AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00071_bsub_reg_300.orf -o00071_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 yhfI 151 similar to hypothetical proteins #5 yhfK 64 similar to hypothetical proteins #6 yhfL 116 similar to long-chain fatty-acid-CoA ligase #7 yhfU 134 similar to biotin biosynthesis #8 yhfV 138 similar to methyl-accepting chemotaxis protein #9 yhfW 111 similar to hypothetical proteins #10 mmgA 137 acetyl-CoA acetyltransferase #11 yqiK 78 similar to glycerophosphodiester phosphodiesterase #12 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #13 yraG 248 similar to spore coat protein #14 lcfA 188 long chain acyl-CoA synthetase #15 yshC 73 similar to DNA polymerase beta #16 yshA 133 yshA #17 gbsA 198 glycine betaine aldehyde dehydrogenase #18 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #19 yusM 300 similar to proline dehydrogenase #20 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #21 aldX 142 aldehyde dehydrogenase Motif number 1 TTTATAAATCTTACTGCTTATTTTCAAAATGTTT 1 81 0 TTCTCTATTT 0.834515 -220 AGATATTGACTTATTGTTTATTTGTCTTACAATT 2 104 1 TTTTTTATTG 0.912492 -123 GTAAGCGCTTTTATTAATTTTTCTTTCACATCCG 2 163 0 TTTTATTTTT 0.839364 -64 ATCAAAACAGTTATTGATTTTTGTAATCTGTTAT 4 46 0 TTTTATTTTT 0.839364 -106 TCTTGAGTGTTTTTTTCTGTTTCTCTATAATGGA 6 37 1 TTTTCTTTTT 0.924495 -80 TTTTTAAGCCTTTTTCTTTTTTATCGGCCAAGGG 8 71 0 TTTTTTTTTT 0.932027 -68 AAAAATATAATTTTTACTTTTTGGCTTTTTAAGC 8 96 0 TTTTCTTTTG 0.937162 -43 CCAATCAGATTTATTCTTAATTTTTCCATATTCT 9 76 0 TTTTTTATTT 0.895406 -36 AAGAAGCAACTTTTTATTCATTTTAAAAAATTTG 12 74 0 TTTTTTATTT 0.895406 -227 TTTCCGCTAATTTTTTCTAATTGGCGCCTCAATT 12 106 1 TTTTCTATTG 0.90302 -195 TGACCACCTCTTCCTGATGTTTGGCTTTTATCTT 12 276 0 TTCTATTTTG 0.807638 -25 AGCGGGAATCTTTTTGTTAATTGGTCTTATATAT 14 58 1 TTTTTTATTG 0.912492 -131 AGATTTACCTTTCTTTTTCTTTTTTTTGCCGTCC 14 116 1 TTTTTTTTTT 0.932027 -73 TTTTTGACTTTTCCTCATGTTTCGTTAAGATAAA 17 66 0 TTCTATTTTG 0.807638 -133 TGAAGACGGATTTTTTTTCTCTCGTACCATTCCC 18 152 1 TTTTTTTCTG 0.755531 -116 AATAGCTAATTTGTTATTTTTTTGTATGAAGCCT 18 219 0 TTTTTTTTTG 0.943508 -49 GCATTTGAGATTGCTGCTGATTATCCATTGTGAT 19 189 1 TTCTCTATTT 0.834515 -112 CCTCCTTTGGTTTCTGTTCATTTTATAGTTTCCT 19 223 1 TTCTTTATTT 0.849562 -78 AGATATGAGTTTGTTATTTTTTCTGACAAACCTT 20 75 1 TTTTTTTTTT 0.932027 -93 TCCGTTTCTCCTTTTTGTAAGGTATGGT 20 150 0 TTCTCTTTTT 0.889832 -18 CTCATTTGCTTTCTTCTTTTCTCGGACCTATTAT 21 107 0 TTTTTTTCTG 0.755531 -36 ** ** ** *** * Masking position 8 Map Score: 24.0105 Number of sites scoring better than the average of aligned sites = 1095 Number in coding regions = 843 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 261 Fraction of orfs with sites within 600 bp upstream = 0.041921 Motif number 2 ACGGTTTATTGAAAAAGACGGATATATACT 1 204 1 GAAAAAGACG 0.596108 -97 CATTTTTCTTGAAAAAAGCATGTTTTAAAC 4 85 0 GAAAAAAGCA 0.901725 -67 TAGAGAAACAGAAAAAAACACTCAAGAGCA 6 34 0 GAAAAAAACA 0.744314 -83 CTATAATGGAGAAGAAAGCTTGGCTTCAAT 6 61 1 GAAGAAAGCT 0.96374 -56 AGGGAAACATGAATGAAGCTGCAGATGAAA 8 45 0 GAATGAAGCT 0.651575 -94 CGATAAAAAAGAAAAAGGCTTAAAAAGCCA 8 79 1 GAAAAAGGCT 0.923786 -60 TCATACATAGGAAGCAGGCATTGTTCATAA 9 40 0 GAAGCAGGCA 0.787952 -72 ATAGTTGTTAGAAGGAGGCTGTTTGACGCA 10 18 1 GAAGGAGGCT 0.960964 -120 ATGAATGAAAAAAGAAGGCTGCGTCAAACA 10 37 0 AAAGAAGGCT 0.577554 -101 TACATTCATAGAAGACAACTAGAAATTGTA 10 86 1 GAAGACAACT 0.741377 -52 AAAATTAGCGGAAAGAAGCAACTTTTTATT 12 90 0 GAAAGAAGCA 0.891227 -211 CATCATACTTGAAAAAAACTTCTCCGGACA 15 23 0 GAAAAAAACT 0.787574 -51 TTATTTACGTCAAGGAGGCTTAT 17 186 1 CAAGGAGGCT 0.644055 -13 TGCTCGCGATGAAAAAAGCGCATTTCATGG 19 99 0 GAAAAAAGCG 0.817686 -202 CGAAATAACGGAAGGCGGCATTTGAGATTG 19 172 1 GAAGGCGGCA 0.867917 -129 CTCCCAGTCTGAAGGAAACTATAAAATGAA 19 239 0 GAAGGAAACT 0.882764 -62 TAAAATGCAGGAAGACAACATTTATTTTTT 20 24 0 GAAGACAACA 0.692384 -144 TCCGAGAAAAGAAGAAAGCAAATGAGGGGG 21 115 1 GAAGAAAGCA 0.954273 -28 ********** Masking position 3 Map Score: 15.2925 Number of sites scoring better than the average of aligned sites = 1778 Number in coding regions = 1597 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 3 GATTCTGTAGTCTCCATTATACAGTAATTA 1 35 0 TCTCCATTAT 0.909405 -266 AATTGGTCCTCCTTCAATATACCCATTTTT 4 108 0 CCTTCAATAT 0.727126 -44 AATGTCCTCCTATCTTTTCAAAAAA 4 137 0 CCTCCTATCT 0.893843 -15 ATCCCTCCTGCCTCCATTATTTCAAAAACA 5 41 0 CCTCCATTAT 0.972162 -24 CAAGCTTTCTTCTCCATTATAGAGAAACAG 6 53 0 TCTCCATTAT 0.909405 -64 GTGAAATCCTCCAAAAAGTAATCAAAT 7 118 0 CCTCCAAAAA 0.857189 -17 GCCGTTATACCTCCAATCAGATTTATTCT 9 93 0 CCTCCAATCA 0.967686 -19 CCTAAAGTTTTCTCCATTATACTTATTTTG 11 44 0 TCTCCATTAT 0.909405 -35 CTTTACAAATTCTCCATTCTGGTCAAAGAT 12 251 1 TCTCCATTCT 0.910944 -50 ATCGAGTGCCTCCTATAAAACCATACTT 13 9 1 CCTCCTATAA 0.857189 -240 CGTTTCTCCTCCATTCCGCGAGAATCC 16 117 0 CCTCCATTCC 0.904322 -17 GAAGCACCCTCCAAAAAAATAAATGTT 20 8 1 CCTCCAAAAA 0.857189 -160 AAAAGACACCTCCAATCATTAGACAGAT 21 9 1 CCTCCAATCA 0.967686 -134 ********** Masking position 3 Map Score: 14.5803 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 160 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 4 AAGATTTATAAAAACCTCATGTTCTGGGTCAAA 1 103 1 AAACCCTGTT 0.926602 -198 TATGTTGATCACATCCTCGCTTTTTATTTTGGG 1 163 0 AATCCCCTTT 0.955646 -138 GGGCCAGTATATATCCGTCTTTTTCAATAAACC 1 206 0 AATCCTTTTT 0.892768 -95 CAATAAGTCAATATCTTTATTTTCTGATATTTT 2 87 0 AATCTTTTTT 0.591482 -140 TCCTTCCCATATATCCTTTTGTTTAATTGTAAG 2 129 0 AATCCTTGTT 0.861754 -98 TTTTTCTTTCACATCCGCTCCTTCCCATATATC 2 147 0 AATCCCCCTT 0.908384 -80 CAACATAACCTCCTGTTATTTGTGTAT 2 210 0 AAACCCTGTT 0.926602 -17 TCCTCCTTCAATATACCCATTTTTCTTGAAAAA 4 99 0 AATACCTTTT 0.570126 -53 TTTCAAAAACACAACCGCTCTTTCAAACGATGT 5 19 0 AAACCCCTTT 0.927507 -46 CCTCATAGACAAATCTGCTCGTTATCTTTCTAA 12 148 1 AATCTCCGTT 0.737212 -153 TGCCTCCTATAAAACCATACTTTTACTGGTCAT 13 17 1 AAACCTCTTT 0.789536 -232 ATTGATGTAACCTCCTTTTATCAACGTTA 13 230 0 GAACCCTTTT 0.64132 -19 AAAGAAAGGTAAATCTTTCTTTTTCTCATAATA 14 99 0 AATCTTTTTT 0.591479 -90 TCGATTTTAGAGATCCACCTTATCATTATAGCA 14 153 0 AATCCCTTAT 0.7912 -36 AAAACCTCCCCTTTCGATTTTAG 14 176 0 AAACCCCCTT 0.854817 -13 TGACAGTTTAAAAACCATATGTTAGATTAAGGT 17 120 1 AAACCTTGTT 0.787306 -79 CTGCGCCATGAAATGCGCTTTTTTCATCGCGAG 19 94 1 AATGCCTTTT 0.662807 -207 TAACAAACTCATATCTGCGTTTTCAGCAGGAAT 20 58 0 AATCTCTTTT 0.831586 -110 TGTAAAATCCCCCTCATTTGCTTTCTT 21 126 0 AATCCCTCAT 0.63554 -17 * **** * **** Masking position 13 Map Score: 15.0183 Number of sites scoring better than the average of aligned sites = 811 Number in coding regions = 639 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 5 TTCAGTTCACCGGCCAGCGGCACCGTAATC 1 246 0 CGGCCAGCGG 0.963615 -55 ACCAAACAGCCGGCTGACCAGGCTGT 2 7 1 CAGCCGGCTG 0.49662 -220 AATCACTGTCCGGCCGGGATTCTGCGCAGC 2 43 0 CGGCCGGGAT 0.869143 -184 GAAATAATGGAGGCAGGAGGGATTCAC 5 48 1 AGGCAGGAGG 0.756015 -17 GCAAAAAAACCGGCCGTATGGCAGACCGGT 7 20 0 CGGCCGTATG 0.780252 -115 ATTCCCGCTGCGGCGAGCAGTATTTTCGCA 14 37 0 CGGCGAGCAG 0.92921 -152 CTGCTCGCCGCAGCGGGAATCTTTTTGTTA 14 47 1 CAGCGGGAAT 0.806046 -142 TGTATCATAACAGCGGGAGGCTCGTCTTTC 16 53 1 CAGCGGGAGG 0.972397 -81 AAGCAGCCGTGGGAAGCAGCTGC 18 4 1 CAGCCGTGGG 0.783887 -264 GCAGTCAGCGCGGCGAGCGTAAAGGGAGAT 18 119 0 CGGCGAGCGT 0.882672 -149 CCGTCTTCAGCGGCAGTCAGCGCGGCGAGC 18 131 0 CGGCAGTCAG 0.869817 -137 GTCGAAATAACGGAAGGCGGCATTTGAGAT 19 170 1 CGGAAGGCGG 0.83198 -131 TTGAAGATGACGGCGGGAGGGAGTCGG 19 284 1 CGGCGGGAGG 0.990081 -17 TCTGCGTTTTCAGCAGGAATTTGATAAAAT 20 48 0 CAGCAGGAAT 0.679003 -120 ********** Masking position 3 Map Score: 9.50611 Number of sites scoring better than the average of aligned sites = 2002 Number in coding regions = 1874 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 6 ATACGACAAAAACATTTTGAAAATAAGCAGTAA 1 72 1 AAATTTAAAA 0.922774 -229 AATAAGCAGTAAGATTTATAAAAACCTCATGTT 1 93 1 AAATTTAAAA 0.922774 -208 TTATTTTCTGATATTTTATAAAAAAGCGGTAAA 2 71 0 ATTTTTAAAA 0.893298 -156 ATGTGAAAGAAAAATTAATAAAAGCGCTTACAG 2 166 1 AAATTAAAAA 0.602898 -61 ATGTCCTCCTATCTTTTCAAAAAAATTGGTCCT 4 128 0 ATTTTTAAAA 0.893294 -24 TCCTGCCTCCATTATTTCAAAAACACAACCGCT 5 33 0 ATATTTAAAA 0.934203 -32 GCAGATGAAAAATATTTGAAAAAACGTTCATTA 8 22 0 AAATTTAAAA 0.922774 -117 CCCTATTCTCAAATTTTTTAAAATGAATAAAAA 12 65 1 AATTTTAAAA 0.875701 -236 AGCAAGTTCCATGATTTTCAAAAGGGCTATACG 12 200 0 ATATTTAAAA 0.934207 -101 TAAAAATTTAATGTTTTTAACAACCTTAATCTA 17 142 0 ATTTTTACAA 0.611889 -57 ATGGTGATTTATTATGTGAAAAATCTCTTCTGC 20 122 0 ATATGTAAAA 0.727816 -46 ** **** **** Masking position 10 Map Score: 5.72705 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 212 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 7 CGGCTGACCAGGCTGTTTTTTTGCTGCGCA 2 21 1 GGCTGTTTTT 0.846036 -206 CTCTTTCAAACGATGTGTTTTGCC 5 5 0 CGATGTGTTT 0.842455 -60 TTGAAAGAGCGGTTGTGTTTTTGAAATAAT 5 26 1 GGTTGTGTTT 0.842736 -39 AAATTGTAAGCGCTGTCTATCTTCTGAATG 10 108 1 CGCTGTCTAT 0.944045 -30 CAAATCTGCTCGTTATCTTTCTAACAACAG 12 157 1 CGTTATCTTT 0.767435 -144 CCTGCATTCGCGTTGTCTTTACAAATTCTC 12 235 1 CGTTGTCTTT 0.971149 -66 TTTTAAGAATCGCTGTTTTTGCTCGTTCTT 13 145 0 CGCTGTTTTT 0.947481 -104 TTACACTTTTCGCTGTATATACCAGTGTAT 16 28 1 CGCTGTATAT 0.763761 -106 GATGGTTCACCGTTGTCTTTCTTACAGAAA 21 65 1 CGTTGTCTTT 0.971149 -78 ********** Masking position 6 Map Score: 4.48869 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 335 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 GATTTATAAAAACCTCATGTTCTGGGTCAA 1 105 1 AACCTCATGT 0.767785 -196 ATAAGTCAATATCTTTATTTTCTGATATTT 2 88 0 ATCTTTATTT 0.539895 -139 CAACATAACCTCCTGTTATTTGTGTA 2 211 0 AACCTCCTGT 0.879584 -16 TGTTTGACGCAGCCTTCTTTTTTCATTCAT 10 37 1 AGCCTTCTTT 0.792817 -101 TCCATACTTCACCCTTATTTCAGATTTAAG 13 95 1 ACCCTTATTT 0.822797 -154 TGTATGCTTCAACTTCATTTCGGGAAATGT 13 201 1 AACTTCATTT 0.806154 -48 ATTGATGTAACCTCCTTTTATCAACGTT 13 231 0 AACCTCCTTT 0.958542 -18 AGAAAGGTAAATCTTTCTTTTTCTCATAAT 14 100 0 ATCTTTCTTT 0.721632 -89 AGAAAGATTTACCTTTCTTTTTCTTTTTTT 14 112 1 ACCTTTCTTT 0.803006 -77 GTAATAATCTCCTTTTTTTACACTT 16 6 1 AATCTCCTTT 0.603625 -128 ACTGACCCTCTTTTCCTTTAGAAA 17 5 1 ACCCTCTTTT 0.680474 -194 TTATTTAACAAACTTTATTTACGTCAAGGA 17 172 1 AACTTTATTT 0.691066 -27 ATCCATTGTGATCCTCCTTTGGTTTCTGTT 19 211 1 ATCCTCCTTT 0.923829 -90 ********** Masking position 1 Map Score: 5.31913 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 355 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 9 AGCTGACCCGGAATTCTTCA 1 291 0 AGCTGACCCG 0.895614 -10 CCAAACAGCCGGCTGACCAGGCTGTTTTTT 2 12 1 GGCTGACCAG 0.986145 -215 GTATATTGAAGGAGGACCAATTTTTTTGAA 4 116 1 GGAGGACCAA 0.818064 -36 CCGGCCGTATGGCAGACCGGTTTTTGATGG 7 11 0 GGCAGACCGG 0.971442 -124 GGTTACGCTTGGCTGACCCACCCGTCAAAC 12 25 1 GGCTGACCCA 0.94616 -276 TCATTAAATTGGATGACCAGTAAAAGTATG 13 32 0 GGATGACCAG 0.942127 -217 GTAATGCTGAGTCGGACCGGCATCTCCCTT 18 98 1 GTCGGACCGG 0.968664 -170 AGCTATTGAAGTCGAACCGGAAATCTTTTA 18 246 1 GTCGAACCGG 0.775377 -22 ********** Masking position 6 Map Score: 3.58797 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 284 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 10 CAAAACAGTTATTGATTTTTGTAATCTGTT 4 48 0 ATTGATTTTT 0.694168 -104 ATTTTTACTTTTTGGCTTTTTAAGCCTTTT 8 91 0 TTTGGCTTTT 0.969573 -48 CTTCCTGATGTTTGGCTTTTATCTTTGACC 12 271 0 TTTGGCTTTT 0.969573 -30 GATTTTTCTTTTTGACTTTTCCTCATGTTT 17 78 0 TTTGACTTTT 0.952583 -121 AAAGTCCCATTTTGATTTTTCTTTTTGACT 17 91 0 TTTGATTTTT 0.926824 -108 TAATCTAACATATGGTTTTTAAACTGTCAA 17 119 0 TATGGTTTTT 0.782618 -80 TACTGCTGATTTTGACTTGTCCGTTTTCCG 18 63 1 TTTGACTTGT 0.860755 -205 GTGATCCTCCTTTGGTTTCTGTTCATTTTA 19 218 1 TTTGGTTTCT 0.860755 -83 ********** Masking position 7 Map Score: 2.64095 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 268 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 ACTACAAAGGGGAAAGAGGGA 4 2 0 GGAAAGAGGG 0.891934 -150 CTTTTTTCAAGAAAAATGGGTATATTGAAG 4 97 1 GAAAAATGGG 0.670309 -55 CAATTTTTTTGAAAAGATAGGAGGACATT 4 133 1 GAAAAGATAG 0.82231 -19 TTGTGTTTTTGAAATAATGGAGGCAGGAGG 5 38 1 GAAATAATGG 0.884091 -27 TCCTATGTATGAAAAGATAGAATATGGAAA 9 58 1 GAAAAGATAG 0.82231 -54 CTAACAACAGGAAATGATCGGGTCGTATAG 12 177 1 GAAATGATCG 0.820599 -124 ACTTAAATCTGAAATAAGGGTGAAGTATGG 13 96 0 GAAATAAGGG 0.924289 -153 GGGGACGGAGAATAGATGGAAAAGCTTGC 14 10 1 GAATAGATGG 0.859851 -179 TTTTCTAAAGGAAAAGAGGGTCAGT 17 6 0 GAAAAGAGGG 0.979625 -193 TGCTCGCGATGAAAAAAGCGCATTTCATGG 19 99 0 GAAAAAAGCG 0.819913 -202 ATCCTTTGTCGAAATAACGGAAGGCGGCAT 19 163 1 GAAATAACGG 0.701221 -138 GTACGGTAACGTATAGATGGTTCACCGTTG 21 50 1 GTATAGATGG 0.415419 -93 AAGAAGAAAGCAAATGAGGGGGATTTTACA 21 123 1 CAAATGAGGG 0.749943 -20 ********** Masking position 3 Map Score: 5.14138 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 637 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 143 Fraction of orfs with sites within 600 bp upstream = 0.0229682 Motif number 12 TACCTTCCGCTATTATGAAAGCGT 1 5 0 TATTATGAAA 0.72323 -296 AATCAATAACTGTTTTGATACAATGTTTAA 4 61 1 TGTTTTGATA 0.657659 -91 TGCAGGTAATTATTATGTCAACTGATTTTT 7 72 0 TATTATGTCA 0.725772 -63 TTTTCAACCTTATTATGTTATGAACAATGC 9 23 1 TATTATGTTA 0.895723 -89 TATCTGTTCATATTATGAGAAAAAGAAAGA 14 89 1 TATTATGAGA 0.876774 -100 GTCCATCTGCTATAATGATAAGGTGGATCT 14 146 1 TATAATGATA 0.634544 -43 AGCCTCCCGCTGTTATGATACACTGGTATA 16 45 0 TGTTATGATA 0.929534 -89 TTAATAAACGTGTTATGATAAGAACTAGGA 16 90 1 TGTTATGATA 0.929534 -44 GATTGTCCCATGTTATGTTTTTTATACTGC 18 39 1 TGTTATGTTT 0.567556 -229 TATGGTGATTTATTATGTGAAAAATCTCTT 20 126 0 TATTATGTGA 0.829782 -42 ********** Masking position 6 Map Score: 1.38317 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 55 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 13 ACTCAGGGCTTTTTGCTCTTGAGTGTTTTT 6 21 1 TTTTGCTCTT 0.794325 -96 CCGTCAAACGATTTGCTCACCCTATTCTCA 12 46 1 ATTTGCTCAC 0.841305 -255 TCATAGACAAATCTGCTCGTTATCTTTCTA 12 150 1 ATCTGCTCGT 0.94493 -151 AAATCATGGAACTTGCTCGCCTGCATTCGC 12 216 1 ACTTGCTCGC 0.915652 -85 GAATCGCTGTTTTTGCTCGTTCTTATGACA 13 139 0 TTTTGCTCGT 0.944087 -110 CTTGCGAAAATACTGCTCGCCGCAGCGGGA 14 35 1 TACTGCTCGC 0.830615 -154 CTGAACTGGAATTTGCTCGCGATGAAAAAA 19 112 0 ATTTGCTCGC 0.976117 -189 GAAAAATCTCTTCTGCTTGTCAATCGCGCA 20 108 0 TTCTGCTTGT 0.732799 -60 AATCCCCCTCATTTGCTTTCTTCTTTTCTC 21 118 0 ATTTGCTTTC 0.647986 -25 ********** Masking position 4 Map Score: 2.40883 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 215 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 ACTGAAATTTTATCCCCTCAATGAAGAATT 1 270 1 TATCCCCTCA 0.766805 -31 TACAATGATCCCCCTTGGGAAAAATAT 8 122 0 ATCCCCCTTG 0.771896 -17 ATCACTCCTTTTCAACCTTATTATGTTATG 9 15 1 TTCAACCTTA 0.860857 -97 GGTTTCACCTCATTCAGAAGAT 10 126 0 TTTCACCTCA 0.870179 -12 CGTTTCACCTCAAACCCTAAAG 11 67 0 TTTCACCTCA 0.870179 -12 GTTTCCATACTTCACCCTTATTTCAGATTT 13 92 1 TTCACCCTTA 0.870179 -157 GATTTTAGAGATCCACCTTATCATTATAGC 14 154 0 ATCCACCTTA 0.93741 -35 TAATGTTTTTAACAACCTTAATCTAACATA 17 137 0 AACAACCTTA 0.65677 -62 ACAGAAAAGGTACCACCTTATAATAGGTCC 21 88 1 TACCACCTTA 0.908497 -55 TGTAAAATCCCCCTCATTTGCTTTCT 21 127 0 ATCCCCCTCA 0.946178 -16 ********** Masking position 8 Map Score: 3.71451 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 175 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 15 ********** No masking Map Score: -1.01015e-11 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