AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_hinf_reg_100.orf -o02010_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 Input sequences: #1 HI0097 272 iron(III) ABC transporter, periplasmic-binding protein (hitA) #2 HI0098 216 iron(III) ABC transporter, permease protein (hitB) #3 HI0126 43 ferric ABC transporter, ATP-binding protein (afuC) #4 HI0129 300 H. influenzae predicted coding region HI0129 #5 HI0131 165 afuA protein #6 HI0213 164 oligopeptide transporter, periplasmic-binding protein, putative #7 HI0354 300 ABC transporter, ATP-binding protein #8 HI0357 21 thiamine biosynthesis protein, putative #9 HI0362 300 iron (chelated) ABC transporter, periplasmic-binding protein (yfeA) #10 HI0408 171 ABC transporter, ATP-binding protein (yebM) #11 HI0498 254 spermidine/putrescine ABC transporter, periplasmic-binding protein (potD) #12 HI0501 167 high affinity ribose transport protein (rbsD) #13 HI0621 175 ABC transporter, ATP-binding protein #14 HI0821 207 galactose operon repressor (galR) #15 HI0822 90 galactose ABC transporter, periplasmic-binding protein (mglB) #16 HI0823 65 galactoside ABC transporter, ATP-binding protein (mglA) #17 HI0853 140 heme-binding lipoprotein (dppA) #18 HI1019 300 thiamin ABC transporter, periplasmic-binding protein (tbpA) #19 HI1079 67 amino acid ABC transporter, permease protein #20 HI1080 300 amino acid ABC transporter, periplasmic-binding protein #21 HI1087 300 ABC transporter, ATP-binding protein #22 HI1110 50 D-xylose ABC transporter, ATP-binding protein (xylG) #23 HI1111 233 D-xylose ABC transporter, periplasmic-binding protein (xylF) #24 HI1123 80 oligopeptide ABC transporter, permease protein (oppB) #25 HI1124 295 oligopeptide ABC transporter, periplasmic-binding protein (oppA) #26 HI1180 126 arginine ABC transporter, ATP-binding protein (artP) #27 HI1187 89 dipeptide ABC transporter, permease protein (dppB) #28 HI1188 300 DNA helicase II (uvrD) #29 HI1344 72 spermidine/putrescine ABC transporter, periplasmic-binding protein (potD) #30 HI1345 25 spermidine/putrescine ABC transporter, permease protein (potC) #31 HI1347 268 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #32 HI1382 90 phosphate ABC transporter, permease protein (pstC) #33 HI1383 300 phosphate ABC transporter, periplasmic-binding protein (pstS) #34 HI1472 67 iron chelatin ABC transporter, periplasmic-binding protein, putative #35 HI1475 227 H. influenzae predicted coding region HI1475 #36 HI1618 95 ABC transporter, ATP-binding protein #37 HI1624 89 H. influenzae predicted coding region HI1624 #38 HI1638 69 peptide ABC transporter, periplasmic-binding protein (sapA) #39 HI1692 173 molybdenum ABC transporter, permease protein (modB) #40 HI1693 137 molybdenum ABC transporter, periplasmic-binding protein (modA) Motif number 1 ATTATAAAGAAAAGTGCGGTGAATTTCACG 5 43 1 AAAGTGCGGT 0.997687 -123 GAAGCCGCAAAAAGTGCGGTGGTGGAAAGG 11 189 0 AAAGTGCGGT 0.997687 -66 TTTCTACAAGAAAGTGCGGTAGATTATTTT 20 148 1 AAAGTGCGGT 0.997687 -153 TACTCGTATTTAAGTGCGGTTAAAAATCGT 24 16 1 TAAGTGCGGT 0.983789 -65 AAATGGGCGAAAAGTGCGGTCAAAAAATAC 24 47 0 AAAGTGCGGT 0.997687 -34 ATTTCTTTGAAGAGTGCGGTGAATTTTTAC 27 42 1 AGAGTGCGGT 0.989004 -48 GTAGATAATAAAAGTGCGGTAAAAATTCAC 27 60 0 AAAGTGCGGT 0.997687 -30 AAATTCATCGAAAGTGCGGTTAAATTTCTC 31 104 1 AAAGTGCGGT 0.997687 -165 GGTTTTGTATAAAGTGCGGTATAAAATAAA 32 17 0 AAAGTGCGGT 0.997687 -74 TAACATTAATAAAGTGCGGTTATCTTAAAT 32 54 1 AAAGTGCGGT 0.997687 -37 ********** Masking position 5 Map Score: 38.3785 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 TCACCGCACTTTTCTTTATAATTGCAAGAATTTTCCTTACATC 5 22 0 TTATAAATTT 0.825854 -144 AAATCGATCATTAAAGAAAAATACCAAAATTTTTATTTTGAC 6 10 1 ATAAAAATTT 0.951047 -155 GGAAACTAATATGCCAAAAAATCCATTTTCTTTTCATTCCATT 7 217 1 ATAAAATTTT 0.912657 -84 GTACGAAATAATTATAAATAAATCTATTATTTTGATAATCATT 9 157 1 ATATAAATTT 0.898139 -144 ACAATTATTCATCGGAGATAATAGTACTACTTTTTATATTGTT 9 210 0 ATATAAATTT 0.898139 -91 ACGCTTAAATATTCGACATAAGAGAGAAAATCTTGAGAATTCT 10 90 1 ATATAAATCT 0.777961 -82 AATCTTGAGAATTCTATAAAAATGCGTTATTTTCCCCAACCAT 10 118 1 ATAAAAATTT 0.951047 -54 TTCCCCAACCATTGTTGAAAACACGGCGATTTT 10 149 1 ATAAAAATTT 0.951047 -23 AAAAAATCCCTTAGGAAAAAACTGGCAAAATCTTACCCCGAAA 11 11 1 TTAAAAATCT 0.805905 -244 ATACTAAATTATTGTAAATAAACCGTGATCTTTGTCACAAAAT 14 54 1 ATATAATTTT 0.825854 -154 TATGAACTAAATCATAAAAAATTTTGCTTATTTTCTTATTTTG 14 91 0 ATAAAATTTT 0.912654 -117 TTTCCTTGTTATAATCTATAAATCTTATATTTTGATCATAAAT 14 170 0 ATATAAATTT 0.898104 -38 AATGAAAATGATTACATAAAAAATTATGAATTTGTGATCCATG 15 18 0 ATAAAAATTT 0.951047 -73 ATTAATTTGTTATAATCCATAGAATTTTTTTATTTAA 17 5 1 ATATAAATTT 0.898139 -136 ATAGAATTTTTTTATTTAAAAAAAGGGAAATTTGCTTATATCT 17 29 1 TTAAAAATTT 0.912657 -112 CCCCTTTATTTTTTCAGAAAATGTAGAAAGTTTATTTCTTTTT 18 88 1 TTAAAAATTT 0.912657 -213 ACATTACAAGTTTATTTATAATCTTAAATTTCTATTAATGCCT 20 35 1 TTATAATTCT 0.503358 -266 TCTTATAAAATTTCAGTAAAAAAATGCCTTTCTAAAGAAAGGC 20 74 0 TTAAAATTCT 0.690706 -227 ATGTGTTGCGATAAAAGAAAAAACTTCATCTTTAAATTAAACA 21 207 1 ATAAAATTTT 0.912656 -94 AAAGTTAGTTTTTCACAAAAATACGAAAAATTTCATCACCTAG 23 24 0 TTAAAAATTT 0.912657 -210 TTAGGCGATATTTTTATAAAAAGTCTTCTATTTATTAGCTCAA 25 247 0 TTAAAATTTT 0.848941 -49 TTGCATAATTATGCATAAAAATGTAATATTTTTTCATCTTATA 26 77 1 ATAAAATTTT 0.912657 -50 AAAGAAATTAATCGGTAAAAAATATAATACTCTTGAATT 27 7 0 ATAAAAATCT 0.885321 -83 TATGCATAAAATGAAAAAAAATCTTATTACGTTTTAACCTTAG 33 74 1 ATAAAAAGTT 0.598449 -227 CAACAGCAAATTATTGCAAAAACGGTTGATTTTGGTGCCTCTG 33 260 1 TTAAAAATTT 0.912657 -41 AATAACAATCATATAGCAAAAGAAAAATTATTTAGTAAAATAT 40 55 0 ATAAAATTTT 0.912657 -83 ** **** * *** Masking position 2 Map Score: 27.3878 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 269 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 3 AAGTTCACATTCCTAAAAGGATTTAACTTTGCCTCGCAG 2 100 1 TAAAAAAATT 0.805093 -117 AGCGAAAAAAATGAATTAACTCGTTAAGT 3 1 1 AAAAAAATAA 0.701797 -43 GGATAAAATAATCCAAAAATAAGCAGAATGCATTATGGA 4 191 0 AAAAAAAGAT 0.708322 -110 ATCGATCATTAAAGAAAAATACCAAAATTTTTATTTTGA 6 13 1 AAAAAAAATT 0.707547 -152 GCTTGTTTGGTAGAAAAAACAAGCAATTAGGTTTCTATC 7 96 0 TAAAAAAATA 0.843064 -205 GTGATGATAAACCTAAAATGACAGAACAAACCAAAACAA 9 43 0 AAAAAAAAAA 0.878078 -258 ATTGAATGTATGAAAAAAGAACAAAACATTTTGGTTAGT 9 111 0 TAAAAAAAAT 0.90435 -190 TGGGAATGATTATCAAAATAATAGATTTATTTATAATTA 9 165 0 TAAAAAATTA 0.637081 -136 ATCATTCCCATTCCAAAACAATATAAAAAGTAGTACTAT 9 194 1 TAAAAAAAAA 0.924791 -107 GATAACAAAAATAGAAAAACAACTAAGAAATTTCAAATT 12 92 0 AAAAAAAAAA 0.878078 -76 ACCAAAACAGATTTAAAAACAATAAATAAAAAGGGCTTA 13 146 1 AAAAAAAAAA 0.878078 -30 GTGATCTTTGTCACAAAATAAGAAAATAAGCAAAATTTT 14 78 1 TAAAAAAAAA 0.924791 -130 GAATTTTTTTATTTAAAAAAAGGGAAATTTGCTTATATC 17 32 1 AAAAAAAATT 0.707547 -109 CCAACGGCTTTTTAAAAAGAAATAAACTTTCTACATTTT 18 105 0 TAAAAAAATT 0.805093 -196 AAGTGATTACTATCAAAATAAGAAAATAATCTACCGCAC 20 161 0 TAAAAAAAAA 0.924791 -140 AAACCAAACTTATGAAAAAAAAAGATTATTTATTTATGG 20 231 0 TAAAAAATAT 0.755477 -70 AATTTTAATCTATAAAAAATAGAAATAAAATTTATCACT 21 134 1 TAAAAAATAA 0.800721 -167 TTTGATGTGGTCATAAAAATAGTGATAAATTTTATTTCT 21 154 0 TAAAAAATAA 0.800721 -147 AGTTAGTTTTTCACAAAAATACGAAAAATTTCATCACCT 23 26 0 TAAAAAAAAT 0.90435 -208 ATAATCAACATAGAAAAATTAAATAACATAATTGATGAA 23 66 0 TAAAAAAAAT 0.90435 -168 TTTCTCATTTTTCCAAAAATACCCATGATGACAATAATA 28 40 0 TAAAAAATAT 0.755477 -261 AAAAAGATATTTTTAAAAGGAGCGAGAAT 31 1 0 TAAAAAAGAT 0.805681 -268 ATAACAATATTTATAAAATTAACGAAGTAAAATTCATCG 31 75 1 TAAAAAAATA 0.843064 -194 AAACTGCCGTTCATAAAAATAACGAGAAATTTAACCGCA 31 118 0 TAAAAAAGAA 0.843559 -151 AAGTATTTTCCAAAATTATTTAAGATAACCGCACTT 32 65 0 TAAAAAAAAT 0.904052 -26 TGGTTGATTTAGTCAAAATGAACCAGAAAAACTAAGAAT 35 54 0 AAAAAAAGAA 0.759514 -174 ATTCTTAGGGAAAGAAAACTAAGAAAAAATCAGATCTTT 35 92 0 AAAAAAAAAA 0.878078 -136 CAAAACAAAGAAAACAAAAGAAATAGGAATTTGGC 35 203 0 AAAAAAAATA 0.758829 -25 TGGCGTCAGATTGAAAAATGAAAAAAATTGGGTAAGCAA 39 145 0 TAAAAAAATT 0.805093 -29 CATATAGCAAAAGAAAAATTATTTAGTAAAATATATAAC 40 50 0 AAAAAAAGAA 0.759407 -88 * **** * ** ** Masking position 11 Map Score: 30.5712 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 353 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 4 GAATGGAACAAGAAAAGCATTTTTAAATTTCTCT 7 61 0 AGAAATTTTT 0.946417 -240 TAATATGCCAAAAAATCCATTTTCTTTTCATTCC 7 223 1 AAAAATTTTC 0.632743 -78 CCCTAAAATAAAAAAGTTTTCAGCATTCAG 10 7 1 AAAAAGTTTT 0.75026 -165 CTTTTTCCATAGGAATGAATTTTCTTTATAATCT 10 46 0 AGAAATTTTC 0.828843 -126 GGTTGGGGAAAATAACGCATTTTTATAGAATTCT 10 125 0 AAAAATTTTT 0.935553 -47 GCGCGCGCGCAGTATAGCATTTTTTTCTAAAAGG 11 69 0 AGATATTTTT 0.867716 -186 TGAGTGAGTGAGCAAAGAATTTTTTCAATTTATT 11 145 0 AGAAATTTTT 0.961041 -110 GGTGGTGGAAAGGAAAAGATTTTTGAGTGAGTGA 11 168 0 AGAAATTTTT 0.961041 -87 GCCTTTCTTTAGAAAGGCATTTTTTTACTGAAAT 20 74 1 AGAAATTTTT 0.957673 -227 TGCATTGTTTAGAAACGTATTTTTCTACAAGAAA 20 127 1 AGAAATTTTT 0.957673 -174 ACCATAAATAAATAATCTTTTTTTTTCATAAGTT 20 230 1 AAAATTTTTT 0.440228 -71 TTATTTGAAGAAAAATTGAGTTTTGTGAGTTGTG 25 182 0 AAAAAGTTTT 0.619877 -114 AAATCTTTACAAAAATGAATTTTTGAGCTAATAA 25 225 1 AAAAATTTTT 0.498144 -71 AAGATGAAAAAATATTACATTTTTATGCATAATT 26 83 0 AAATATTTTT 0.799707 -44 AATTCAAGAGTATTATATTTTTTACCGATTAA 27 9 1 AGATATTTTT 0.867667 -81 CCATATGCTTTGAAAGCTATTTTTATACTATTTA 28 125 0 TGAAATTTTT 0.627386 -176 CGTTAAACTAAAAAAGATATTTTTAAAAGGAGCG 31 16 0 AAAAATTTTT 0.785285 -253 AAATCAACCAAAGATCTGATTTTTTCTTAGTTTT 35 83 1 AAATATTTTT 0.802825 -145 TAACTTTAGAATCAAGTCATTTTTTAAGGAAATT 37 12 0 ATAAATTTTT 0.684378 -78 TATATATTTTACTAAATAATTTTTCTTTTGCTAT 40 52 1 ACAAATTTTT 0.762529 -86 ** ** ****** Masking position 11 Map Score: 18.6468 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 112 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 GAAAGTCAGGTTTTCTTTACTGCGAGGTTGT 4 142 1 TTTTCTTTCT 0.782326 -159 TTGGATTATTTTATCCTTGTTAGCGTTTGCA 4 214 1 TTATCCTTTT 0.449316 -87 TCACGGTATTATTTCTATTTTTCAAGTAGGA 5 112 1 ATTTCTATTT 0.505743 -54 ATTTCTTATCCTTTCTTTTTTATTACGCACT 7 257 1 CTTTCTTTTT 0.806278 -44 TTTTTCTCCTTTAATGAAAAG 8 10 0 TTTTCTCCTT 0.809746 -12 GGCATTCAATCTATCTTTTTTAAATAAGGAC 9 275 1 CTATCTTTTT 0.53626 -26 ATTCTCAAGATTTTCTCTCTTATGTCGAATA 10 99 0 TTTTCTCTTT 0.831742 -73 TCTTAGTTGTTTTTCTATTTTTGTTATCTAT 12 103 1 TTTTCTATTT 0.857324 -65 TCTATTTTTGTTATCTATATTTGTCTTATCG 12 116 1 TTATCTATTT 0.6254 -52 ATATGTCAGATTATCTTTTTTAGACAGATTA 13 88 0 TTATCTTTTT 0.810651 -88 ATTTTGCTTATTTTCTTATTTTGTGACAAAG 14 83 0 TTTTCTTATT 0.774739 -125 AACTTTTTCCTTGTTATAATCTATA 14 193 0 TTTTCCTTTT 0.745977 -15 TATGTAATCATTTTCATTTTTGCAAATTTGC 15 43 1 TTTTCATTTT 0.651275 -48 TTACAATGAGTTATCTTCATTTTTATAGACT 18 33 1 TTATCTTCTT 0.786605 -268 AAGAAATAAACTTTCTACATTTTCTGAAAAA 18 97 0 CTTTCTACTT 0.582883 -204 GAATATAACCTTATCTCCTTTTCGTCATTAT 18 247 1 TTATCTCCTT 0.541815 -54 CGGTAGATTATTTTCTTATTTTGATAGTAAT 20 164 1 TTTTCTTATT 0.774739 -137 TTTTTCTTCCTTGTGTTGTGTT 20 289 0 TTTTCTTCTT 0.929909 -12 GAAGCTTTACATTTCTTCATTATTTATTGAA 21 68 0 ATTTCTTCTT 0.693179 -233 GATAAATTTTATTTCTATTTTTTATAGATTA 21 139 0 ATTTCTATTT 0.505743 -162 AACATTTTCCTCTCTAGGTGATGAA 23 5 1 TTTTCCTCCT 0.370965 -229 GTTATTTAATTTTTCTATGTTGATTATTTGC 23 78 1 TTTTCTATTT 0.857324 -156 ATTATAAAATCTTTCTCCATTATTACGTTTT 23 136 0 CTTTCTCCTT 0.534795 -98 TTTTCTTCTCTATGCTTTATA 26 116 0 TTTTCTTCCT 0.755766 -11 CCTTTTAAAAATATCTTTTTTAGTTTAACGA 31 20 1 ATATCTTTTT 0.421647 -249 TATCAAGATGTTTTCTATTTTTCTCGTTAAA 31 43 0 TTTTCTATTT 0.857324 -226 CATTAAGTCCTTTTCATTATTAACAATTCAC 31 171 1 TTTTCATTTT 0.651275 -98 CACAATTATTTTCTACACTTCGCTACGCA 33 9 1 TTTTCTACCT 0.546834 -292 TATAATGATATTTTCTTACTTAAAATAAGGA 34 41 1 TTTTCTTATT 0.774739 -27 TAAACGGGCGTTTTCTTTTTTGTTTAAATTC 35 27 1 TTTTCTTTTT 0.939058 -201 AGATCTGATTTTTTCTTAGTTTTCTTTCCCT 35 94 1 TTTTCTTATT 0.774739 -134 ATTTCTTTTGTTTTCTTTGTTTTG 35 214 1 TTTTCTTTTT 0.939058 -14 TACCCAATTTTTTTCATTTTTCAATCTGACG 39 150 1 TTTTCATTTT 0.651275 -24 ******** ** Masking position 4 Map Score: 26.516 Number of sites scoring better than the average of aligned sites = 583 Number in coding regions = 407 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 6 TGGTCAGCACAAAGAAGCCGCTACGGCT 1 255 1 AAAGAGCCGC 0.845662 -18 TTCTCTAACAAAATTAACCGCTTGCGTGCGT 2 61 1 AAATAACCGC 0.980755 -156 AAGTACTTTCAAACAAACCGTAATCAAGTGC 4 260 0 AAACAACCGT 0.724397 -41 AATAACGTGAAATTCACCGCACTTTTCTTT 5 48 0 AAATCACCGC 0.96609 -118 AAATTATTGTAAATAAACCGTGATCTTTGTC 14 59 1 AAATAACCGT 0.918365 -149 CATACTTATGAAAGTAACCGCTTTCAATTTA 14 130 1 AAAGAACCGC 0.969621 -78 AACTTGATTGAAATCAACCGCACT 26 4 0 AAATAACCGC 0.980755 -123 AGTGCGGTAAAAATTCACCGCACTCTTCAAA 27 47 0 AAATCACCGC 0.96609 -43 AATAACGAGAAATTTAACCGCACTTTCGATG 31 109 0 AATTAACCGC 0.855127 -160 AGAGGCACCAAAATCAACCGTTTTTGCAATA 33 271 0 AAATAACCGT 0.918365 -30 TTTAAACAAAAAAGAAAACGCCCGTTTAAAT 35 24 0 AAAGAAACGC 0.696063 -204 AAAAAAGGGGCAATGCACCGCCAAAGCCCCT 35 132 1 CAATCACCGC 0.830243 -96 **** ****** Masking position 2 Map Score: 12.9626 Number of sites scoring better than the average of aligned sites = 465 Number in coding regions = 273 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 7 ACCGCACTTTTCTTTATAATTGCAAGAATTT 5 32 0 TCTTTATAAT 0.514805 -134 ATAATAGATTTATTTATAATTATTTCGTACA 9 156 0 TATTTATAAT 0.734364 -145 AAATCTATTATTTTGATAATCATTCCCATTC 9 176 1 TTTTGATAAC 0.48666 -125 GAATGAATTTTCTTTATAATCTGTAGTCTGA 10 37 0 TCTTTATAAC 0.783488 -135 TAAGCAAAATTTTTTATGATTTAGTTCATAC 14 104 1 TTTTTATGAT 0.637527 -104 TATCGTAAATTATTTATGATCAAAATATAAG 14 159 1 TATTTATGAC 0.857113 -49 AACTTTTTCCTTGTTATAATCTATAAATCTT 14 187 0 TTGTTATAAC 0.647884 -21 ATTAATTTGTTATAATCCATAGAATTT 17 7 1 TTGTTATAAC 0.647884 -134 ATTACATCCTTATTTATGATTAAAAGGCAGC 18 279 0 TATTTATGAT 0.637527 -22 ATTACAAGTTTATTTATAATCTTAAATTTCT 20 37 1 TATTTATAAC 0.90411 -264 TTATATTAATTTTTTATAACTAAAATTCATA 20 198 1 TTTTTATAAT 0.734364 -103 ATAAGTTTGGTTTTTATAATCACGCTTAGAC 20 257 1 TTTTTATAAC 0.90411 -44 TTATTATTTATAAGCATTTATCAAT 21 5 1 TATTTATAAC 0.90411 -296 TTTATCACTATTTTTATGACCACATCAAAGT 21 164 1 TTTTTATGAC 0.857113 -137 TTGAACTTTTTATTTATAAACGAGATATTA 21 281 1 TATTTATAAC 0.90411 -20 AAAAGTCTTCTATTTATTAGCTCAAAAATTC 25 241 0 TATTTATTAC 0.620691 -55 TTCTTGGGATTTTTTATTAATAGCACTTGCA 26 51 1 TTTTTATTAT 0.324232 -76 ATTTTTATACTATTTATAAACAAACTTTTAA 28 110 0 TATTTATAAC 0.90411 -191 TATATAACAATATTTATAAAATTAACGAAGT 31 72 1 TATTTATAAA 0.364651 -197 TTTCTCGTTATTTTTATGAACGGCAGTTTTT 31 128 1 TTTTTATGAC 0.857113 -141 ********* * Masking position 7 Map Score: 14.4591 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 78 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 TCGTAATAGTAGTTCCCCTTTGGGACAGCT 4 55 1 AGTTCCCCTT 0.642061 -246 GAGTTACTGTAATTATCCTAGGGCCTACTT 4 103 1 AATTATCCTA 0.400121 -198 CCTAGGGCCTACTTACCCTAGGCGAAAGTC 4 119 1 ACTTACCCTA 0.658865 -182 TAATTGCAAGAATTTTCCTTACATCGAAAC 5 17 0 AATTTTCCTT 0.763654 -149 TCATTCCATTTCTTATCCTTTCTTTTTTAT 7 250 1 TCTTATCCTT 0.728948 -51 AGGTTTGACATATTTCCCTTTCGGGGTAAG 11 42 0 TATTTCCCTT 0.868897 -213 CACTCAAAAATCTTTTCCTTTCCACCACCG 11 173 1 TCTTTTCCTT 0.820184 -82 GGGAAGATCCACTTCCCCTTAGATTACAAC 16 27 0 ACTTCCCCTT 0.915526 -39 GGGAAGTGGATCTTCCCCTTTTTAAAGAGG 16 40 1 TCTTCCCCTT 0.915526 -26 GATATAAGCAAATTTCCCTTTTTTTAAATA 17 41 0 AATTTCCCTT 0.868897 -100 TGTATTCTCCTTGAATGGACTT 25 3 1 TATTCTCCTT 0.789158 -293 TTCCTACATAAATTACCCTTTTAATGCTAA 25 64 0 AATTACCCTT 0.796236 -232 CTATTGTAAATATTTTCCTACATAAATTAC 25 78 0 TATTTTCCTA 0.530797 -218 AAACATAACAAATTCTCCTTGAGTGTTATT 33 45 0 AATTCTCCTT 0.789158 -256 TGCTGGAGCGTCTTTCCCTTATCCAATTTA 33 154 1 TCTTTCCCTT 0.903438 -147 TTCTTAGTTTTCTTTCCCTAAGAATAAAAA 35 106 1 TCTTTCCCTA 0.766122 -122 ********** Masking position 4 Map Score: 10.4918 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 128 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 9 AAGTTTGAAATGTTTAAATTGCATTGAAAA 1 164 0 TGTTTAAATT 0.895591 -109 TTGGATAAAATGTTTGAATCCTACTTGAAA 5 131 0 TGTTTGAATC 0.720268 -35 AAGAAAAGCATTTTTAAATTTCTCTTGCTA 7 56 0 TTTTTAAATT 0.81855 -245 CAATCTATCTTTTTTAAATAAGGACATCTT 9 281 1 TTTTTAAATA 0.660771 -20 TTATTTATTGTTTTTAAATCTGTTTTGGTA 13 145 0 TTTTTAAATC 0.895591 -31 AATTTCCCTTTTTTTAAATAAAAAAATTCT 17 31 0 TTTTTAAATA 0.660771 -110 AAAAACTTCATCTTTAAATTAAACAAATCT 21 225 1 TCTTTAAATT 0.752224 -76 TGAATGGACTTGTTTAAATCTAATCAGGTT 25 22 1 TGTTTAAATC 0.942217 -274 TCAATCAAGTTTTTTAAATCCCAAAATTTC 26 24 1 TTTTTAAATC 0.895591 -103 ATCTTTAATCTGTTTAAATTTACAGTTATT 28 276 0 TGTTTAAATT 0.895591 -25 GTTTAAATGGCGTTTAAATCT 35 2 0 CGTTTAAATC 0.720263 -226 TTTTCTTTTTTGTTTAAATTCTTAGTTTTT 35 37 1 TGTTTAAATT 0.895591 -191 AAATAGCCTCTCTTTAAATCCCTTGTTTAT 39 100 0 TCTTTAAATC 0.852358 -74 ********** Masking position 7 Map Score: 8.60514 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 80 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 10 AAGTCAAAATAAAAATTTTGGTATTTTTCTTTAATG 6 19 0 AAAATTTTTT 0.450019 -146 CCATTCGGATAGAAACCTAATTGCTTGTTTTTTCTA 7 89 1 AAAACTTCTT 0.381091 -212 TGGAATGAAAAGAAAATGGATTTTTTGGCATATTAG 7 222 0 AAAATGTTTT 0.487822 -79 ATAATTATAAATAAATCTATTATTTTGATAATCATT 9 164 1 AAAACTATTT 0.908383 -137 ACCATTGTTGAAAACACGGCGATTTT 10 156 1 AAACCGATTT 0.608535 -16 CGTTCATCATAAAACACGCAAATTTTGCGCGCGCGC 11 93 0 AAACCGATTT 0.607876 -162 TCACTCACTCAAAAATCTTTTCCTTTCCACCACCGC 11 168 1 AAAACTCTTT 0.558183 -87 ATTATTGTAAATAAACCGTGATCTTTGTCACAAAAT 14 61 1 AAAACGTTTT 0.908582 -147 TACGATAAATTGAAAGCGGTTACTTTCATAAGTATG 14 130 0 TAAACGATTT 0.354453 -78 GTTATAATCTATAAATCTTATATTTTGATCATAAAT 14 170 0 AAAACTATTT 0.908773 -38 ATGATTACATAAAAAATTATGAATTTGTGATCCATG 15 18 0 AAAATTATTT 0.487215 -73 TTTTTTATTTAAAAAAAGGGAAATTTGCTTATATCT 17 36 1 AAAAAGATTT 0.522684 -105 ACCATAAATAAATAATCTTTTTTTTTCATAAGTTTG 20 230 1 ATAACTTTTT 0.285907 -71 GCGATAAAAGAAAAAACTTCATCTTTAAATTAAACA 21 214 1 AAAACTTTTT 0.895472 -87 TTTAAATTAAACAAATCTAACTTTTTCAGGTCATAT 21 237 1 AAAACTTTTT 0.888772 -64 GTTTTTCACAAAAATACGAAAAATTTCATCACCTAG 23 24 0 AAATCGATTT 0.362215 -210 AAGTGCGGTTAAAAATCGTCGTATTTTTTGACCGCA 24 27 1 AAAACGTTTT 0.90799 -54 GACACAACTCACAAAACTCAATTTTTCTTCAAATAA 25 180 1 AAAACTTTTT 0.887646 -116 ACAAATCTTTACAAAAATGAATTTTTGAGCTAATAA 25 223 1 AAAAATTTTT 0.453242 -73 TTTTGAGCTAATAAATAGAAGACTTTTTATAAAAAT 25 245 1 AAAAAGATTT 0.522862 -51 AATTATGCATAAAAATGTAATATTTTTTCATCTTAT 26 83 1 AAAAGTATTT 0.488643 -44 TGGAAAAATGAGAAACCTTGCATTTTAGGAATGAGA 28 64 1 AAAACTATTT 0.908706 -237 TGATATACTCACAAATCTTATTGTTTCACAAGATAG 28 230 1 AAAACTTTTT 0.89649 -71 AAAAGGTTTCACAAACCTTTGAATTTAAAATAGAAT 29 16 1 AAAACTATTT 0.908779 -57 AAAAAAACGCCTTGATTGTGCGTCAAG 29 56 0 AAAACGTATT 0.322937 -17 CCGTTCATAAAAATAACGAGAAATTTAACCGCACTT 31 115 0 AATACGATTT 0.347658 -154 AAATTATTGCAAAAACGGTTGATTTTGGTGCCTCTG 33 267 1 AAAAGGATTT 0.541521 -34 AAATGAACCAGAAAAACTAAGAATTTAAACAAAAAA 35 42 0 GAAACTATTT 0.414605 -186 TAAATCAACCAAAGATCTGATTTTTTCTTAGTTTTC 35 82 1 AAGACTTTTT 0.375722 -146 * *** ** * *** Masking position 15 Map Score: 13.7367 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 241 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 GCAAAATGACATACAGAAACGGCAAACATAACGGAAGC 2 178 0 ACGAACGAAA 0.986843 -39 GATACCCGTGAACCTGAAACAGTTAGCACTGACGTAGG 7 181 1 ACGAACGAGA 0.946019 -120 AAAATCCCTTAGGAAAAAACTGGCAAAATCTTACCCCG 11 13 1 AAAAACGAAA 0.706743 -242 TTATTGGCAAAAGCGGAAGCCGCAAAAAGTGCGGTGGT 11 196 0 ACGAACGAAA 0.986843 -59 ATTTACATTCAATCGGAATCGGAGAATAAA 12 3 0 ACGAACGAAA 0.986843 -165 CATACCCGTGAACCTGAAACAGTTAATACTGACGTAGG 18 202 1 ACGAACGAAA 0.986843 -99 TCTTTATATGAGAAAGAAACTGGGAATAAAGTTAATTA 33 197 1 AAGAACGAAA 0.960912 -104 TGATTTAGTCAAAATGAACCAGAAAAACTAAGAATTTA 35 51 0 AAGAACGAAC 0.851713 -177 GCCCTGCTGAAAGCTGAAACGGCGCAAATGGCGTTAAA 36 63 1 ACGAACGCAA 0.946019 -33 * * *** * * ** * Masking position 8 Map Score: 4.5972 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 9 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 TCCAAATATTGCGTGCGTGTATTTGAAAAA 2 11 1 GCGTGCGTGT 0.974079 -206 AATTGTAAACGCGTGCGTGAATTTTTTCAA 2 33 0 GCGTGCGTGA 0.993477 -184 TTAACCGCTTGCGTGCGTGAACTGAAAAGT 2 74 1 GCGTGCGTGA 0.993477 -143 ATGTCATTTTGCGTGCGACAGAA 2 204 1 GCGTGCGACA 0.914334 -13 TGATTAAAGGGAGTGCGTAATAAAAAAGAA 7 269 0 GAGTGCGTAA 0.907947 -32 AAAGATTTTTGAGTGAGTGAGCAAAGAATT 11 158 0 GAGTGAGTGA 0.888429 -97 ********** Masking position 4 Map Score: 2.45674 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 22 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 13 TACTGCGAGGTTGTATGAACGCAAAAAAACTTTC 4 159 1 TTGTTAAGAA 0.671014 -142 CCGCACTTTTCTTTATAATTGCAAGAATTTTCCT 5 28 0 CTTTTATGAA 0.643132 -138 ACGATCTCCGTTGTATCTTAGCAAGAGAAATTTA 7 38 1 TTGTTTTGAA 0.520564 -263 AAGTTTACGCTTGTTTGGTAGAAAAAACAAGCAA 7 109 0 TTGTTGTGAA 0.616751 -192 TTTTATATTGTTTTGGAATGGGAATGATTATCAA 9 188 0 TTTTGATGAA 0.672564 -113 TGAATAATGCTTTTTCCATAGGAATGAATTTTCT 10 55 0 TTTTCATGAA 0.8463 -117 TTATCTATATTTGTCTTATCGAAACGTTTCGATA 12 126 1 TTGTTATGAA 0.931114 -42 AAAAGCTCCTTTTTGTTATCGAAACGTTTCGATA 12 142 0 TTTTTATGAA 0.938029 -26 GACTCCTGTTTTTTATCAATGTAAACGATTACAT 14 14 1 TTTTTAAGAA 0.695508 -194 TAAACTTGTAATGTCTAATAGAAAAGCAGCGTAT 20 15 0 ATGTTATGAA 0.520565 -286 TAGAAAGGCATTTTTTTACTGAAATTTTATAAGA 20 83 1 TTTTTACGAA 0.657481 -218 ATTATTTTCTTATTTTGATAGTAATCACTTATAT 20 170 1 TATTTATGAA 0.533949 -131 TTAATAATACTTTGTTTATGGAAAATAAACATTG 21 32 0 TTTGTATGAA 0.629356 -269 AGATTAAAATTTTTGTAATAGTAACATTCTTTTT 21 111 0 TTTTTATGAA 0.938038 -190 ATGAAGTTTTTTCTTTTATCGCAACACATCTCTT 21 202 0 TTCTTATGAA 0.722129 -99 TGGAGAAAGATTTTATAATTGAAAGCCTTTTTTA 23 148 1 TTTTTATGAA 0.938037 -86 TTAATGCTAATTGTGCTATCGTAACCTGATTAGA 25 40 0 TTGTCATGAA 0.830991 -256 ATGTATTGATTTTTCCTATTGTAAATATTTTCCT 25 89 0 TTTTCATGAA 0.8463 -207 **** * ** * ** Masking position 13 Map Score: 6.19372 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 90 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 TACAATTCTCTAACAAAATTAACCGCTTGC 2 56 1 TAACAAAATT 0.6765 -161 AGCATTGTGGTAACAAAAGTCAAAATAAAA 6 41 0 TAACAAAAGT 0.892571 -124 AACTTAATACTAACCAAAATGTTTTGTTCT 9 103 1 TAACCAAAAT 0.718414 -198 CAAATATAGATAACAAAAATAGAAAAACAA 12 109 0 TAACAAAAAT 0.936955 -59 AACGTTTCGATAACAAAAAGGAGCTTTTAG 12 148 1 TAACAAAAAG 0.882389 -20 CATGTCAAATTGACAAAAATTATCTATTTA 13 27 1 TGACAAAAAT 0.756062 -149 CCTTAGATTACAACAAAAATTGATGGGAAA 16 11 0 CAACAAAAAT 0.700962 -55 TAATTTTTTATAACTAAAATTCATAAACCA 20 204 1 TAACTAAAAT 0.632541 -97 AATGTTACTATTACAAAAATTTTAATCTAT 21 117 1 TTACAAAAAT 0.786667 -184 AGTTAGTTTTTCACAAAAATACGAAAAATT 23 35 0 TCACAAAAAT 0.756062 -199 TGACAAATCTTTACAAAAATGAATTTTTGA 25 221 1 TTACAAAAAT 0.786667 -75 TTAACAAAAGGTTTCACAAAC 29 2 1 TAACAAAAGG 0.807482 -71 TGCTCTATAATAACAAAAGGGCAGAAATAT 39 40 0 TAACAAAAGG 0.807482 -134 ********** Masking position 6 Map Score: 4.09554 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 46 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 15 CTTTCAAACAAACCGTAATCAAGTGCATTG 4 256 0 AACCGTAATC 0.823234 -45 GAATTTTAAAAACTGTGAACTTCATCACGG 5 88 1 AACTGTGAAC 0.910493 -78 CTGAGATGATACCCGTGAACCTGAAACAGT 7 174 1 ACCCGTGAAC 0.961476 -127 ATTGTAAATAAACCGTGATCTTTGTCACAA 14 64 1 AACCGTGATC 0.96785 -144 CTGAGATCATACCCGTGAACCTGAAACAGT 18 195 1 ACCCGTGAAC 0.961476 -106 GTTTTTTCACAACTGTGATCCACGCCACAG 23 111 0 AACTGTGATC 0.910493 -123 ********** Masking position 6 Map Score: 2.089 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 12 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701