AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_hinf_reg_300.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 HI0062 258 dnaK suppressor protein (dksA) #2 HI0063 247 poly(A) polymerase (pcnB) #3 HI0393 48 conserved hypothetical GTP-binding protein #4 HI0394 166 peptidyl-tRNA hydrolase (pth) #5 HI0405 72 pyridoxine kinase, putative #6 HI0406 89 acetyl-CoA carboxylase, carboxyl transferase (accA) #7 HI0408 171 ABC transporter, ATP-binding protein (yebM) #8 HI0638 128 conserved hypothetical protein #9 HI0639 22 adenylosuccinate lyase (purB) #10 HI0640 271 ribosomal protein L10 (rpL10) #11 HI0641 54 ribosomal protein L7/L12 (rpL7/L12) #12 HI0642 159 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #13 HI1334 126 cell division protein (ftsJ) #14 HI1335 90 cell division protein (ftsH) #15 HI1336 111 dihydropteroate synthase (folP-1) #16 HI1337 37 mrsA protein (mrsA) #17 HI1603 207 conserved hypothetical protein #18 HI1604 24 phosphate permease, putative #19 HI1605 65 conserved hypothetical protein #20 HI1607 62 hemM protein (hemM) #21 HI1630 166 ribosomal protein L25 (rpL25) Motif number 1 GTTAATTTTAACCGCACTTTTGTATTTTTC 2 22 0 ACCGCACTTT 0.998796 -226 GTTAAAATTAACCGCACTTTTTTGCATTTA 2 40 1 ACCGCACTTT 0.998796 -208 ATTAAAAGTCACCGCACTTTTCCGTTATAA 4 41 0 ACCGCACTTT 0.998796 -126 GGTAAAAATCACCGCTCTTTTAGAATGTTA 5 12 0 ACCGCTCTTT 0.996983 -61 GGTGATTTTTACCGCTCTTTTTTGATCTAA 5 29 1 ACCGCTCTTT 0.996983 -44 GTAAAAATCGACCGCACTTTATCAAGGAAT 6 50 0 ACCGCACTTT 0.998796 -40 TGGGGAAAATAACGCATTTTTATAGAATTC 7 126 0 AACGCATTTT 0.909686 -46 GAGAAAATCAACCGCTCTTTTTTATTAGGA 13 17 0 ACCGCTCTTT 0.996983 -110 CTAAAAATTAACCGCATTTT 15 102 1 ACCGCATTTT 0.992238 -10 GTTAAAATTAACCGCACTTTTTATTGAGAT 19 14 0 ACCGCACTTT 0.998796 -52 GTTAATTTTAACCGCACTTTTGTTGTGATG 19 32 1 ACCGCACTTT 0.998796 -34 ********** Masking position 1 Map Score: 45.9838 Number of sites scoring better than the average of aligned sites = 1183 Number in coding regions = 748 Number in noncoding regions = 435 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 2 TGAAAAATACAAAAGTGCGGTTAAAATTAA 2 21 1 AAAAGTGCGG 0.994855 -227 TTAAATGCAAAAAAGTGCGGTTAATTTTAA 2 41 0 AAAAGTGCGG 0.994855 -207 TTTTGCATTTAAAAATGCAGGAAAATCCAC 2 59 1 AAAAATGCAG 0.758617 -189 TCTTTACAAGAAAAGAGCCAAGTCATTTAT 2 98 1 AAAAGAGCCA 0.931428 -150 ATTATAACGGAAAAGTGCGGTGACTTTTAA 4 40 1 AAAAGTGCGG 0.994855 -127 CTAACATTCTAAAAGAGCGGTGATTTTTAC 5 11 1 AAAAGAGCGG 0.995406 -62 TTTAGATCAAAAAAGAGCGGTAAAAATCAC 5 30 0 AAAAGAGCGG 0.995406 -43 AATTCCTTGATAAAGTGCGGTCGATTTTTA 6 49 1 TAAAGTGCGG 0.939512 -41 TGTTATCCTAAAAAGACCGTAAAAATCGAC 6 68 0 AAAAGACCGT 0.906512 -22 AGAATTCTATAAAAATGCGTTATTTTCCCC 7 125 1 AAAAATGCGT 0.911338 -47 CTCGAACATTAAAAAAGCCTAGAGTTTCTG 8 51 0 AAAAAAGCCT 0.735804 -78 TATTGTTGAAAAAAGAGCCAAATTC 10 6 0 AAAAGAGCCA 0.931428 -266 TTTAAAATTCAAAAAACCGATGGGAAACCA 12 27 1 AAAAAACCGA 0.771215 -133 TTTATATAAGAAAAAACCGATGGTTTCCCA 12 47 0 AAAAAACCGA 0.771215 -113 TTCCTAATAAAAAAGAGCGGTTGATTTTCT 13 16 1 AAAAGAGCGG 0.995406 -111 GATCTCAATAAAAAGTGCGGTTAATTTTAA 19 13 1 AAAAGTGCGG 0.994855 -53 ACATCACAACAAAAGTGCGGTTAAAATTAA 19 33 0 AAAAGTGCGG 0.994855 -33 ********** Masking position 4 Map Score: 40.918 Number of sites scoring better than the average of aligned sites = 1662 Number in coding regions = 1115 Number in noncoding regions = 547 Number of orfs with sites within 600 bp upstream = 345 Fraction of orfs with sites within 600 bp upstream = 0.0554128 Motif number 3 TAAAAATAAATTTTTCAGGAAAATTTACTTGCT 1 102 1 TTTAGGAAAA 0.526606 -157 AGTTGTTTGTTTTAGCAAGTAAATTTTCCTGAA 1 115 0 TTAAAGTAAA 0.587543 -144 TTGCATTTAAAAATGCAGGAAAATCCACTTGCC 2 61 1 AATAGGAAAA 0.815081 -187 TTCCAACAACAAAACGGAGTAAATTATTCTTAC 2 128 1 AAAGAGTAAA 0.901099 -120 GTTTTACTCAAAATAAGGGAAAAATT 3 33 1 AATGGGAAAA 0.876776 -16 AAATTTTTTAACAAAGAAGTAAAA 4 2 0 AAAAAGTAAA 0.849491 -165 TAAATATACAACAAAGGAGAAAATATA 5 56 1 AAAGAGAAAA 0.967428 -17 CAGACTACAGATTATAAAGAAAATTCATTCCTA 7 38 1 ATAAAGAAAA 0.938063 -134 AATATTCGACATAAGAGAGAAAATCTTGAGAAT 7 97 1 AAAGAGAAAA 0.967428 -75 TAGTAAATATCAGGAAAACGTTTCCGTT 8 111 0 ATAAGGAAAA 0.903646 -18 CAGGCGCAGGATTATAGAGAAAAGCTATGTTCT 10 45 0 ATAGAGAAAA 0.960706 -227 TTCGGCGCCCAGAAGCAAGAAAAATTCTTATTC 10 180 0 AAAAAGAAAA 0.948451 -92 TAACAAACTTTTATATAAGAAAAAACCGATGGT 12 53 0 TATAAGAAAA 0.685885 -107 GTTATTGATGAATAAAGAGAAAATTT 12 144 1 ATAGAGAAAA 0.960706 -16 ATCAGTAAAAAACATTGAGAAAATCAACCGCTC 13 30 0 ACAGAGAAAA 0.903693 -97 CAAGAACAAAATCATTAGGAAAAAATAAAGCCT 15 34 0 ACAAGGAAAA 0.782581 -78 TTTTCGCTTTAAAAGCGAGAAAATTTGAAAGGT 17 17 0 AAAGAGAAAA 0.967428 -191 TTTCAAAAAAATTTGTAAGAAAAAAGGTTTATC 17 112 0 ATTAAGAAAA 0.854212 -96 TTAACCCCTTAATTTGGAGTAAATCACTT 17 189 1 ATTGAGTAAA 0.743693 -19 TGTTGTGATGTTTAAGGGGAAAAA 19 52 1 TTAGGGAAAA 0.822822 -14 AGGATTTAGTTTAATTGAGTAAAGTTACTTTTA 20 15 0 TAAGAGTAAA 0.736486 -48 AATTAATGTTAAAAGAAAGAAAATCGCAGGCGA 21 128 0 AAAAAGAAAA 0.948451 -39 * ** ******* Masking position 11 Map Score: 30.0068 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 307 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 4 TTCCTGCATTTTTAAATGCAAAAAAGTGCGGTTA 2 48 0 TTAAAGAAAA 0.950017 -200 GGCTCTTTTCTTGTAAAGAAAAAGGCAAGTGGAT 2 83 0 TTTAAGAAAG 0.858409 -165 CACTTTTCCGTTATAATGGCTAAAATTTTTTAAC 4 23 0 TTTAAGTAAA 0.887127 -144 GTGCGGTGACTTTTAATGATAAATCACGCGCAAT 4 54 1 TTTAAGAAAT 0.689617 -113 TAGTGGCGTATTGTAGCGAAAAAGCCTTAAATTC 4 121 0 TTTAGGAAAG 0.806549 -46 AGAAAATTCATTCCTATGGAAAAAGCATTATTCA 7 55 1 TTCTAGAAAA 0.761404 -117 AAAAGCATTATTCAAACGCTTAAATATTCGACAT 7 75 1 TTAAAGTAAA 0.81903 -97 TCGGAGTGTATTCAGGAGCTAAAAGCCA 10 254 1 TTAGGGAAAA 0.845514 -18 TTTTTGAATTTTAAAGTGGTTAAAATAGAAA 12 8 0 TTAAGGTAAA 0.860067 -152 AAATGGTAAGTTTTTAAGTAAAAACTATAACAAA 12 79 0 TTTTAGAAAA 0.813013 -81 TAACCTACCTTTCCTAAGTTAAAAAATTTCGTCA 14 54 0 TTCTAGAAAA 0.761319 -37 TGGTTTTATAACGATAAAAAATTAAAGGA 16 6 1 TTTAAGAAAA 0.950156 -32 GCGAGAAAATTTGAAAGGTAAAAAA 17 2 0 TTAAAGAAAA 0.964633 -206 ATTTTCTCGCTTTTAAAGCGAAAAGTGTATTGAG 17 26 1 TTTAAGAAAA 0.95602 -182 TTACTCCAAATTAAGGGGTTAAAAATTCGTGCGC 17 177 0 TTAGGGAAAA 0.845105 -31 TGTTGTGATGTTTAAGGGGAAAAA 19 52 1 TTAAGGAAAA 0.949408 -14 GCTTTTTGATTTGAAAAGATTAAAAT 21 3 0 TTAAAGTAAA 0.899334 -164 ** *** * **** Masking position 12 Map Score: 17.8989 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 188 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 GCCAAACAAATTTTTGATATAAGTAAGAATAA 2 151 0 TTTTTGATTA 0.950316 -97 TACGCCACTATTTTTTACATCATCAAATAAAA 4 145 1 TTTTTTACTA 0.841629 -22 TTACCGCTCTTTTTTGATCTAAATATACAACA 5 37 1 TTTTTGATTA 0.950327 -36 TGCTGAAAACTTTTTTATTTTAGGG 7 4 0 TTTTTTATTA 0.932649 -168 AAGCCTAGAGTTTCTGATATGATGTGTGAACA 8 35 0 TTTCTGATTA 0.951208 -94 TTATTAAGCGTTTCTTACTTCATCTAACTTTA 11 11 1 TTTCTTACTA 0.844131 -44 TCATCTAACTTTATTTATTTTAGGAATTGATT 11 30 1 TTATTTATTA 0.865043 -25 CCATCGGTTTTTTCTTATATAAAAGTTTGTTA 12 54 1 TTTCTTATTA 0.933365 -106 TCAATGTTTTTTACTGATTTCAATTAGCTTCG 13 45 1 TTACTGATTA 0.900251 -82 TGTGACGAAATTTTTTAACTTAGGAAAGGTAG 14 52 1 TTTTTTAATA 0.66083 -39 GTGTATTGAGTTACTTATCTTACCACACTAGG 17 50 1 TTACTTATTA 0.867225 -158 ACCGCACTTTTTATTGAGATCAA 19 2 0 TTATTGAGTA 0.648757 -64 TTTTCTAGGCTTTTTGATTTGAAAAGATTAAA 21 13 0 TTTTTGATTA 0.950327 -154 ******** * * Masking position 7 Map Score: 12.9164 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 113 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 6 AAAAATAAATTTTTCAGGAAAATTTACTTG 1 103 1 TTTTCAGGAA 0.841365 -156 TGCCTTTTTCTTTACAAGAAAAGAGCCAAG 2 90 1 TTTACAAGAA 0.934061 -158 AAGTCATTTATTTCCAACAACAAAACGGAG 2 117 1 TTTCCAACAA 0.931011 -131 TGGCTAAAATTTTTTAACAAAGAAGTAAAA 4 11 0 TTTTTAACAA 0.769781 -156 TTGATCTAAATATACAACAAAGGAGAAAAT 5 50 1 TATACAACAA 0.784223 -23 AATCGCCGTGTTTTCAACAATGGTTGGGGA 7 150 0 TTTTCAACAA 0.973069 -22 TTTGGCTCTTTTTTCAACAATATTCTTTAC 10 14 1 TTTTCAACAA 0.973069 -258 AACAATATTCTTTACAAGAACATAGCTTTT 10 29 1 TTTACAAGAA 0.934061 -243 TAGTTAAAATTTTTCAAAAAAATTTGTAAG 17 126 0 TTTTCAAAAA 0.835951 -82 ********** Masking position 6 Map Score: 7.26868 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 144 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 TATAAAAGATTAATTCCAGCCTCTCTAAGCCT 1 14 1 TAATCAGCCT 0.950943 -245 CATATTTAAATAAAACTAGCCTAGGCTTAGAG 1 36 0 TAAACAGCCT 0.925298 -223 AAAGTGCGGTTAATTTTAACCGCACTTTTGTA 2 28 0 TAATTAACCG 0.741462 -220 AAAACGGTTGTAAAACTAACCGCACTT 3 6 0 TAAACAACCG 0.866575 -43 ATCATATCAGAAACTCTAGGCTTTTTTAATGT 8 44 1 AAATCAGGCT 0.747568 -85 AATATTGTTGAAAAAAGAGCCAAATTC 10 6 0 AAAAAAGCCA 0.494994 -266 ACAATCTGTCAAATTCAAGCCGAAGCTAATTG 13 65 0 AAATCAGCCG 0.972331 -62 ATCGTTCAAAGTCTAACCTACCTTTCCTA 14 72 0 AAATCAACCT 0.932119 -19 TCATTAGGAAAAAATAAAGCCTTTCCGAAGAA 15 24 0 AAATAAGCCT 0.895393 -88 AAATCACTCTAAAAATTAACCGCATTTT 15 94 1 AAAATAACCG 0.741462 -18 AAAGTGCGGTTAATTTTAACCGCACTTTTGTT 19 24 1 TAATTAACCG 0.741462 -42 TTACTCAATTAAACTAAATCCTTAAAATATGC 20 26 1 AAATAATCCT 0.488713 -37 AAAACCGCTCAAAGACAAGCCTTGAGAGCCGT 21 80 0 AAAACAGCCT 0.950943 -87 *** ** ***** Masking position 8 Map Score: 5.9235 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 204 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 TAGAGAGGCTGGAATTAATCTTTTATAAAA 1 11 0 GGAATTAATC 0.964244 -248 TTTTGTTGTTGGAAATAAATGACTTGGCTC 2 112 0 GGAAATAAAT 0.881808 -136 ACTTTATCAAGGAATTAAACTGTGGCGCAA 6 35 0 GGAATTAAAC 0.953939 -55 TTTTTCCATAGGAATGAATTTTCTTTATAA 7 49 0 GGAATGAATT 0.872957 -123 CCGATTACTCGGAATTAATTTACCTAATCC 10 228 0 GGAATTAATT 0.957139 -44 ATTTATTTTAGGAATTGATTGTT 11 42 1 GGAATTGATT 0.872957 -13 ACAAAACATAGGAAATAAACT 18 14 1 GGAAATAAAC 0.900096 -11 ********** Masking position 4 Map Score: 4.11144 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 56 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 AAACGGTTGCTTCAAATTTTGCGATCCATAT 1 69 1 TCAAATTTTG 0.7308 -190 ATATCGTAAAAATAAATTTTTCAGGAAAATT 1 96 1 ATAAATTTTT 0.682352 -163 TATTTTAGGAACCCAATTTTTGCGGGCGGTA 1 159 0 ACCAATTTTT 0.796055 -100 CTTCTTGCCAAACAAATTTTTGATATAAGTA 2 158 0 ACAAATTTTT 0.959182 -90 GTCTGAATGCTGAAAACTTTTTTATTTTAGG 7 12 0 TAAAACTTTT 0.641433 -160 ACAATTCTGGAGCAAACATTT 9 12 1 ACAAACATTT 0.659151 -11 TAGTCAATCTAACAAATTTCTGGTTGGTGCT 10 81 1 ACAAATTTCT 0.794418 -191 TAAAAACTATAACAAACTTTTATATAAGAAA 12 64 0 ACAAACTTTT 0.947796 -96 GTATCTTGTGACGAAATTTTTTAACTTAGGA 14 46 1 AGAAATTTTT 0.762123 -45 TTTTTTACCTTTCAAATTTTCTCGCTTTTAA 17 11 1 TCAAATTTTC 0.7308 -197 CCTTTTTTCTTACAAATTTTTTTGAAAAATT 17 118 1 TCAAATTTTT 0.940471 -90 TTGTTGATAGTTAAAATTTTTCAAAAAAATT 17 132 0 TAAAATTTTT 0.70894 -76 TTATTTTCAAATCAAACTTTTTTCTAGGCTT 21 33 0 ACAAACTTTT 0.94784 -134 * ********* Masking position 6 Map Score: 5.99312 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 245 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 10 TGGCTCTTTTCTTGTAAAGAAAAAGGCAAG 2 88 0 CTTGTAAAGA 0.706314 -160 AATTTTAGCCATTATAACGGAAAAGTGCGG 4 30 1 ATTATAACGG 0.481755 -137 ATAGTGGCGTATTGTAGCGAAAAAGCCTTA 4 126 0 ATTGTAGCGA 0.889453 -41 CAGACTACAGATTATAAAGAAAATTCATTC 7 38 1 ATTATAAAGA 0.852592 -134 AAGCTATGTTCTTGTAAAGAATATTGTTGA 10 27 0 CTTGTAAAGA 0.706314 -245 CAGGCGCAGGATTATAGAGAAAAGCTATGT 10 48 0 ATTATAGAGA 0.914915 -224 GTTATTGATGAATAAAGAGAAAATTT 12 144 1 AATAAAGAGA 0.346297 -16 TTGGTGGGCGATTATAGCGAAATACATCCA 15 65 0 ATTATAGCGA 0.916369 -47 TGGTTTTATAACGATAAAAAATTA 16 5 1 TTTATAACGA 0.832207 -33 TTTTCTCGCTTTTAAAGCGAAAAGTGTATT 17 27 1 TTTAAAGCGA 0.810199 -181 AACCGCACTTTTTATTGAGATCAA 19 5 0 TTTATTGAGA 0.490563 -61 GGCTTTTTGATTTGAAAAGATTAAAAT 21 8 0 TTTGAAAAGA 0.623291 -159 TTAACATTAATTTAAAGAGAACATTAAA 21 149 1 TTTAAAGAGA 0.807288 -18 ********** Masking position 3 Map Score: 3.36092 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 161 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 11 CAAGTAAATTTTCCTGAAAAATTTATTTTTA 1 102 0 TTCCTAAAAA 0.843819 -157 GAAAATTTACTTGCTAAAACAAACAACTTCT 1 120 1 TTGCTAAACA 0.919834 -139 TTTTGTCTTCTTGCCAAACAAATTTTTGATA 2 164 0 TTGCCAACAA 0.950328 -84 TCAAAAGAGGTTGCCAAAACAAGTGCTCATT 2 198 1 TTGCCAAACA 0.962168 -50 TTTTACTTCTTTGTTAAAAAATTTTAGCCAT 4 11 1 TTGTTAAAAA 0.52086 -156 GCTTGCCCAACCAGTGAAAACCA 6 3 1 TTGCCAACCA 0.934285 -87 TTTGTTATCCTAAAAAGACCGTAAAA 6 74 0 TATCCAAAAA 0.611372 -16 ATGCGTTATTTTCCCCAACCATTGTTGAAAA 7 139 1 TTCCCAACCA 0.834191 -33 GTAAAGAATATTGTTGAAAAAAGAGCCAAAT 10 13 0 TTGTTAAAAA 0.52086 -259 GTTATAGTTTTTACTTAAAAACTTACCATTT 12 82 1 TTACTAAAAA 0.66995 -78 AAATAAAGCCTTTCCGAAGAAAGGCTTTGAT 15 14 0 TTTCCAAGAA 0.754797 -98 AGTTAAAATTTTTCAAAAAAATTTGTAAGAA 17 124 0 TTTCAAAAAA 0.622477 -84 ACCCAGCAATTTTCCTAAAAACCGCTCAAAG 21 98 0 TTTCCAAAAA 0.936213 -69 ***** ***** Masking position 7 Map Score: 4.3256 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 447 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 12 AGTGCGGTTAATTTTAACCGCACTTTTGTA 2 28 0 ATTTTAACCG 0.960665 -220 AAAATGCGTTATTTTCCCCAACCATTGTTG 7 136 1 ATTTTCCCCA 0.850886 -36 TTTCTATTTTAACCACTTTAAAATT 12 6 1 ATTTTAACCA 0.925544 -154 CTAAGATAGAATATTACCCGTTGTTATTGA 12 122 1 ATATTACCCG 0.974967 -38 AATTTGACAGATTGTACCCAAATATAGGCG 13 82 1 ATTGTACCCA 0.850886 -45 ATCACTCTAAAAATTAACCGCATTTT 15 96 1 AAATTAACCG 0.757576 -16 ACACTAGGAAATATTACCCAGTTGCTTACT 17 74 1 ATATTACCCA 0.951977 -134 ATTCGTGCGCATATTACCCGATTTTTGTTG 17 157 0 ATATTACCCG 0.974967 -51 AGTGCGGTTAATTTTAACCGCACTTTTGTT 19 26 1 ATTTTAACCG 0.960665 -40 ********** Masking position 5 Map Score: 10.5371 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 58 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 TCCAGCCTCTCTAAGCCTAGGCTAGTTTTAT 1 28 1 CTAAGCTAGG 0.961872 -231 CGAACATTAAAAAAGCCTAGAGTTTCTGATA 8 48 0 AAAAGCTAGA 0.840793 -81 TGTTCGAGTTCAAAAGCTAGGTTAAAAATGC 8 73 1 CAAAACTAGG 0.973825 -56 TTACCTAATCCTAAGACTAGGATGACTTCGG 10 208 0 CTAAGCTAGG 0.961872 -64 CAGATTGTACCCAAATATAGGCGAAACGACT 13 89 1 CCAAAATAGG 0.841797 -38 GAAACGACTACAAAAAATAGAAGATT 13 111 1 CAAAAATAGA 0.850526 -16 TCAACAAAACATAGGAAATAAACT 18 5 1 CAAAAATAGG 0.935719 -20 TTTCAAATCAAAAAGCCTAGAAAAAAGTTTG 21 21 1 AAAAGCTAGA 0.840793 -146 ***** ***** Masking position 4 Map Score: 2.454 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 35 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 ATTTAAATATGCAAACGGTTGCTTCAAATT 1 57 1 GCAAACGGTT 0.959424 -202 AAAGAAAAAGGCAAGTGGATTTTCCTGCAT 2 73 0 GCAAGTGGAT 0.924158 -175 AAACTGTGGCGCAAATGGTTTTCACTGGTT 6 19 0 GCAAATGGTT 0.981305 -71 TAGAAAGATAGCAAATGGTAAGTTTTTAAG 12 95 0 GCAAATGGTA 0.941016 -65 GACTAAGTAAGCAACTGGGTAATATTTCCT 17 79 0 GCAACTGGGT 0.947535 -129 ********** Masking position 4 Map Score: 0.107414 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 34 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 15 ********** No masking Map Score: -3.65686e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0