AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -irpoN_bsub_opreg_300.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yckK 114 similar to glutamine ABC transporter (glutamine-binding protein) #2 yclA 89 similar to transcriptional regulator (LysR family) #3 yfjN 300 similar to hypothetical proteins #4 yfjM 195 yfjM #5 yfjL 29 alternate gene name: yztA #6 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #7 acoR 115 transcriptional regulator #8 spoVK 300 alternate gene name: spoVJ; disruption leads to the production of immature spores (stage V sporulation) #9 ynbA 220 similar to GTP-binding protein protease modulator #10 ynbB 187 similar to hypothetical proteins #11 glnR 110 transcriptional regulator #12 glnA 60 glutamine synthetase #13 yqiY 80 similar to amino acid ABC transporter (permease) #14 yqiX 268 similar to amino acid ABC transporter (binding protein) #15 yqiW 162 similar to hypothetical proteins from B. subtilis #16 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #17 glnQ 155 glutamine ABC transporter (ATP-binding protein) #18 glnH 21 glutamine ABC transporter (glutamine-binding protein) #19 glnM 60 glutamine ABC transporter (integral membrane protein) #20 ytmM 29 similar to amino acid ABC transporter (permease) #21 ytmL 21 similar to amino acid ABC transporter (permease) #22 ytmI 152 similar to hypothetical proteins from B. subtilis #23 yufT 300 similar to NADH dehydrogenase #24 yxeN 22 similar to amino acid ABC transporter (permease) #25 yxeM 24 similar to amino acid ABC transporter (binding protein) #26 yxeK 185 similar to monooxygenase #27 yxeI 154 similar to penicillin amidase #28 yxeH 39 similar to hypothetical proteins #29 yxeF 87 yxeF #30 rocR 240 transcriptional regulator (NtrC/NifA family) Motif number 1 AAATCAACCAGAAAAGTGGGGAATAAG 1 98 1 GAAAAGTGGG 0.777848 -17 TAAAAGGTATGATAAGGAGGCGCTTTCTT 2 71 1 GATAAGGAGG 0.927256 -19 GAGATATCATATAAAGGGGGAGAGGAAA 4 178 1 ATAAAGGGGG 0.791057 -18 TAAAGGAAAAAGCAGGCGCATGGATA 7 7 1 AAAAAGCAGG 0.854925 -109 TTCAACAATAAAAAAGCAGGCGCCTTATAT 7 34 0 AAAAAGCAGG 0.854925 -82 CGATTGCTTTGAAAAGGCGGAAATACGAGC 9 41 0 GAAAAGGCGG 0.98321 -180 ACTAAGTTAAGAAAAGGAGGAAATTGAG 11 93 1 GAAAAGGAGG 0.987376 -18 AAAAAAGCGGCTCAACTTTT 13 1 1 AAAAAAGCGG 0.803428 -80 TTTCCTGTAAGAAAAGGAGACAAAGGCT 13 63 1 GAAAAGGAGA 0.943276 -18 AAAAGTAATGAATACGGGGGAAATGGATC 14 250 1 AATACGGGGG 0.737779 -19 CTGCTTACAGAAAAAGGGGATTATATAACC 15 38 0 AAAAAGGGGA 0.93474 -125 ACAGATGATGAAAAAGGAGAGGTCTTCA 15 145 1 AAAAAGGAGA 0.923798 -18 GAAATGAAAAGATAAAGGGGTTTTCTGAAG 16 11 0 GATAAAGGGG 0.590474 -142 AACAGAAATGGGGGAGCTTGT 18 5 1 GAAATGGGGG 0.856329 -17 TAATGATGAAAAACAGGAGGGAGCACA 22 8 0 AAACAGGAGG 0.826068 -145 TAAGTCTAACAAAAAAGAGGTTATTTGTAT 23 45 0 AAAAAAGAGG 0.845177 -256 TTGAGAACGAGAAAAGGAGGTCTTATCTTT 23 202 1 GAAAAGGAGG 0.987376 -99 AAAGCAAATAAAAAAGGCGATAAAATAGCA 23 247 0 AAAAAGGCGA 0.90076 -54 GAAACGGCGGTGACTCACCA 24 1 1 GAAACGGCGG 0.937526 -22 AAATAGAAAAGGCGGGAAAATCAA 25 6 1 GAAAAGGCGG 0.98321 -19 AATCTGAATTGAAAAGGGGACTGATCAA 27 137 1 GAAAAGGGGA 0.951567 -18 CATTCGCCCAAAAAAGGAGGAAAGA 29 73 1 AAAAAGGAGG 0.982764 -15 TGAAACAGAAAACAAGGGGGAATTCAAAT 30 10 0 AACAAGGGGG 0.865594 -231 ATTTTATAAAAAAACGGAGAGGATATGCAA 30 181 0 AAAACGGAGA 0.756496 -60 ********** Masking position 9 Map Score: 41.0503 Number of sites scoring better than the average of aligned sites = 901 Number in coding regions = 560 Number in noncoding regions = 341 Number of orfs with sites within 600 bp upstream = 375 Fraction of orfs with sites within 600 bp upstream = 0.0602313 Motif number 2 AATCCCTTTATTTTGTTAGCCTTTTTTGAATCAAGCACTGCTG 4 10 0 TTTTTTTTAA 0.982732 -186 CAGCCTGTCTTTTCTCTAATTTATTGTAAGAAAATAATGGTATA 4 127 1 TTTCTTTTAA 0.917357 -69 ATATCCGGTCTTTTTTTTGCATGCTGTAAAACGAGACAAATGAA 6 60 1 TTTTTTTTAA 0.98273 -172 AATTTCCTCCTTTTCTTAACTTAGTTTCATTATAGGTGATGTTA 11 74 0 TTTTTTTTAA 0.982667 -37 CGGCTCAACTTTTTCGTTGAGCCTTTTTATTGAATAGGAAACTT 13 18 1 TTTTTCTTAA 0.892493 -63 AGCGATTTAATTTTTATCTAGTAATATCAGAAGAGATCACTGGA 14 112 1 TTTTTTTTAA 0.982672 -157 CAGTTTCTCATTTTTATGCAATACTATTTTTAAAAATTATCTTT 14 167 0 TTTTTTTTTA 0.848458 -102 GCTCCTTTATTTTCCTTCTGGTTATATAATCCCCTTTTTCTGTA 15 19 1 TTTCTTTTAC 0.827435 -144 GACCTCTCCTTTTTCATCATCTGTTCTTATGATAGCAAGGAAAC 15 125 0 TTTTTTTTAA 0.982732 -38 ATCATTTACTTTTTGGTCAAATTTTCTGATAGGAGGATTGCG 17 124 1 TTTTTTTTAA 0.982732 -32 CTGTAATGGATTTTTATGAGTTCTTTTGACCTCAAAATAAGTCT 23 68 0 TTTTTTTTAA 0.982732 -233 TTTATCGCCTTTTTTATTTGCTTTTATCATTCCCTTCTTGGCAA 23 253 1 TTTTTTTTAC 0.942919 -48 CAAAGGTACATTTTGATTTATTCATATTAAACGACTAGGAATAT 26 97 1 TTTTTTTTAA 0.982732 -89 ATTTTCTTAATATTGCTTCTATTTTATAAAAAAACGGAGAGGAT 30 187 0 TATTTTTTAA 0.848501 -54 **** * * * * * * Masking position 15 Map Score: 17.2176 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 72 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 AAAAATCAAATCCTTTCATTATGGGATACG 3 278 0 TCCTTTCATT 0.811165 -23 TGTGTAAAAATCCCTTTATTTTGTTAGCCT 4 32 0 TCCCTTTATT 0.7398 -164 AAATATACCATTATTTTCTTACAATAAATT 4 144 0 TTATTTTCTT 0.816119 -52 ATCGACGTATTTATTTCCTTGGAAATCTTT 6 11 0 TTATTTCCTT 0.695086 -221 TTTGTGCGCCTCCTTCTATTTAGGGTTCAC 6 212 0 TCCTTCTATT 0.841793 -20 CAAATGGATGTTCCTTTCTTTTGCATATTG 9 117 0 TTCCTTTCTT 0.790288 -104 GTCATACTGTTCATTTTCTTCATTAAAATA 10 91 0 TCATTTTCTT 0.947334 -97 CTCAATTTCCTCCTTTTCTTAACTTAGTTT 11 91 0 TCCTTTTCTT 0.978226 -20 TTGGTAAAATTCCTCCTCTTAAAAGGTAAA 12 41 0 TCCTCCTCTT 0.76224 -20 AGCCTTTGTCTCCTTTTCTTACAGGAAAAA 13 61 0 TCCTTTTCTT 0.978226 -20 CTTTATCTTTTCATTTCCTTTATTGTCCAG 16 24 1 TCATTTCCTT 0.902333 -129 TTACCACGTTTTCTTCTCTTGACAAAATAT 16 62 0 TTCTTCTCTT 0.875813 -91 AAAAGTTTGATCATTTACTTTTTGGTCAAA 17 115 1 TCATTTACTT 0.63904 -41 CACTGCTCCCTCTCTTTTTAC 21 6 0 TCCCTCTCTT 0.906688 -16 AGATAAGACCTCCTTTTCTCGTTCTCAATT 23 200 0 TCCTTTTCTC 0.907768 -101 TTTGCTTTTATCATTCCCTTCTTGGCAAAA 23 269 1 TCATTCCCTT 0.854605 -32 GGCGATACTCCTTTTATCATGTTTTTAG 26 168 0 TCCTTTTATC 0.646922 -18 CCTCCCTCAATTATTTTCTTAATATTGCTT 30 213 0 TTATTTTCTT 0.816119 -28 ********** Masking position 9 Map Score: 15.8505 Number of sites scoring better than the average of aligned sites = 1503 Number in coding regions = 1233 Number in noncoding regions = 270 Number of orfs with sites within 600 bp upstream = 290 Fraction of orfs with sites within 600 bp upstream = 0.0465789 Motif number 4 TACAAATCTAAAGGATAACTTTTTTTTAGTATGA 1 43 0 AGGATATTTT 0.727629 -72 ATTATGGGATACGGCTGAACCTTTATCCCAAATT 3 257 0 AGGCTGCTTT 0.95757 -44 CCCATAATGAAAGGATTTGATTTTTGTT 3 283 1 AGGATTTTTT 0.949967 -18 TATTGTTGAAAGCGCTTTATTTTTCCCCTACAAT 7 54 1 ACGCTTTTTT 0.90934 -62 CATGTGTCGAAACAATTGCTTTTTTCGGGAACAA 8 215 0 ACAATTTTTT 0.555295 -86 GTTCGTTCAAATGGATGTTCCTTTCTTTTGCATA 9 120 0 AGGATGCTTT 0.967893 -101 GCCGCATATCACGGATGAGCATTTTGAAAATTCT 9 197 1 AGGATGATTT 0.770976 -24 CGGCAAGTGAAGGGAAGCTCCTTTCCAGAATCAA 10 32 1 AGGAAGCTTT 0.819769 -156 ACGATGGTAGACCGCTTCTATTTTAATGAAGAAA 10 73 1 ACGCTTTTTT 0.909341 -115 TCTTTAATTCACCGATGATACTTTGCTCTTCTTG 10 136 0 ACGATGCTTT 0.955095 -52 CGGATTGTACAGCGATTTAATTTTTATCTAGTAA 14 102 1 ACGATTTTTT 0.930541 -167 GAGGTTTACAAGGAATTATTCTTTATGTTTCTTT 17 37 1 AGAATTCTTT 0.690381 -119 TACTGAAGTGAAGGTTTACTTTTTTTGATTAGTC 22 42 1 AGGTTTTTTT 0.687409 -111 CAGCCTTTAGAAGGCTGGATTTTTTA 27 3 0 AGGCTGTTTT 0.947101 -152 CAGCCTTCTAAAGGCTGGATCTTTTCGTTTTATT 27 20 1 AGGCTGCTTT 0.957319 -135 TCTTTGACGAATCGATTTGACTTTCGTTATGCTG 27 69 1 ACGATTCTTT 0.944074 -86 ACATATTGTGAACGAATTGGTTTTATCAGCATAA 27 95 0 ACGAATTTTT 0.669022 -60 * ***** **** Masking position 12 Map Score: 12.0159 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 439 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 TGATAAGAAATGCTTTCGCATGCGATAAGTG 3 203 1 TGCTTTCCAT 0.949593 -98 CTGACCATGCTTCTTTTACACTTATCGCATG 3 221 0 TTCTTTTCAC 0.697846 -80 TACTCAGCCTGTCTTTTCTCTAATTTATTGT 4 123 1 GTCTTTTTCT 0.724485 -73 GTGATATCCGGTCTTTTTTTTGCATGCTGTA 6 57 1 GTCTTTTTTT 0.470489 -175 TCCATGCGCCTGCTTTTTCCTTTA 7 4 0 TGCTTTTCCT 0.943451 -112 ATAAGGCGCCTGCTTTTTTATTGTTGAAAGC 7 36 1 TGCTTTTTAT 0.879778 -80 TTCTCATTATTTCTTTTTCATACAACGGGCT 8 64 0 TTCTTTTCAT 0.947949 -237 TATAGTGAGCTTCTTTCTCATTATTTCTTTT 8 78 0 TTCTTTCCAT 0.931672 -223 GGATGTTCCTTTCTTTTGCATATTGGGCAGT 9 111 0 TTCTTTTCAT 0.947949 -110 CGACTAAAATGGCTTTCTCCTGAATCGTTTC 9 156 0 GGCTTTCCCT 0.903404 -65 TGAAGACCTCTCCTTTTTCATCATCTGTTCT 15 142 0 TCCTTTTCAT 0.928402 -21 CTGCTTTCACCTCACCTATATC 17 2 1 TGCTTTCCCT 0.925878 -154 CTATTTTATCGCCTTTTTTATTTGCTTTTAT 23 249 1 GCCTTTTTAT 0.738466 -52 TGATTTTCCCGCCTTTTCTATTT 25 3 0 GCCTTTTTAT 0.738466 -22 CATGTTATCCTGCTTTCCCTTTATATAAATG 30 41 1 TGCTTTCCTT 0.80846 -200 AAGTGCAAAATTCTTTTGCATATCCTCTCCG 30 166 1 TTCTTTTCAT 0.947949 -75 ******* *** Masking position 6 Map Score: 11.5945 Number of sites scoring better than the average of aligned sites = 1046 Number in coding regions = 891 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 6 GATTTCACGTGGGATGATTATCTACCCTAT 3 154 0 GGGATGATTA 0.765296 -147 CGGCGTGTAAGGGAGGAGCGATCAAGGAA 7 97 1 GGGAGGAGCG 0.959925 -19 CCGCATATCACGGATGAGCATTTTGAAAAT 9 198 1 CGGATGAGCA 0.925169 -23 TTGAGCATCCGGGTTGTTCGTCT 14 4 0 GGGTTGTTCG 0.790498 -265 TGGTAACATAGGGTTGTGCAAATTATTGCA 16 86 1 GGGTTGTGCA 0.944588 -67 CAACCATCCCGGGATGAGCAGGCGATGCTC 19 11 1 GGGATGAGCA 0.98679 -50 TTATCAAATTGGGATGAGCATCGCCTGCTC 19 26 0 GGGATGAGCA 0.98679 -35 AAATAATTGAGGGAGGTTCATACA 30 227 1 GGGAGGTTCA 0.911559 -14 ********** Masking position 6 Map Score: 5.60967 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 113 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 GGGTCTTTTTTGTACGCAGCTTTTACTCAGCCTGTCT 4 100 1 TGTCATTTAT 0.768125 -96 AGATTTTGTTTTTAATCATTTTGTCAGAGTATTATAG 8 104 0 TTTCATTTCG 0.936631 -197 ATTTTTTAAAAATTTCTCCTGGATTTGATG 11 4 1 TTTAATTTCT 0.932229 -107 TGCAATACTATTTTTAAAAATTATCTTTAGGCTTATC 14 158 0 TTTAATTTCT 0.93223 -111 TAATTTGTATTTTAAACAGTTTCTCATTTTTATGCAA 14 190 0 TTTCATTTCT 0.977089 -79 ACCTCTCCTTTTTCATCATCTGTTCTTATGATAGCAA 15 131 0 TTTCATGTCT 0.879827 -32 CACAACCCTATGTTACCACGTTTTCTTCTCTTGACAA 16 67 0 TGTCATTTCT 0.959746 -86 AATAAATAGGTGTGCAAATTTTTTCATACAAAGGGGT 16 120 1 TGTAATTTCT 0.884926 -33 TCATTTACTTTTTGGTCAAATTTTCTGATAGGAGGAT 17 125 1 TTTCATTTCG 0.936631 -31 TTCCTATTTGTTTACTAAGCTTTTATTGTTTATACTA 22 96 0 TTTAATTTAT 0.656503 -57 TTGTTTTCTGTTTCAACATGTTATCCTGCTTTCCCTT 30 25 1 TTTCATTTCT 0.977089 -216 TATCAGAATGTTTTTGCACCTTGTCCTCGAAAATTGT 30 109 0 TTTCATTTCT 0.977089 -132 *** ** ** ** * Masking position 8 Map Score: 10.6218 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 118 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 AAATGCTTTCGCATGCGATAAGTGTAAAAGA 3 210 1 GCTGCGATAA 0.780238 -91 AGTAAAAGCTGCGTACAAAAAAGACCCGGAT 4 96 0 GCTACAAAAA 0.897107 -100 ACCATTATTTTCTTACAATAAATTAGAGAAA 4 137 0 TCTACAATAA 0.59278 -59 TCGTTTTACAGCATGCAAAAAAAAGACCGGA 6 63 0 GCTGCAAAAA 0.950646 -169 GTAATACGTTTCGTACAAAAATCAGCCCGTT 8 41 1 TCTACAAAAA 0.866613 -260 AGGCGGAAATACGAGCAAAAAACAGACCTCT 9 26 0 ACAGCAAAAA 0.684002 -195 TTCGTTTACTGCTTACAGAAAAAGGGGATTA 15 45 0 GCTACAGAAA 0.829765 -118 TCCTTTATTGTCCAGCGGAAAAAATATTTTG 16 39 1 TCAGCGGAAA 0.827441 -114 TCAAAATAAGTCTAACAAAAAAGAGGTTATT 23 50 0 TCAACAAAAA 0.825157 -251 AAGCGTGGCAGCTTGCAGAAAAGTGCGATAT 23 119 1 GCTGCAGAAA 0.915026 -182 TTTTTTCTATTCAAGCGAAAAGACCCTTGCG 26 35 0 TCAGCGAAAA 0.895587 -151 TTCTGATATTTCGAGCGAAAATTTCAGCAAG 30 138 1 TCAGCGAAAA 0.895587 -103 ** ******** Masking position 10 Map Score: 5.5242 Number of sites scoring better than the average of aligned sites = 503 Number in coding regions = 440 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 TTCAATCATACTCCTGATATATCC 2 2 1 TCATCATTCC 0.862642 -88 AATAAATACGTCGATCATTGTCAAAGGCCGGGT 6 26 1 TCATCATTCA 0.917291 -206 GATCCATTTCCCCCGTATTCATTACTTTTGG 14 248 0 TCCCCGTTCA 0.904071 -21 CTGCCTATTCACTCCTTATCAAATTGGGATG 19 40 0 TCCTCCTTCA 0.983221 -21 TCTTCTCCCCCCTCATCCGAAGAAATAT 20 12 0 TCCCCCTTCC 0.949471 -18 TTTTGTCACTCCTCTTCACAAAATATAT 22 135 0 TCCTCCTTCA 0.983221 -18 ATATTTAAAATCAATCCTGATCAAGCTGAAGGA 23 14 0 TCATCCTTCA 0.958169 -287 TCAATGCCGTTCCCTCATGGTCACGCAAGGGTC 26 12 1 TCCTCATTCA 0.965955 -174 ** ***** *** Masking position 8 Map Score: 5.03663 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 62 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 GTGTAAAAATCCCTTTATTTTGTTAGCCTT 4 31 0 CCCTTTATTT 0.902641 -165 TTTCCTCTCCCCCTTTATATGATATCTCCA 4 176 0 CCCTTTATAT 0.978098 -20 GTCTTTTGAGCCCGTAAAATCAGTCTTCTC 6 157 0 CCCGTAAAAT 0.52094 -75 CAAAAATCAGCCCGTTGTATGAAAAAGAAA 8 56 1 CCCGTTGTAT 0.925156 -245 ATTGAATAATCCCTTAATATTTATTCATAT 14 72 0 CCCTTAATAT 0.933828 -197 TTATATAATCCCCTTTTTCTGTAAGCAGTA 15 40 1 CCCTTTTTCT 0.840001 -123 TTCAGAAAACCCCTTTATCTTTTCATTTCC 16 12 1 CCCTTTATCT 0.96196 -141 CCCGATACCCCTTTGTATGAAAAAATTT 16 135 0 CCCTTTGTAT 0.96196 -18 ATCCTGCTTTCCCTTTATATAAATGCAAGT 30 47 1 CCCTTTATAT 0.978098 -194 ********** Masking position 5 Map Score: 7.55238 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 75 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 11 CACTAAGAAAGACGAAGGTCAGCGCCAGTT 3 108 1 GACGAAGGTC 0.918236 -193 GTCGATCATTGTCAAAGGCCGGGTGATATC 6 35 1 GTCAAAGGCC 0.961948 -197 GACAAAACGAGACACACGTCTCAAACTGTC 6 113 1 GACACACGTC 0.902199 -119 TGCCGATTGTGACAAACGCCTATCATGTGT 8 242 0 GACAAACGCC 0.974917 -59 AAGAAAAGGAGACAAAGGCT 13 71 1 GACAAAGGCT 0.843302 -10 TTTTTGATTAGTCAAAGATCAGAGTATGCT 22 63 1 GTCAAAGATC 0.716592 -90 AAAATATACGGTCAAACGACCTAGTCCAAA 23 152 0 GTCAAACGAC 0.836995 -149 TTAACTCATTGACAAACGTCCAAGACAAAG 26 72 1 GACAAACGTC 0.974918 -114 AAACGTCCAAGACAAAGGTACATTTTGATT 26 85 1 GACAAAGGTA 0.845928 -101 ********** Masking position 6 Map Score: 4.11324 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 159 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 12 TAAAATCAACCAGAAAAGTGGGGAATAAG 1 96 1 CAGAAAGTGG 0.766895 -19 ATTACCAACGCAAAATAATTGCCCTGTTA 3 9 0 CAAAAAATTG 0.906442 -292 AAAAGGCTAACAAAATAAAGGGATTTTTACA 4 29 1 CAAAAAAAGG 0.909043 -167 ATAAATTAGAGAAAAGACAGGCTGAGTAAAA 4 120 0 GAAAAACAGG 0.650638 -76 TTTATTGTAAGAAAATAATGGTATATTTAGT 4 146 1 GAAAAAATGG 0.92623 -50 TACATATGAGGAAAAGAGTGGGAAC 5 15 1 GAAAAAGTGG 0.903851 -15 TTTACGGGCTCAAAAGACTGGCACACTTCTT 6 169 1 CAAAAACTGG 0.870554 -63 TATCATGTGTCGAAACAATTGCTTTTTTCGG 8 221 0 CGAAAAATTG 0.666669 -80 GCCCAATATGCAAAAGAAAGGAACATCCATT 9 114 1 CAAAAAAAGG 0.909043 -107 ATGTATATAGCAAAACAGTTGCTAACGGA 12 9 0 CAAAAAGTTG 0.878846 -52 AAAGGCTCAACGAAAAAGTTGAGCCGCTTTT 13 13 0 CGAAAAGTTG 0.599589 -68 TAACCAGAAGGAAAATAAAGGAGCAGTTGTA 15 12 0 GAAAAAAAGG 0.854964 -151 TTACTGCTTACAGAAAAAGGGGATTATATAA 15 40 0 CAGAAAAGGG 0.669107 -123 ACGAAGAGGCCAAAAAAAGTGCACGGCGAAG 15 71 1 CAAAAAAGTG 0.816809 -92 CCCTTTGTATGAAAAAATTTGCACACCTATT 16 124 0 GAAAAATTTG 0.398289 -29 ATAAGTCTAACAAAAAAGAGGTTATTTGTAT 23 45 0 CAAAAAGAGG 0.882114 -256 TGTTGAAACAGAAAACAAGGGGGAATTCAAA 30 12 0 GAAAAAAGGG 0.852464 -229 AGAGGATATGCAAAAGAATTTTGCACTTGCT 30 163 0 CAAAAAATTT 0.299559 -78 GCAATATTAAGAAAATAATTGAGGGAGGTTC 30 215 1 GAAAAAATTG 0.851076 -26 ***** ***** Masking position 5 Map Score: 16.469 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 623 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 13 CCTCCTTATCATACCTTTTAGGTATTAATTATA 2 58 0 ATACCTTTGT 0.794453 -32 AAAGCGCAGGATTCCTTATTGTTCCCGAAAAAA 8 197 1 ATTCCTTTGT 0.968172 -104 TCTACCATCGTTTCCGATTTGATTCTGGAAAGG 10 51 0 TTTCCGATGT 0.800543 -137 CTTAACTTAGTTTCATTATAGGTGATGTTATAT 11 71 0 TTTCATTTGT 0.740137 -40 AGGAAAAAAGTTTCCTATTCAATAAAAAGGCTC 13 36 0 TTTCCTATAT 0.766542 -45 GCTCCTTTATTTTCCTTCTGGTTATATAATCCC 15 19 1 TTTCCTTTGT 0.97308 -144 AGTTTGATCATTTACTTTTTGGTCAAATTTTCT 17 118 1 TTTACTTTGT 0.740137 -38 AAAATATATAATTCCTATTTGTTTACTAAGCTT 22 111 0 ATTCCTATGT 0.947188 -42 AAACTCCTATATTCCTAGTCGTTTAATATGAAT 26 116 0 ATTCCTATGT 0.947188 -70 GTGATCAGTCTCCTTGTGGGTGAATTCCTTA 29 9 1 TCTCCTTTGT 0.871915 -79 TTGTGGGTGAATTCCTTATAACTTATGTAGTCA 29 24 1 ATTCCTTTAT 0.824137 -64 ******* * * * Masking position 9 Map Score: 3.53361 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 171 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 14 ********** No masking Map Score: 1.15701e-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 Motif number 15 CGTTTTCATCTATTGTAGGGGAAAAATAAAGC 7 67 0 TATTTAGGGA 0.798919 -49 AGAAATAAAGTATTTCTCGGGAAAGCGCAGGA 8 176 1 TATTCTGGGA 0.833008 -125 CTCTATATGATATTCAAGCGGATGCCGATTGT 8 262 0 TATTAACGGA 0.963238 -39 TGAGCCTTTTTATTGAATAGGAAACTTTTTTC 13 35 1 TATTAAAGGA 0.802116 -46 ATTAAGGGATTATTCAATCGGATTGTACAGCG 14 84 1 TATTAACGGA 0.963238 -185 TTGTGCAAATTATTGCAACGGAATAAATAGGT 16 99 1 TATTCACGGA 0.962522 -54 TATATTTCTTCGGATGAGGGGGGA 20 3 1 TATTCTCGGA 0.8903 -27 TAATTTTTTCTATTCAAGCGAAAAGACCCTTG 26 37 0 TATTAACGAA 0.719784 -149 AACTTGCATTTATATAAAGGGAAAGCAGGATA 30 46 0 TATAAAGGGA 0.717416 -195 **** ** **** Masking position 3 Map Score: 2.06154 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 91 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