AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_bsub_reg_100.orf -o00251_bsub_100.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 yacL 115 similar to hypothetical proteins #2 gltX 90 glutamyl-tRNA synthetase #3 glmS 300 L-glutamine-D-fructose-6-phosphate amidotransferase #4 nadE 139 NH3-dependent NAD+ synthetase #5 ycnG 106 similar to 4-aminobutyrate aminotransferase #6 ycnH 68 similar to succinate-semialdehyde dehydrogenase #7 guaA 232 GMP synthetase #8 purE 300 phosphoribosylaminoimidazole carboxylase I #9 purC 72 phosphoribosylaminoimidazole succinocarboxamide synthetase #10 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #11 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #12 ykrV 94 similar to aspartate aminotransferase #13 pyrB 145 aspartate carbamoyltransferase #14 glnR 110 transcriptional regulator #15 glnA 60 glutamine synthetase #16 gltA 146 glutamate synthase (large subunit) #17 aspB 22 aspartate aminotransferase #18 ypmA 142 ypmA #19 ypcA 155 similar to glutamate dehydrogenase #20 yrpC 300 similar to glutamate racemase #21 ysmB 243 similar to transcriptional regulator (MarR family) #22 yugG 147 similar to transcriptional regulator (Lrp/AsnC family) #23 ywfB 151 alternate gene name: ipa-80d #24 rocA 226 pyrroline-5 carboxylate dehydrogenase #25 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase Motif number 1 TTAATGTTGGTTTTTGTTTATTCTGATATTCGTAGGATG 1 42 1 TTTTTTTTAT 0.909141 -74 CCCCACCTCCTTTTTTAACATTTTAATTTCACAAAGTCT 1 85 0 TTTTTACTTT 0.77822 -31 GATCATGTGATTTCTCTTTGTTCAAGGAGTCACCCCCTT 3 181 0 TTTCTTTTAG 0.700257 -120 ATTTTTCTTCCTCCTAAGATTGTAAAAGGA 3 281 0 TTTTTTCTAT 0.971241 -20 TTTGTAGTTTCTCCTTCTGATACCATCAAAAAGTTA 5 8 1 TTTCTTTTAT 0.89656 -99 CTGTCGGTATTTTCTTATCATTCTGACTTCTCTTTGGTA 5 66 0 TTTCTTCTTT 0.94024 -41 TGAACATTCCTTTCTTTTCATGATTACTTAAAATGATAG 6 38 0 TTTCTTCTTT 0.94024 -31 ATTTTTGTATCGTTCGATAATATCGTTGACA 8 3 1 TTTTGTCTAT 0.7215 -298 AGAGCGGGTATTTTTTATTTTCTGAAAACAAAAGCATTA 8 256 1 TTTTTTTTAC 0.649314 -45 ATATTTAATATTTTTATTCATTTATAAATTTTCTGTTCA 10 107 0 TTTTTTCTAT 0.971241 -100 ATTGAATTAATTTTTATTCATGTTATAATGTTAAATAAT 10 149 1 TTTTTTCTAT 0.971241 -58 TTTTTTTTCGATATAAAGGCATAAAAATTCAT 11 4 1 TTTTTATTAT 0.659058 -67 ACCCCAAATTTTTCTTTACTTTTTTCATTTAACCATATA 12 20 1 TTTCTACTTT 0.752446 -75 ATTTCCTCCTTTTCTTAACTTAGTTTCATTATAGGTGAT 14 78 0 TTTCTACTAT 0.849655 -33 TTTTTCATCCTCCAGTTTGAACAAATATT 18 124 0 TTTTTTCTTG 0.830386 -19 ATTTCAGCAGTTTTTTTTCGTTAAAAAACATGGAAAAAC 19 32 1 TTTTTTCTAC 0.862051 -124 TTTTTTTTCGTAATTTCATCCACTGACTC 20 1 1 TTTTTTCTAT 0.971241 -300 GTCTCATTCTTTTTTTATCATATGACTTTATATCATCTG 20 255 0 TTTTTTCTTT 0.947818 -46 TCACTCCCTTTTTTTGATGGTTGTATTATGCCCTGAAAT 22 17 1 TTTTTTGTAT 0.700407 -131 CTAGCGGAAGTTTCTCCTCGTTTTTTCTTAGCATTCGTC 22 64 1 TTTCTTCTTT 0.94024 -84 TTAAAAAGGGTTTTTAATTATAGGAATTTAGAAACTTTG 23 12 0 TTTTTTTTTT 0.843302 -140 TTAAAGGGTTTTTTTGTTTGTATGGGAATAATTATCAAT 23 47 1 TTTTTTTTAT 0.909141 -105 TATTTTGCGTTTTTTGCTCTTTACGCAAAAAACAAATGC 24 38 0 TTTTTTCTAA 0.801586 -189 GGTGATCACCTTTCTCTTTTTCCGATCTTGAACGCAAAT 24 78 0 TTTCTTTTTT 0.823375 -149 ATCATGCCATTTTCTTGTCTTTTGCTGAAAAAACTTGTT 24 142 0 TTTCTTCTAA 0.777753 -85 GATTCTTGCATTTTTATTCATATGCGAAGATATATTTCA 24 178 1 TTTTTTCTAG 0.901015 -49 ***** ** * ** Masking position 11 Map Score: 28.8227 Number of sites scoring better than the average of aligned sites = 826 Number in coding regions = 641 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 2 TTAAAATGTTAAAAAAGGAGGTGGGGGT 1 98 1 AAAAAAAGGG 0.936377 -18 ATGATCTTCCAAAAAACATGTAGGAGGGGACGATT 3 214 1 AAAAAATGGA 0.964773 -87 TTGACACAGAAAAAAACGAGGACAGATATGAAGCT 7 180 0 AAAAAAAGAG 0.870109 -53 TTTCTGTGTCAAAAAACTTAGAGGAGATTAGGTGA 7 203 1 AAAAAATAGA 0.854393 -30 TCAGCCGCATAAAAAAACAGGCTGACCGCG 10 6 0 AAAAAAAGGA 0.978778 -201 TTCCGCTCAAAAAAAATCAGCACGACTCCAGCACA 10 65 0 AAAAAAAGGA 0.978778 -142 TGGTTAAATGAAAAAAGTAAAGAAAAATTTGGGGT 12 20 0 AAAAAAAAAA 0.818102 -75 TTTTTAACGAAAAAAAACTGCTGAAATCAGCAGTT 19 24 0 AAAAAATGAA 0.925736 -132 TTTTTTCGTTAAAAAACATGGAAAAACATAACGTT 19 44 1 AAAAAATGAA 0.925736 -112 GTCATATGATAAAAAAAGAATGAGACAGAAAGCGT 20 268 1 AAAAAAAAGA 0.9081 -33 CATTTTCTTCAAAAAAGAAGGAAAATAGACACGGA 21 177 1 AAAAAAAGAA 0.954529 -67 TACAACCATCAAAAAAAGGGAGTGACACAGA 22 7 0 AAAAAAGGGA 0.879143 -141 GAATGCTAAGAAAAAACGAGGAGAAACTTCCGCTA 22 65 0 AAAAAAAGAA 0.954529 -83 AGCATTCGTCAAAAAACGTGATATAATGTCATGAG 22 93 1 AAAAAATGTA 0.662741 -55 CTCTTTACGCAAAAAACAAATGCAAAATTATTTTG 24 26 0 AAAAAAAAAA 0.818102 -201 TCTTTTGCTGAAAAAACTTGTTGAATCGAACAGAA 24 129 0 AAAAAATGAA 0.925736 -98 TTCGCATATGAATAAAAATGCAAGAATCATGCCAT 24 171 0 AATAAATGGA 0.6501 -56 TTGAATCCACAAAAAAAGAGACTGAAAACATCTCA 25 34 0 AAAAAAAGGA 0.978778 -143 TAAGCGCTTTAAAAAATCAGCCCGCCAATTCCTTT 25 115 0 AAAAAAAGGC 0.845922 -62 ACAGCCGGCCAAAAAAACAATGAGGTGAAAAAG 25 154 1 AAAAAAAAGG 0.759226 -23 ****** ** ** Masking position 6 Map Score: 27.3269 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 467 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 AGCAATAATCCCGTCTTCTTTTCCTATTGA 3 21 0 CCGTCTTCTT 0.897624 -280 TCGATAACCTCCATCCTCGTCAACTAAGCC 3 92 0 CCATCCTCGT 0.914382 -209 GCAGACCCGGCCATTTTCTTTCCAATGA 6 9 0 CCATTTTCTT 0.860195 -60 GCGGTCAAGACCATCTTCTTTTAATTAAAT 7 55 0 CCATCTTCTT 0.928723 -178 GAAGCTCGCTCCGCCCTCTTTGGCAAGGCC 7 156 0 CCGCCCTCTT 0.947863 -77 AACAAGTTCACCCTCTTGGTCTTTGTG 10 190 0 TCACCCTCTT 0.905372 -17 CTAACAGCCCACCTCTTGATGAATAAT 11 54 0 CCCACCTCTT 0.907806 -17 CATTGAAGCTTCCTTCTCTTCATAACCCTT 13 42 0 TCCTTCTCTT 0.921275 -104 GTTCTTTCCCCTCTCTTTTCAACTTAA 13 129 0 CCCCTCTCTT 0.96042 -17 CTCAATTTCCTCCTTTTCTTAACTTAGTTT 14 91 0 TCCTTTTCTT 0.80561 -20 TTGGTAAAATTCCTCCTCTTAAAAGGTAAA 15 41 0 TCCTCCTCTT 0.961214 -20 CAGGTGATCACCTTTCTCTTTTTCCGATCT 24 89 0 CCTTTCTCTT 0.810831 -138 AAGAATCATGCCATTTTCTTGTCTTTTGCT 24 155 0 CCATTTTCTT 0.860195 -72 ATGTAGTCCCCCTCGTGTTATGAAAT 24 211 0 TCCCCCTCGT 0.840818 -16 ********** Masking position 7 Map Score: 13.8267 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 350 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 AACATTTTAATTTCACAAAGTCTTATGCATCCTAC 1 73 0 TTTCCACTTA 0.415398 -43 AACTAAGCCTTTTTCCGGGCGCTTAGTTCGGGCGC 3 66 0 TTTTCGCTTA 0.783222 -235 GGTTATCGAATTTCGCGGATCCTCCCGGCTGAGTG 3 113 1 TTTCCGCTCC 0.887181 -188 TTCCCATAACTCTCTCGAATCATTCCATAGCGCCG 7 19 0 TCTCCGATTC 0.799401 -214 AGTCGTTCGCTTCTGCGATATATCCATGTCAGTTT 8 169 0 TTCTCGATCC 0.737259 -132 AAGAAGCTTTTACGGCTTCTTCTAAGCCGCCG 9 8 1 TTTTCGCTTC 0.973127 -65 TGCTGATTTTTTTTGAGCGGAATTCCCATTGAACA 10 78 1 TTTTAGATTC 0.603021 -129 AAATCAGCAGTTTTCCGTTGCATTC 19 1 0 TTTTCGATTC 0.966373 -155 GAATCTTCTGTTTCTCACATGCTCCCTTTCAGAGA 19 115 0 TTTCCACTCC 0.735789 -41 CCTTCTCAAGTTTTGCTCCCTATTCGAATAATCGA 20 170 1 TTTTCTATTC 0.815749 -131 AAAATGGTTCTTTTTCGTTTGATTCAGATGATATA 20 231 1 TTTTCGATTC 0.966373 -70 CTTGCCTACGTTTTGCACAGCATTCCAAATATGGT 21 74 0 TTTTCAATTC 0.910533 -170 CTCCTGCGAGTCTTGCATTTTCTTCAAAAAAGAAG 21 162 1 TCTTCACTTC 0.762022 -82 TTCTCCTCGTTTTTTCTTAGCATTCGTCAAAAAAC 22 75 1 TTTTCTATTC 0.815749 -73 TGCAAAATTATTTTGCGGAGGCTTCTCAAA 24 6 0 TTTTCGCTTC 0.973127 -221 GCCAATTCCTTTCTTCATTGGATTCACCCTTATCA 25 92 0 TTCTCAATTC 0.717612 -85 **** ** **** Masking position 13 Map Score: 10.4064 Number of sites scoring better than the average of aligned sites = 1199 Number in coding regions = 1096 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 5 AATATCAGAATAAACAAAAACCAACATTAA 1 42 0 TAAACAAAAA 0.625889 -74 GGTGACTCCTTGAACAAAGAGAAATCACAT 3 186 1 TGAACAAAGA 0.734495 -115 GAAGTCAGAATGATAAGAAAATACCGACAG 5 75 1 TGATAAGAAA 0.53342 -32 TAAGTAATCATGAAAAGAAAGGAATGTTCA 6 47 1 TGAAAAGAAA 0.905274 -22 TTTTATTTTCTGAAAACAAAAGCATTAGAA 8 268 1 TGAAAACAAA 0.686643 -33 GGAATTCCGCTCAAAAAAAATCAGCACGAC 10 74 0 TCAAAAAAAA 0.544656 -133 GAATTCCCATTGAACAGAAAATTTATAAAT 10 97 1 TGAACAGAAA 0.886886 -110 AATTTATAAATGAATAAAAATATTAAATAT 10 116 1 TGAATAAAAA 0.822885 -91 CATTATAACATGAATAAAAATTAATTCAAT 10 149 0 TGAATAAAAA 0.822885 -58 GCCTTTATATCGAAAAAAAA 11 1 0 CGAAAAAAAA 0.934058 -70 AACTTAAGGCTGAAAAAAAACCCCGGTCTA 13 106 0 TGAAAAAAAA 0.945292 -40 AGCCTTAAGTTGAAAAGAGAGGGGAAAGAA 13 125 1 TGAAAAGAGA 0.650959 -21 TCCTCCAGTTTGAACAAATATTGTTAGTCA 18 116 0 TGAACAAATA 0.503532 -27 TGTTTTTTAACGAAAAAAAACTGCTGAAAT 19 32 0 CGAAAAAAAA 0.934058 -124 GATGAAATTACGAAAAAAAA 20 1 0 CGAAAAAAAA 0.934058 -300 CTGAATCAAACGAAAAAGAACCATTTTACT 20 228 0 CGAAAAAGAA 0.723839 -73 TAAAGTCATATGATAAAAAAAGAATGAGAC 20 264 1 TGATAAAAAA 0.673949 -37 GCATTTTCTTCAAAAAAGAAGGAAAATAGA 21 176 1 CAAAAAAGAA 0.236251 -68 TATTCCCATACAAACAAAAAAACCCTTTAA 23 47 0 CAAACAAAAA 0.578325 -105 CTTGTTGAATCGAACAGAAATTTGTCTAAC 24 118 0 CGAACAGAAA 0.865368 -109 TCTTCGCATATGAATAAAAATGCAAGAATC 24 178 0 TGAATAAAAA 0.822885 -49 ********** Masking position 6 Map Score: 17.4112 Number of sites scoring better than the average of aligned sites = 1126 Number in coding regions = 900 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 6 TACCCGTATTCATAAGGTTTTAACCGAAA 1 3 0 CAAGTTTAGA 0.955578 -113 TTTTCTTCCTCCTAAGATTGTAAAAGGAGACGAAGAA 3 272 0 CAAGTTTAGG 0.980547 -29 CTGATACCATCAAAAAGTTATAATTGGTACTTTTCAT 5 27 1 CAAATTTAGG 0.94877 -80 TTCATGATTACTTAAAATGATAGCAGACCCGGCCATT 6 24 0 CAAATGTAGA 0.831935 -45 GGGCCATATTCCCAAGATTATATGAGGTCGTGTTTTG 8 76 0 CAAGTTTAGG 0.980036 -225 GAATATGGCCCATAAGTTTCTACCCGGCAACCGTAAA 8 102 1 CAAGTTTAGG 0.980548 -199 TTTTTTCAGCCTTAAGTTGAAAAGAGAGGGGAAAGAA 13 118 1 CAAGTGAAGA 0.631257 -28 CCGGTATTATCGGAAATTGATCGGGGGAGAGGAATT 16 121 1 CAAATGTCGG 0.816574 -26 ATGTGAGAAACAGAAGATTCTAGGAGGTTAACTCAA 19 130 1 CAAGTTTAGG 0.980548 -26 TCAATTCTAGCGGAAGTTTCTCCTCGTTTTTTCTTAG 22 58 1 CAAGTTTCGT 0.715051 -90 ATAAAATTTACTTAAAATTTTAAAAGATTGGTTGGTG 23 122 1 CAAATTTAGA 0.887683 -30 * *** ** ** ** Masking position 5 Map Score: 8.9562 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 50 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 GTGAATATCCCCCTGTCGGTATTTTCTTATCAT 5 84 0 CCTGTCGATT 0.977067 -23 AAGAAAATGGCCGGGTCTGCTATCATTTTAAGT 6 19 1 CCGGTCGTAT 0.864461 -50 TTGACATTATCCATGTCCGTTGTTAAGATAAAC 8 36 1 CCTGTCGTGT 0.956492 -265 TGCGATATATCCATGTCAGTTTTATCGATCACT 8 158 0 CCTGTCGTTT 0.989484 -143 GATACATGTACCATGCCCGGTTTGTATTGCTTC 8 207 1 CCTGCCGTTT 0.985293 -94 ATAAAAAATACCCGCTCTGCATTGCACTTATGA 8 241 0 CCGCTCGATT 0.848025 -60 TCTTATCTCCCCTTCTCAAGTTTTGCTCCCTAT 20 160 1 CCTCTCATTT 0.832058 -141 TCCTTGCCGGTATTCCTTCTTTTG 21 2 1 CCTGCCGATT 0.968087 -242 CAAAAGCGTTCCGTGTCTATTTTCCTTCTTTTT 21 188 0 CCTGTCATTT 0.942082 -56 CATGCAAGATCCGTACCAGCTTTTGAATCCACA 25 58 0 CCTACCGTTT 0.882093 -119 ** **** * *** Masking position 13 Map Score: 6.9835 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 197 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 ACCCCCACCTCCTTTTTTAACA 1 104 0 CCCCACCTCC 0.957128 -12 TTTCAATCGTCCCCTCCTACATGTTTTTTG 3 223 0 CCCCTCCTAC 0.848922 -78 TTTGTAGTTTCTCCTTCTGATACCATC 5 8 1 TTTCTCCTTC 0.672342 -99 TCTGTTCCCCACCTTCTAATGCTTTT 8 285 0 CCCCACCTTC 0.957942 -16 CTATTCTCACCTTCTAAAAAAATC 12 81 0 TCTCACCTTC 0.963021 -14 GTTTGTCTCACATCCATCTATCTCA 16 6 1 TCTCACATCC 0.863443 -141 AATTCCTCTCCCCCGATCAATTTC 16 133 0 CCTCTCCCCC 0.901595 -14 ATCTTCTGTTTCTCACATGCTCCCTTTCAG 19 118 0 TCTCACATGC 0.812764 -38 TTCGATCTTATCTCCCCTTCTCAAGTTTTG 20 155 1 TCTCCCCTTC 0.904964 -146 GTCCTCTATTTCTCTCCTGCGAGTCTTGCA 21 149 1 TCTCTCCTGC 0.946017 -95 TTGTCCATCCCTCACTCAAGGATCTCT 21 227 0 TCCCTCACTC 0.698376 -17 ********** Masking position 6 Map Score: 5.01818 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 213 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 9 GAACTAAGCGCCCGGAAAAAGGCTTAGTTGACGAG 3 72 1 CCCGAAACTT 0.951673 -229 CAGATCACAGCCGTAAGAATTTCTTCAAACCAAGG 3 150 1 CCGAAGACTT 0.974563 -151 TGGCCTGACTCCGGCAAACGGCCTTGCCAAAGAGG 7 137 1 CCGCAAACTT 0.943043 -96 TTAGAAGAAGCCGTAAAAGCTTCTT 9 1 0 CCGAAAACTT 0.981755 -72 CTTTTTAACACCCCAAATTTTTCTTTACTTTTTTC 12 11 1 CCCAAATCTT 0.869049 -84 TTTAACCATACCCCGAGTCTATCTTAGACCGGGGT 13 82 1 CCCGAGTCTT 0.795814 -64 TACTCCCACACCGCAAAAGCCGCTTTATGCGGCTT 18 11 0 CCGAAAACTT 0.981755 -132 GTATCACAGAGCGGGAAATCCGCTTTTAAATAAAA 18 54 0 GCGGAAACTT 0.92229 -89 ACGCTTTTGTGCGTAAGAGATCCTTGAGTGAGGGA 21 212 1 GCGAAGACTT 0.91107 -32 TGAGAAGCCTCCGCAAAATAATTTTGCATTTGTTT 24 13 1 CCGAAAATTT 0.824599 -214 *** **** *** Masking position 6 Map Score: 4.04086 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 155 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 CACCAAATAGACCCGGCATCAAAACAAG 2 6 0 ACCGCATAAA 0.944488 -85 CTGAGGCCATACATGACATGAAAGGAAGTATTT 2 64 1 ACAGCATAAA 0.959833 -27 GTTAAGATAAACATGAAATCAAAACACGACCTC 8 57 1 ACAGAATAAA 0.805103 -244 TGAAATCAAAACACGACCTCATATAATCTTGGG 8 70 1 ACAGCCTATA 0.832873 -231 AGCAATACAAACCGGGCATGGTACATGTATCGT 8 205 0 ACCGCATGTA 0.799004 -96 TTCCGATAATACCGGTCATAAAATCTAACAACT 16 103 0 ACCGCATAAA 0.944488 -44 CCATTTCAGGACACGCCATACTAGTATCACAGA 18 79 0 ACAGCATCTA 0.848097 -64 TCAAACAACATCAAGAAATAAAATTTAATTTAT 21 111 0 TCAGAATAAA 0.651628 -133 ATTGACAATTTCAGGGCATAATACAACCATCAA 22 30 0 TCAGCATATA 0.915399 -118 TCAAGAAATCTCATGACATTATATCACGTTTTT 22 104 0 TCAGCATATA 0.915399 -44 *** * *** *** Masking position 9 Map Score: 2.4127 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 85 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 GAGGGGACGATTGAAAGTCCCCTTGAAATTTG 3 237 1 TTGAATCCCC 0.98513 -64 GTGAATATCCCCCTGTCGGTAT 5 95 0 GTGAATCCCC 0.95256 -12 ATTGAACATTCCTTTCTTTTCAT 6 56 0 TTGAATTCCT 0.937377 -13 CTTCTTTTAATTAAATTTTCCCATAACTCTCT 7 39 0 TTAAATTCCC 0.876982 -194 CCGCCGCAGTTTGAAAATTCCCAACATTCGGG 9 37 1 TTGAATTCCC 0.981452 -36 GAGGGCAGCATTGAAGCTTCCTTCTCTTCATA 13 48 0 TTGAATTCCT 0.937377 -98 CTTGAACTCCCCCTAATTCGTC 17 10 0 TTGAACCCCC 0.953324 -13 ***** ***** Masking position 5 Map Score: 3.50605 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 23 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 CTACCACCAAATAGACCCGGCATCAAAACA 2 13 0 ATAGACCCGG 0.966155 -78 ATAAGAAAATACCGACAGGGGGATATTCAC 5 87 1 ACCGACAGGG 0.849924 -20 TAAAATGATAGCAGACCCGGCCATTTTCTT 6 19 0 GCAGACCCGG 0.964808 -50 AGGAAGCAATACAAACCGGGCATGGTACAT 8 212 0 ACAAACCGGG 0.878627 -89 TAAGTGCAATGCAGAGCGGGTATTTTTTAT 8 244 1 GCAGAGCGGG 0.947283 -57 CCGGTCTAAGATAGACTCGGGGTATGGTTA 13 84 0 ATAGACTCGG 0.787361 -62 CGAGTCTATCTTAGACCGGGGTTTTTTTTC 13 95 1 TTAGACCGGG 0.883146 -51 CTTAAGTTGAAAAGAGAGGGGAAAGAAC 13 128 1 AAAGAGAGGG 0.650825 -18 TACTAGTATCACAGAGCGGGAAATCCGCTT 18 64 0 ACAGAGCGGG 0.973518 -79 AAGAAGGAAAATAGACACGGAACGCTTTTG 21 191 1 ATAGACACGG 0.903437 -53 ********** Masking position 5 Map Score: 5.7385 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 170 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 ATTTTTTAAAAATTTCTCCTGGATTTGAT 14 10 1 AAATTTCTCC 0.930954 -101 CTCAATTTCCTCCTTTTCTTAAC 14 98 0 AATTTCCTCC 0.968132 -13 TTGGTAAAATTCCTCCTCTTAAAAGG 15 45 0 AAATTCCTCC 0.954957 -16 TTTTTTTCGTAATTTCATCCACTGACTCTG 20 12 1 AATTTCATCC 0.911231 -289 ATTCTAGCGGAAGTTTCTCCTCGTTTTTTC 22 61 1 AAGTTTCTCC 0.918914 -87 ATTTTAAGTAAATTTTATCCAGTGGAAATT 23 110 0 AATTTTATCC 0.867166 -42 ********** Masking position 5 Map Score: 2.55851 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 78 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 AGAAATTCTTACGGCTGTGATCTGCACACT 3 144 0 ACGGCTGTGA 0.453273 -157 ACAATCTTAGGAGGAAGAAAAAT 3 288 1 GAGGAAGAAA 0.670612 -13 AATATTATCGGAGTCTGGGAGCGAGTTGGC 7 111 1 GAGTCTGGGA 0.642394 -122 TCAAACTGCGGCGGCTTAGAAGAAGCCGTA 9 21 0 GCGGCTTAGA 0.854906 -52 GTTTTTTTATGCGGCTGAAATGCGGCACCG 10 23 1 GCGGCTGAAA 0.958405 -184 TTTCGATATAAAGGCATAAAAATTCATTTT 11 16 1 AAGGCATAAA 0.416594 -55 AAAGTCCAGAGAGGCTTGGAAGGGTTATGA 13 23 1 GAGGCTTGGA 0.801785 -123 TTTTCAACTTAAGGCTGAAAAAAAACCCCG 13 111 0 AAGGCTGAAA 0.900973 -35 GTTCAAACTGGAGGATGAAAAA 18 131 1 GAGGATGAAA 0.851333 -12 AAAAAAGAATGAGACAGAAAGCGTGAGAAG 20 279 1 GAGACAGAAA 0.784003 -22 TTTGTAGTCAGAGACTGAGATGTTTTCAGT 25 19 1 GAGACTGAGA 0.922035 -158 CACAAAAAAAGAGACTGAAAACATCTCAGT 25 32 0 GAGACTGAAA 0.910788 -145 ********** Masking position 10 Map Score: 1.72003 Number of sites scoring better than the average of aligned sites = 1067 Number in coding regions = 964 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 15 AATAGATTCATACATTTTTGCCTGAGGCCA 2 43 1 TACATTTTTG 0.746482 -48 ACAGTCATGATTCATTTTCATTGATTTAGG 4 75 1 TTCATTTTCA 0.917046 -65 ATTCCTCCTGTACATTTTCCCTTATTACTG 4 113 0 TACATTTTCC 0.677053 -27 GTGTTTTGATTTCATGTTTATCTTAACAAC 8 54 0 TTCATGTTTA 0.76404 -247 AATATTTTTATTCATTTATAAATTTTCTGT 10 110 0 TTCATTTATA 0.686001 -97 TACGATTGAATTAATTTTTATTCATGTTAT 10 145 1 TTAATTTTTA 0.575616 -62 GGCATAAAAATTCATTTTTATAATTAATTA 11 28 1 TTCATTTTTA 0.93949 -43 TTTTGCTATATACATTTTTACCTTTTAAGA 15 25 1 TACATTTTTA 0.92645 -36 TAAATACTCCTACATTTTCAAAGCTAATTT 20 48 1 TACATTTTCA 0.899715 -253 GCATGATTCTTGCATTTTTATTCATATGCG 24 174 1 TGCATTTTTA 0.850215 -53 ********** Masking position 5 Map Score: 1.78628 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 324 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011