AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -icytR_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 yhjM 103 similar to transcriptional regulator (LacI family) #2 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #3 yjlC 300 yjlC #4 yjlD 39 similar to NADH dehydrogenase #5 yjmA 197 similar to glucuronate isomerase #6 yjmB 67 similar to Na+:galactoside symporter #7 yjmC 104 similar to malate dehydrogenase #8 yjmE 24 similar to D-mannonate hydrolase #9 yjmG 47 similar to hexuronate transporter #10 yjmH 87 similar to transcriptional regulator (LacI family) #11 deoD 300 purine nucleoside phosphorylase #12 drm 160 phosphodeoxyribomutase #13 ripX 300 integrase/recombinase #14 cdd 118 cytidine/deoxycytidine deaminase #15 yqfF 78 yqfF #16 yqfC 56 yqfC #17 yqfB 24 yqfB #18 yqfA 21 yqfA #19 yqeZ 130 yqeZ #20 rpsU 163 ribosomal protein S21 #21 ccpA 274 transcriptional regulator (Lacl family) #22 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #23 ytxJ 23 alternate gene name: csb40; similar to general stress protein #24 ytxH 27 alternate gene name: csb40; similar to general stress protein #25 ytxG 161 alternate gene name: csb40; similar to general stress protein #26 murC 249 UDP-N-acetyl muramate-alanine ligase #27 ytpS 159 ytpS #28 ytpP 234 similar to thioredoxin H1 #29 pdp 29 pyrimidine-nucleoside phosphorylase #30 nupC 115 pyrimidine-nucleoside transport protein #31 dra 105 deoxyribose-phosphate aldolase #32 deoR 90 transcriptional regulator #33 yxxB 72 yxxB #34 yxeR 69 similar to ethanolamine transporter #35 yxeN 22 similar to amino acid ABC transporter (permease) #36 yxeM 24 similar to amino acid ABC transporter (binding protein) #37 yxeK 185 similar to monooxygenase #38 yxeI 154 similar to penicillin amidase #39 yxeH 39 similar to hypothetical proteins #40 yxeF 87 yxeF Motif number 1 TTTTATTTACGAAAGGGGTTAGACACG 2 7 0 GAAAGGGGTA 0.837978 -117 TATTATAAGGAAATGGAGGTACACTTTAAAA 2 44 0 AAATGGAGGA 0.627613 -80 CCTTATAATAAAAAGGGATAGAAACGATACT 2 65 1 AAAAGGGATG 0.395013 -59 ATCCGACTTAAAAAGGAGGATGATTCAA 2 106 1 AAAAGGAGGT 0.971614 -18 CAAAAAACTGAAAAGGAAGGAGGCACTTGC 7 85 1 AAAAGGAAGA 0.790563 -20 AATATAGTGGGAGAGGCGGTATGTTTGATGA 10 17 1 GAGAGGCGGA 0.631006 -71 CCTAACCGCAGGAAGGAGGGGTGGGACATGG 11 106 0 GGAAGGAGGG 0.666265 -195 CGTATAGAAAAAAAGGAGGCTTTCAAG 12 144 1 AAAAGGAGGT 0.971614 -17 ATCAGGATGAAAAAGGCGGATGGTTCGACCG 13 242 1 AAAAGGCGGT 0.916533 -59 TTTTTTTACCAAAACGGGGAGTAGATCAAGA 13 280 1 AAAACGGGGG 0.708705 -21 TTGATGTTTCAAGAGGAGGTTCTT 15 65 1 AAGAGGAGGT 0.858722 -14 TGTATGATTTGAAAGGAGGTTCTAACACT 16 9 0 GAAAGGAGGT 0.962276 -48 CACATGAGATGAAAGGGGGTTCTTTTTGT 16 38 1 GAAAGGGGGT 0.93352 -19 ATAGAAACGAGGAGAAGTTAT 18 4 1 GAAACGAGGG 0.767092 -18 CACTTATTATAAAAGGAAGGAGGGATACACC 19 106 1 AAAAGGAAGA 0.790563 -25 TATAATGAAAGAAAGGGGTTG 20 1 0 GAAAGGGGTG 0.838513 -163 TGTATCCAGTAAAAGGAGTGGTTTTAGG 21 257 1 AAAAGGAGTG 0.926779 -18 AAAAAATACTAAGAGGAGGAATA 24 15 1 AAGAGGAGGA 0.877347 -13 TAAAAAGCAGTGATCTCACTGCT 25 3 1 AAAAGCAGTA 0.706442 -159 CAGATAAATAAAAAGCAGTGAGATCACTGCT 25 16 0 AAAAGCAGTA 0.706442 -146 ATGATTGAAGAAAACGGGTAAACAGCAGTAT 25 118 1 AAAACGGGTA 0.431321 -44 ATATCCTGCAGCAAGGAGGTTTGAG 25 147 1 GCAAGGAGGT 0.628215 -15 ATGGATATACATAAGGAGGGATTTTTATT 28 9 0 ATAAGGAGGA 0.642906 -226 TCAGAAAACGGAAAGCAGTCTGCCTTCCGTC 30 51 0 GAAAGCAGTT 0.603784 -65 ATCTTAACAAAAAAGGAAGTGTGCGAAGG 31 87 1 AAAAGGAAGG 0.791216 -19 TCAGGTGGATGAAAGCCGGCGCCAGCCTGTA 32 14 1 GAAAGCCGGG 0.648562 -77 AAAGCAAATCAAAAGCAGTTTTATCAGGACT 32 50 1 AAAAGCAGTT 0.671578 -41 ATACGTTTGAAAAAGGAGAAAACC 34 56 1 AAAAGGAGAA 0.738544 -14 AAATAGAAAAGGCGGGAAAATCAA 36 7 1 AAAAGGCGGA 0.928174 -18 AAAACATGATAAAAGGAGTATCGCC 37 171 1 AAAAGGAGTT 0.914624 -15 ATCTGAATTGAAAAGGGGACTGATCAA 38 138 1 AAAAGGGGAT 0.569215 -17 ATTCGCCCAAAAAAGGAGGAAAGA 40 74 1 AAAAGGAGGA 0.975776 -14 ********* * Masking position 4 Map Score: 30.5692 Number of sites scoring better than the average of aligned sites = 1860 Number in coding regions = 1045 Number in noncoding regions = 815 Number of orfs with sites within 600 bp upstream = 879 Fraction of orfs with sites within 600 bp upstream = 0.141182 Motif number 2 TGAATATGGCAAGATGAAAAACTGGGTAGTA 3 147 1 AAATGAAAAA 0.813638 -154 CGCTGTCATAAACATAAAAAAAGACATTGCC 5 63 0 AAATAAAAAA 0.671449 -135 ATATAAAGGTAAAATAAAAACAAATCAAAAT 5 134 1 AAATAAAAAC 0.750263 -64 ATTTTGAAATAGAATGAAAGACGGTGAGGAC 5 177 1 AGATGAAAGA 0.788808 -21 AACGAATGTCATGATGAAACAAACTTCAGCA 11 231 0 ATATGAAACA 0.699045 -70 ACCGGTAAACAGGATGAAAACTTTCAATGCA 13 106 0 AGATGAAAAC 0.941693 -195 GTGAATCAAGAGTATGAAAACTATCATCGGT 13 170 1 AGATGAAAAC 0.941693 -131 GAAATGGATCAGGATGAAAAAGGCGGATGGT 13 235 1 AGATGAAAAA 0.916575 -66 TATACATAAAAAAATGAAACCTTTGATACAT 19 54 1 AAATGAAACC 0.685713 -77 GCCTGTCTATATAATGAAAGAAAGGGGTTG 20 10 0 ATATGAAAGA 0.699045 -154 TAAACGAGAAAGCATAAAAAAAGGCCGCACG 21 32 0 AGATAAAAAA 0.83721 -243 GTTTTTATAGATGATGAAAACGTATACTTGG 21 77 0 ATATGAAAAC 0.909452 -198 AATTTGATGAATAATGAAAAATAATGTACAC 21 134 1 ATATGAAAAA 0.872327 -141 TGATAACTACAAAATAAAAAATGAATGTGCA 22 198 1 AAATAAAAAA 0.671449 -38 GTGCAGGGAAAGGATGAAAAAA 22 224 1 AGATGAAAAA 0.916575 -12 CAGCAGTGGTATACTAAAAACCGTCCCAGAA 27 113 1 ATCTAAAAAC 0.649956 -47 AAAGTCGGTTATGCTAAAAAATATCTTAACA 31 65 1 ATCTAAAAAA 0.558131 -41 GCCAGCCTGTATAATAAAAGCAAATCAAAAG 32 34 1 ATATAAAAGC 0.615134 -57 TTCAGATGATATGATAAAACCAATCATACGT 34 31 1 ATATAAAACC 0.615134 -39 CGCATTATTCAGCCTAAAAACATGATAAAAG 37 155 1 AGCTAAAAAC 0.749106 -31 TGGGACTATAGCCTGAAAACGACATGAAGG 39 10 1 AGCTGAAAAC 0.86447 -30 ** ******** Masking position 5 Map Score: 18.2446 Number of sites scoring better than the average of aligned sites = 1035 Number in coding regions = 818 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 3 AATCGAATTGGAGTTTTTTGTGTTTGCTATT 3 56 1 GGTTTTTTGT 0.77131 -245 TTTCTGGCAATGTCTTTTTTTATGTTTATGA 5 58 1 TTCTTTTTTT 0.806286 -140 GTATATGATTGTTCTTTTTTTGGCCGGTGAT 11 55 1 GTCTTTTTTT 0.941369 -246 AGGTGGCTGCGGCTTTTTTGTTTAGAGCGAC 12 15 1 GCTTTTTTGT 0.806863 -146 CTTGAAAGCCTCCTTTTTTTCTATACGTCT 12 141 0 CCCTTTTTTT 0.715605 -20 TCGACCGGTTGATCTTTTTTTACCAAAACGG 13 266 1 GTCTTTTTTT 0.941369 -35 ACATAATCGCGCGCTTTTTTTCACGCCCATT 14 48 0 GGCTTTTTTT 0.945637 -71 ATGAAAGGGGGTTCTTTTTGT 16 46 1 GTCTTTTTGT 0.929513 -11 TTAGAAAGATGTCCTTTTCTTTGCCAT 19 7 0 GCCTTTTCTT 0.852601 -124 CTAAGAGAGATGTCTTTTTTTATACATAAAA 19 34 1 TTCTTTTTTT 0.806286 -97 GCCGCCGTGCGGCCTTTTTTTATGCTTTCTC 21 27 1 GCCTTTTTTT 0.955647 -248 ATATCATCTGGCGCTTTTTTTTGTAAAAAAC 22 25 1 GGCTTTTTTT 0.945637 -211 TTCACATGATTCGTTTTTTTTGGCGGATTTA 27 18 0 TGTTTTTTTT 0.515629 -142 TTCGCACACTTCCTTTTTTGTTAAGATATTT 31 83 0 TCTTTTTTGT 0.519924 -23 CTAAAGGCTGGATCTTTTCGTTTTATTTGAT 38 27 1 GTCTTTTCGT 0.779744 -128 * ********* Masking position 6 Map Score: 11.064 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 305 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 4 CAACTTTTTTAAGGAAGGGAAAAT 1 90 1 AAGGAAGGGA 0.876887 -14 TATAATAAAAAGGGATAGAAACGATACTTC 2 68 1 AGGGATAGAA 0.730045 -56 AGCGTGAGACAGGGAGAGGCACTACCCTTT 3 238 1 AGGGAGAGGC 0.971996 -63 GGAAATATAGTGGGAGAGGCGGTATGTTTG 10 14 1 TGGGAGAGGC 0.773557 -74 CCGGTATGATAAGGAAGGGAATTAG 10 73 1 AAGGAAGGGA 0.876887 -15 CGCAGGAAGGAGGGGTGGGACATGGGTAAA 11 101 0 AGGGGTGGGA 0.75039 -200 CTGGAACCATAGGGAAAGGATCGATTAGGA 13 46 1 AGGGAAAGGA 0.966028 -255 GTGTATTCGGAGGGAGGGAAAGAGA 20 149 1 AGGGAGGGAA 0.905289 -15 ATGAATGTGCAGGGAAAGGATGAAAAAA 22 218 1 AGGGAAAGGA 0.966028 -18 GCAGGGAAGGAAGAGCTTGAGT 23 3 1 AGGGAAGGAA 0.876887 -21 AAACAACTGGAGGGATATGAA 28 224 1 AGGGATATGA 0.730045 -11 ACTGATCCACAGGGAGGTGCAGA 32 78 1 AGGGAGGTGC 0.896842 -13 CGTGACCATGAGGGAACGGCATTGAT 37 7 0 AGGGAACGGC 0.872929 -179 AAACGACATGAAGGAGATGCAGG 39 27 1 AAGGAGATGC 0.532891 -13 ********** Masking position 4 Map Score: 11.8047 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 265 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 5 TGGGTAGTAAACATTTATTTTTGTAAATGAT 3 169 1 ACATTTATTT 0.940551 -132 GACAGCGTTAACATTTCATTTTCAAAAAAGA 5 87 1 ACATTTCTTT 0.950076 -111 GTTAACGTTAACATTTTGATTTGTTTTTATT 5 146 0 ACATTTTATT 0.825546 -52 CCCTACAAACACATTTTATTTACAAATTATT 7 35 0 ACATTTTTTT 0.958608 -70 AGATCCTCGAACATTTCTTTTTTCGATATAT 11 186 1 ACATTTCTTT 0.950271 -115 GAAAATTCTTACATTTATTTTACATTTTTAG 14 16 1 ACATTTATTT 0.940551 -103 ACACATATAAACATGTACTTTGACATTATAA 20 98 0 ACATGTATTT 0.83331 -66 TCAGTAGTGTACATTATTTTTCATTATTCAT 21 140 0 ACATTATTTT 0.728524 -135 CTTTCCCTGCACATTCATTTTTTATTTTGTA 22 205 0 ACATTCATTT 0.730946 -31 TATCATTATCATATTTTATTTGCATTATCAA 28 84 0 ATATTTTTTT 0.604115 -151 TTATGTTCTTACATGTTTTTTATCGATACTC 28 195 0 ACATGTTTTT 0.879805 -40 CCTTCGCACACTTCCTTTTTTGTTAAGA 31 88 0 ACACTTCTTT 0.750883 -18 AGACAAAGGTACATTTTGATTTATTCATATT 37 94 1 ACATTTTATT 0.825546 -92 ******* *** Masking position 3 Map Score: 7.04124 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 117 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 AGAAACTGAACCAACATAGGGGTGAGGTTGAG 9 26 1 CAACATATGA 0.909816 -22 AAAAAAAGAACAATCATATACCTGAAAAAGATATC 11 41 0 CATCATATGA 0.986244 -260 TTCTATTATGCTATGATATGGGTGAATCAAGAGTA 13 149 1 CATGATATGA 0.950426 -152 AGTATGAAAACTATCATCGGTATGATAAACCGGAA 13 180 1 CATCATCTGA 0.968582 -121 AGCCCATAAGCAATCATAAAAATGACCCGATAACG 15 31 0 CATCATATGA 0.986244 -48 ACCTCCTTTCAAATCATACACATGAGATGAAAGGG 16 20 1 AATCATATGA 0.862335 -37 CCGTTTTCTTCAATCATAAACATGTGTACTGGGCT 25 100 0 CATCATATGT 0.909815 -62 AAATTTTGTTCAATGAAAGGTTTGAACGTG 31 6 0 CATGAAATGA 0.729558 -100 CTGGCGCCGGCTTTCATCCACCTGATTT 32 4 0 CTTCATCTGA 0.812659 -87 ATGATAAAACCAATCATACGTTTGAAAAAGGAGAA 34 41 1 CATCATATGA 0.986244 -29 * ****** *** Masking position 6 Map Score: 5.86486 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 37 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 AACATTTATTTTTGTAAATGATTGTGCATGA 3 178 1 TTTGAAATGA 0.961274 -123 AAGGAATGCTTTTGGCAATGCCAGATTCATT 5 18 0 TTTGCAATGC 0.865993 -180 CAATCTCTTTTTTGAAAATGAAATGTTAACG 5 92 0 TTTGAAATGA 0.961274 -106 TTTAAAATAATTTGTAAATAAAATGTGTTTG 7 30 1 TTTGAAATAA 0.850244 -75 TGACAATGTATTTGGAAATAATGAGAAACTT 12 57 0 TTTGAAATAA 0.850244 -104 CCATGTTTGGTGTGAAAATGAACCCATA 26 8 0 TGTGAAATGA 0.933582 -242 GTCTTGGACGTTTGTCAATGAGTTAAGATTA 37 67 0 TTTGCAATGA 0.960522 -119 TGCGTGCCACTGTGCCAATGACTACATAAGT 40 44 0 TGTGCAATGA 0.93233 -44 **** ****** Masking position 7 Map Score: 5.00531 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 127 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 AGGTAAAATAAAAACAAATCAAAATGTTAA 5 140 1 AAAACAAATC 0.882116 -58 TTTAGTTATAAAAACCAAGTATACGTTTTC 21 63 1 AAAACCAAGT 0.82176 -212 CCTAAAACCACTCCTTTTACTGG 21 262 0 AAAACCACTC 0.942329 -13 TCCGCCAAAAAAAACGAATCATGTGAAAAG 27 22 1 AAAACGAATC 0.862815 -138 GCTATCAGCAGAAACCAAGCCGCTAAACAA 27 63 0 GAAACCAAGC 0.773121 -97 TGATAATGGGAAAGCCAATCTTACATATTC 28 110 1 AAAGCCAATC 0.942329 -125 TGCTTGAGGCAAAACCACTTATATGCAACG 28 143 0 AAAACCACTT 0.821759 -92 CTGTATAATAAAAGCAAATCAAAAGCAGTT 32 40 1 AAAGCAAATC 0.762894 -51 ATGATATGATAAAACCAATCATACGTTTGA 34 36 1 AAAACCAATC 0.97436 -34 TTATGCTGATAAAACCAATTCGTTCACAAT 38 95 1 AAAACCAATT 0.914692 -60 ********** Masking position 7 Map Score: 5.08244 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 221 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 9 GAACAGTACCTCCAATGATTTTA 1 4 1 CAGTACCTCC 0.776979 -100 GCAAGTGCCTCCTTCCTTTTCA 7 93 0 AAGTGCCTCC 0.966992 -12 CTTGAAAGCCTCCTTTTTTTCTA 12 148 0 GAAAGCCTCC 0.859219 -13 AAGAACCTCCTCTTGAAACA 15 69 0 AAGAACCTCC 0.961963 -10 AGTGTTAGAACCTCCTTTCAAATCA 16 6 1 TAGAACCTCC 0.799469 -51 ACAAAAAGAACCCCCTTTCATCTCA 16 42 0 AAGAACCCCC 0.826468 -15 CTTTTATAATAAGTGCCTTCTCTTCATACG 19 91 0 AAGTGCCTTC 0.697731 -40 AAAAAAGCGTCCAGATATCATC 22 3 1 AAAAGCGTCC 0.8616 -233 GCGGCGGCTGAAAAGCCTCCCTTAGCGGCG 26 166 0 AAAAGCCTCC 0.963132 -84 TGGTATACTAAAAACCGTCCCAGAAAACTA 27 119 1 AAAACCGTCC 0.724284 -41 AATAAAAATCCCTCCTTATGTATAT 28 6 1 AAATCCCTCC 0.866658 -229 ********** Masking position 2 Map Score: 4.93457 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 211 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 10 GCCAGAAAGCACTCGGAAAGGAATGCTTTT 5 36 0 ACTCGGAAAG 0.718662 -162 GTGCCCAAAAAACTGAAAAGGAAGGAGGCA 7 80 1 AACTGAAAAG 0.680508 -25 TGAAGAAGCACACGGGAAAGAA 11 3 0 CACGGGAAAG 0.740062 -298 ATACATTGTCAACGGGAATGAAAACGGTTT 12 77 1 AACGGGAATG 0.610533 -84 CCATATGCCAAATCAGAAAGGTTTTA 13 7 0 AATCAGAAAG 0.754169 -294 AATGGATCAGGATGAAAAAGGCGGATGGTT 13 237 1 GATGAAAAAG 0.399349 -64 TCGCACTCATGACGGAAAAGTGAACTCACT 20 43 1 GACGGAAAAG 0.808788 -121 TAACTAAATAAACGAGAAAGCATAAAAAAA 21 41 0 AACGAGAAAG 0.736172 -234 TTATTTATCTGATGGGAAAGCTTATTAAAG 25 36 1 GATGGGAAAG 0.893516 -126 ATCTGGGTTTAATCGGAAAGAAATAACCTG 26 107 1 AATCGGAAAG 0.955473 -143 TGATAATGATAATGGGAAAGCCAATCTTAC 28 104 1 AATGGGAAAG 0.955473 -131 ACTTAATCGAAAAGGATCGGTGAC 29 5 1 AATCGAAAAG 0.922436 -25 TTTCCTCAGAAAACGGAAAGCAGTCTGCCT 30 57 0 AAACGGAAAG 0.841878 -59 AAATAGAAAAGGCGGGAAAAT 36 2 1 AATAGAAAAG 0.570452 -23 TTTTCTATTCAAGCGAAAAGACCCTTGCGT 37 34 0 AAGCGAAAAG 0.712656 -152 ACATCAAATAAAACGAAAAGATCCAGCCTT 38 30 0 AAACGAAAAG 0.746885 -125 TATTAATCTGAATTGAAAAGGGGACTGATC 38 133 1 AATTGAAAAG 0.700759 -22 ********** Masking position 7 Map Score: 9.13301 Number of sites scoring better than the average of aligned sites = 695 Number in coding regions = 609 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 11 AGATATCATTGCAGCTGAAGAAGCACACGG 11 18 0 GCAGCTGAAG 0.803246 -283 AATCCAAAAGGCCGCCGTGCGGCCTTTTTT 21 17 1 GCCGCCGTGC 0.983605 -258 TAACAGCTATGCCGCTTTACAGCAGCTGTG 26 60 1 GCCGCTTTAC 0.861566 -190 CCGCTTTACAGCAGCTGTGCATAGACAAAT 26 71 1 GCAGCTGTGC 0.960255 -179 TATAAAATACGCCGCTAAGGGAGGCTTTTC 26 157 1 GCCGCTAAGG 0.96113 -93 AGGCTTTTCAGCCGCCGCGGTCGCAAATTG 26 178 1 GCCGCCGCGG 0.933018 -72 CATGTGAAAAGCCGCTAAGCCCTTGTTTAG 27 41 1 GCCGCTAAGC 0.979584 -119 CAGAAACCAAGCCGCTAAACAAGGGCTTAG 27 55 0 GCCGCTAAAC 0.940211 -105 GCGAATGCGTGCCACTGTGCCAATGACTAC 40 50 0 GCCACTGTGC 0.923271 -38 ********** Masking position 5 Map Score: 4.32096 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 569 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 GAGGTACACTTTAAAACGTTGATTTTATTTACGAAAGGG 2 21 0 TTATTTTTTT 0.940845 -103 GAATTGGAGTTTTTTGTGTTTGCTATTTTCAGAGAGAGT 3 60 1 TTTTTCTTTT 0.630766 -241 GGATTTTGACTTATTCAATTGTTTATTTTTAGATAAAAA 3 102 1 TTATTTTTTT 0.940845 -199 AATGTTAACGTTAACATTTTGATTTGTTTTTATTTTACC 5 141 0 TTATTTTGTT 0.698802 -57 TACAAATTATTTTAAATATTCTTTATATTATATTG 7 7 0 TTTTTTTTTT 0.900708 -98 TCCTCGAACATTTCTTTTTTCGATATATTCCTTTATAAT 11 189 1 TTTTTATTTT 0.744397 -112 GTTTACCGGTTTTACCGCTTTGTTCTATTATGCTATGAT 13 127 1 TTTTTTTTTT 0.900708 -174 AACAAATGTATCAAAGGTTTCATTTTTTTATGTATAAAA 19 51 0 TCATTTTTTT 0.821955 -80 AGTAGAGTTTTTATAAAATTTTTTGTATTTCAGTATTTC 22 131 1 TTATTTTTTT 0.940845 -105 GCGGCGTATTTTATATGTTTTGTTATGTTTAGTATCAGG 26 133 0 TTATTTTTTT 0.940845 -117 TAGCGGCTTTTCACATGATTCGTTTTTTTTGGCGGATTT 27 19 0 TCATTTTTTT 0.821955 -141 CTCCAGTTGTTTATGTTCTTACATGTTTTTTATCGATAC 28 197 0 TTATTATTTT 0.836231 -38 ATGTGTTTCTCCTTTATTTGTATTCGCTTACAAT 30 92 0 TTTTTTTTTT 0.900708 -24 AAAATTTCAATTACCAATTTACATATGTTCAAAAGTCGG 31 34 1 TTATTATTTT 0.836231 -72 *** ** ** * ** Masking position 10 Map Score: 9.83965 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 242 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 13 TTTTCATCTTGCCATATTCAGTATTATTTTTA 3 135 0 GCCAATCAGT 0.948923 -166 TGTGAATTCATGCACAATCATTTACAAAAATA 3 184 0 TGCAAACATT 0.70187 -117 TTTTGGCAATGCCAGATTCATTAAAAGGA 5 8 0 GCCAATCATT 0.967387 -190 ATCTGGCATTGCCAAAAGCATTCCTTTCCGAG 5 23 1 GCCAAACATT 0.921967 -175 GCTCGCACCTCCGGATTCAGTCAT 8 4 0 TCCGATCAGT 0.786188 -21 TCTCATTATTTCCAAATACATTGTCAACGGGA 12 62 1 TCCAATCATT 0.956717 -99 GCCTTTTTCATCCTGATCCATTTCAACAACTT 13 227 0 TCCTATCATT 0.909162 -74 ATCCTTTCCCTGCACATTCATTTTTTATTTTG 22 207 0 TGCAATCATT 0.855293 -29 AAGCCAATCTTACATATTCATTCGTTGCATAT 28 121 1 TACAATCATT 0.684236 -114 AAGTGGTTTTGCCTCAAGCAGTTTGGTATGAT 28 153 1 GCCTAACAGT 0.770156 -82 AGTTGTCTCCGCCTGATGCATTTTCTCCTT 30 9 0 GCCTATCATT 0.930707 -107 **** ** **** Masking position 6 Map Score: 4.98092 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 167 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 TCGAATTGGAGTTTTTTGTGTTTGCTATTT 3 58 1 GTTTTTTGTG 0.773642 -243 TTCCTTTTCAGTTTTTTGGGCACTCTCCAA 7 73 0 GTTTTTTGGG 0.945524 -32 AGCGCCAGATGATATCTGGACGCTTTTTT 22 10 0 GATATCTGGA 0.467662 -226 GACAAATCTTGATATCTGGGTTTAATCGGA 26 94 1 GATATCTGGG 0.909546 -156 TTTTTTGGCGGATTTATGGGAGT 27 4 0 GATTTATGGG 0.824315 -156 ATAGCTTAATCTTTTCTGGGCCGACCAGCA 27 88 1 CTTTTCTGGG 0.934042 -72 CTCCCTTATAGTTTTCTGGGACGGTTTTTA 27 127 0 GTTTTCTGGG 0.981467 -33 ACTGCTTTCCGTTTTCTGAGGAAACAGTAA 30 63 1 GTTTTCTGAG 0.855364 -53 TTACAGTAAAGATTTCTGTGAAAGAGGGTT 33 47 1 GATTTCTGTG 0.876892 -26 TCTTTCCTCCTTTTTTGGGCGAATGCGTG 40 69 0 CTTTTTTGGG 0.822732 -19 ********** Masking position 5 Map Score: 5.79693 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 157 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 ATCTAAAAATTTATTACAAATTTATCCTAGT 1 36 1 TTATTACAAT 0.674681 -68 TTCAGTATTATTTTTATCTAAAAATAAACAA 3 120 0 TTTTTATCAA 0.838389 -181 GTTACGATGTTTTTTACCCATGTCCCACCCC 11 89 1 TTTTTACCAT 0.857783 -212 GGTTGATCTTTTTTTACCAAAACGGGGAGTA 13 272 1 TTTTTACCAA 0.892508 -29 GAGATGTCTTTTTTTATACATAAAAAAATGA 19 40 1 TTTTTATAAT 0.764877 -91 GAGAAGGCACTTATTATAAAAGGAAGGAGGG 19 99 1 TTATTATAAA 0.64069 -32 ATTATACACGTTTTTATAGATGATGAAAACG 21 86 0 TTTTTATAAT 0.764877 -189 GTTCAAGGGTTTTTTACAAAAAAAAGCGCCA 22 33 0 TTTTTACAAA 0.877447 -203 AAACTCTACTTTATTACCCAAACGCTTTTAA 22 110 0 TTATTACCAA 0.767836 -126 TAAAGTAGAGTTTTTATAAAATTTTTTGTAT 22 128 1 TTTTTATAAA 0.81735 -108 TTAAAGGATTTTCTTACATAACGGAGAATAG 25 60 1 TTCTTACAAA 0.626095 -102 TCTTACATGTTTTTTATCGATACTCGTCCAT 28 189 0 TTTTTATCAT 0.790286 -46 ******** ** Masking position 6 Map Score: 4.26071 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 198 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257