAGCCGT 0.959062 -157 TTATTTTGATAAAAATCAGTTGCTTTAATG 18 64 1 AAAAATCAGT 0.578024 -138 CTGGGGAGCTTAAAAGCATTAACAACCCAN 27 79 1 TAAAAGCATT 0.655989 -210 TAGGCATCATTAAAATCCTTAGCTGACACA 27 133 1 TAAAATCCTT 0.82449 -156 CATTCAGGGTTAAAAGCCCTGACCAACAGG 27 202 1 TAAAAGCCCT 0.85816 -87 ACCTAAAAGCAAAAAGCTGTTGAAATCAAC 27 254 0 AAAAAGCTGT 0.892432 -35 TATTTTCCTATAAAAGCCATTTAGCAAACG 29 74 1 TAAAAGCCAT 0.796392 -87 TTAATTTTTATAAAATCTTTCTTGATAAAA 31 63 1 TAAAATCTTT 0.624564 -76 CATTAAAAGCAAAAATCTTTATTTAGCTTT 34 32 0 AAAAATCTTT 0.730611 -124 ********** Masking position 5 Map Score: 13.4062 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 214 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 TAAAAAATACAAAACCAAAACAAAAAAATA 6 155 0 AAAACCAAAA 0.541952 -146 TGAGAAAGAAAAAATGAAAAAATTACTATT 9 158 0 AAAATGAAAA 0.698554 -103 ATCAGATTTAAACAGGAAAATTTT 9 247 1 AACAGGAAAA 0.852848 -14 AATTAAAACAAAAAGGAAAAATT 11 122 1 AAAAGGAAAA 0.955731 -13 AATTTCAAAAATATGCAAAAATAGGGCGAC 13 127 1 ATATGCAAAA 0.36626 -61 ATAGATTATAACAAGGAAAAAGTT 16 5 0 ACAAGGAAAA 0.802591 -203 AAATAAGAAAATAAGCAAAATTTTTTATGA 16 106 0 ATAAGCAAAA 0.87104 -102 GAATAGGTATAAAAGCAAAT 17 1 0 AAAAGCAAAT 0.528776 -181 TCATTGGGAGAAAAGGAAAAATAA 22 124 1 AAAAGGAAAA 0.955731 -14 TTTTATAATGAAAAACAAGGGGCA 27 5 1 ATAATGAAAA 0.54411 -284 AGCCCTGACCAACAGGAAAAAGTATAGATA 27 216 1 AACAGGAAAA 0.852848 -73 ATTCATACCTAAAAGCAAAAAGCTGTTGAA 27 260 0 AAAAGCAAAA 0.92915 -29 CAACACATACATAAGGAAAAGCT 31 126 1 ATAAGGAAAA 0.917485 -13 TTTGTGCATTAAAAGCAAAAATCTTTATTT 34 38 0 AAAAGCAAAA 0.92915 -118 ACACTAGACAAAGAGGAAAAGTGCGGTTAT 34 68 1 AAGAGGAAAA 0.758993 -88 CTAATTATTAGTAAGGAAAATAT 34 143 1 GTAAGGAAAA 0.585078 -13 ********** Masking position 7 Map Score: 14.639 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 203 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 9 TTACCTGTTCTAGGCAATACAAAAATATCCAGA 5 54 0 TACAATCAAA 0.915274 -197 AAATTTTACATAAAAAATACAAAACCAAAACAA 6 162 0 TAAAATCAAA 0.94519 -139 TAGATTATTTTATTAAATTCTAATAATACTAAA 7 119 1 TAAAATCTAA 0.935421 -182 ATAGGATATCTAATAAATGCAAACTAAGGAGAT 12 50 1 TAAAATCAAA 0.945137 -28 AAAGCCTTTTTATAAATTTCAAAAATATGCAAA 13 113 1 TAAATTCAAA 0.683494 -75 GCCGTTTGAATAAACAATTCAAACGGCTTTTTT 18 27 0 TACAATCAAA 0.914824 -175 CTTTTGGATATAAAAAATACTTATGACTGAGGC 22 33 0 TAAAATCTTA 0.648003 -105 TGACTAAATATATAAAATATAAATTCCCTTTAT 24 33 0 TAAAATTAAA 0.576123 -51 ATTGGAAATTTAGTAAATCCTACGGCTTAA 33 8 0 TAAAATCTAC 0.732178 -117 GCTTTGTGCATAAAAAATCCTAATTT 34 4 0 TAAAATCTAA 0.935537 -152 ATCGATTATTTATTCAATTCTAATTATTAGTAA 34 124 1 TACAATCTAA 0.900786 -32 ** **** **** Masking position 6 Map Score: 4.62763 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 59 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 ACCGCTTTAATTGTGTGCATACGGTTTTCT 6 52 0 TTGTGTGCAT 0.950875 -249 GTTGTGTGCCTGTTTTAGTTA 9 2 1 TTGTGTGCCT 0.904411 -259 AAATCTTTCATTTTGTCCATTTTATTTGTA 11 21 0 TTTTGTCCAT 0.933378 -114 AAATGAAAGATTTTGTCCATTTTTGTTTTA 11 38 1 TTTTGTCCAT 0.933378 -97 ATTATTCTATTATTGTGCATATTTATTCAT 11 91 0 TATTGTGCAT 0.861926 -44 TTTTTGTTCCTAAATTAGCTT 26 290 0 TTTTGTTCCT 0.715157 -11 CTTTATTTAGCTTTGTGCATAAAAAATCCT 34 16 0 CTTTGTGCAT 0.902459 -140 TTGTCTAGTGTTTTGTGCATTAAAAGCAAA 34 49 0 TTTTGTGCAT 0.975369 -107 AATAATCGATTTTTGTGAATAAAAATTCTA 34 104 0 TTTTGTGAAT 0.79517 -52 ********** Masking position 6 Map Score: 5.66725 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 54 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 TTTTGTGTAGTTTATTCTTATTGTTATTTC 1 32 1 TTTATTCTTA 0.864872 -43 CAGAATAAAATTACTTGTTATGTTTAACTA 3 65 0 TTACTTGTTA 0.474491 -45 TTAAAATAAATATATTCTTACTTTAGTTTT 5 123 1 TATATTCTTA 0.475477 -128 ATCGTGTTATTTTATTCTAAATAAATCTAT 5 169 1 TTTATTCTAA 0.326316 -82 AATCTAACTCTTTATTGTTATTTGTTTGAT 7 95 0 TTTATTGTTA 0.848918 -206 CAATTTTTTATTTCTCGATAAATTTAAACT 8 22 0 TTTCTCGATA 0.537267 -89 CCATTTTTGTTTTATTATTAATATAGAATA 11 54 1 TTTATTATTA 0.385546 -81 ATTGTGCATATTTATTCATAAAGCAATATT 11 80 0 TTTATTCATA 0.580494 -55 CTTTTATCTCCTTAGTTTGCATTT 12 64 0 TATCTCCTTA 0.464215 -14 CAAAAAACAATTTCTTGTTAA 13 2 0 TTTCTTGTTA 0.918312 -186 CGACTTAGTTTTTATTTTTATTATGGGTAA 13 153 1 TTTATTTTTA 0.525265 -35 AACTTTTTCCTTGTTATAATCTATAA 16 7 1 TTCCTTGTTA 0.572328 -201 TTTCTTTCTTCTTAATTGCTATAA 20 109 0 TTTCTTCTTA 0.927564 -14 CTATCCTGTTTTTCTTCTTACTGATGATAC 23 49 0 TTTCTTCTTA 0.927564 -23 AGGATAAAATTTTATCCTTAAAGTTGCAAT 29 42 1 TTTATCCTTA 0.753553 -119 AATATTTCTCGTTAAATTTACGAA 30 56 0 TTTCTCGTTA 0.843026 -14 TTATAAAATCTTTCTTGATAAAATAAAATG 31 70 1 TTTCTTGATA 0.708486 -69 AGGATTTTTATTTCTTTTTAAAAAATAGCA 33 80 1 TTTCTTTTTA 0.688827 -45 ********** Masking position 5 Map Score: 9.98297 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 141 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 AAATATCCAGAAATTAATCTATGGAGACTCT 5 34 0 AAATTATCTA 0.925603 -217 ATTTTATTCTAAATAAATCTATTGCGTTATT 5 177 1 AAATAATCTA 0.612528 -74 CTCTTCATCAAAAATAAACTAAAACATATTT 7 38 1 AAAATAACTA 0.645402 -263 ATTTTCGTTTAAATTCATCTACTATTAGAAA 7 65 1 AAATTCTCTA 0.700866 -236 AGAATTTAATAAAATAATCTAACTCTTTATT 7 109 0 AAAATATCTA 0.880031 -192 TTGTTTTAATTAATTATTCTATTATTGTGCA 11 102 0 TAATTATCTA 0.612528 -33 AGTAAATTTGAAATTAGTGTAAACCTTTGTA 15 137 0 AAATTATGTA 0.912523 -34 AATTTATACTAAATTATTGTAAATAAACCGT 16 149 0 AAATTATGTA 0.912523 -59 AATTTAGTATAAATTAATGTAATCGTTTACA 16 165 1 AAATTATGTA 0.912523 -43 AAAATAAAGTAAAAGTATTTA 17 171 0 AAAATAAGTA 0.604126 -11 AAAATAATGTAGTACTTTTAT 19 1 1 AAAATATGTA 0.860149 -30 ****** **** Masking position 3 Map Score: 3.63257 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 41 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 TTTATTATTTTTTTGTTTTGGTTTTGTATT 6 150 1 TTTTGTTTTG 0.836507 -151 AATAATCTCCTTGTGTTTTGACTATACATT 7 281 0 TTGTGTTTTG 0.958639 -20 TAACCCGAAATGGCGTTTTATGCTATTATT 8 60 1 TGGCGTTTTA 0.808382 -51 TTTTGTCCATTTTTGTTTTATTATTAATAT 11 48 1 TTTTGTTTTA 0.698427 -87 AATTTTTCCTTTTTGTTTTAATTAATTATT 11 115 0 TTTTGTTTTA 0.698427 -20 TAACAAGAAATTGTTTTTTGAATAATCTGA 13 12 1 TTGTTTTTTG 0.624488 -176 GGTTTTATTTTGGAGTTTTGGCAAAAAGCC 13 89 1 TGGAGTTTTG 0.857659 -99 TGGAGAAAAGTGGTGTTTTGTGGAGATTTT 18 141 1 TGGTGTTTTG 0.9559 -61 GGGTTGTGGCGTTTTATAAATAGCCT 22 7 1 TGGCGTTTTA 0.808382 -131 GCACTTTTAGTTGAGTTTTGTCATTGGGAG 22 104 1 TTGAGTTTTG 0.865643 -34 TGCCTACCCCTTGTGTTTTAATAGTCGGTA 27 37 1 TTGTGTTTTA 0.912977 -252 CCTCTTTGTCTAGTGTTTTGTGCATTAAAA 34 54 0 TAGTGTTTTG 0.80596 -102 ********** Masking position 6 Map Score: 9.63205 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 111 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 TTAATAAGATCCCCTATGTTC 2 1 1 TAATAAGATC 0.931972 -38 TATTTTAAATTAAATAAGATCAAGTTAATTT 5 100 0 TAATAAGATC 0.931972 -151 AAATTGTTTTTGACTAAGATCACATTTTTTA 6 196 1 TACTAAGATC 0.930692 -105 TATATTTTCCTGAAAAAGATCAAGCTCAACA 9 68 0 TAAAAAGATC 0.95648 -193 TCTTATTTTGTGACAAAGATCACGGTTTATT 16 128 1 TACAAAGATC 0.955638 -80 TTTACTAACGTAAAAAAGGTCGCTCTTTCAA 20 40 0 TAAAAAGGTC 0.853746 -83 TGATGAATATTTAAAAATATCAAAGCGTGGT 31 33 1 TAAAAATATC 0.740309 -106 GAATTTTTATTCACAAAAATCGATTATTTAT 34 106 1 TACAAAAATC 0.736441 -50 * ********* Masking position 6 Map Score: 2.22236 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 28 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 AATTGCACCTTAGTTTAAATT 8 1 1 AATTGCCCTT 0.964884 -110 AATTGCTCCTTTTTACTGAAA 8 100 0 AATTGCCCTT 0.964884 -11 ACTTATCGGTAAATCCGCCTTTCACAAGCTT 9 187 1 AAATCCCCTT 0.899028 -74 ACTTGCAAGTAATTCCACATTAAAGCAACTG 18 80 0 AATTCCCATT 0.94585 -122 TGGCTGTTCTAATTCCCCATTGACTTCTTCT 26 46 1 AATTCCCATT 0.9455 -255 AATAGCATATAATTCCACACTTTATCACACA 26 190 0 AATTCCCACT 0.843185 -111 AGGGGTAGGCAACTGCCCCTTGTTTTTCATT 27 17 0 AACTGCCCTT 0.909477 -272 ****** **** Masking position 2 Map Score: 1.65742 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 34 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678