AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00790_bsub_reg_300.orf -o00790_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 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 yacA 103 similar to cell-cycle protein #5 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #6 yacB 194 similar to hypothetical proteins #7 yacC 85 similar to hypothetical proteins #8 yacD 46 similar to protein secretion PrsA homolog #9 cysK 75 cysteine synthetase A #10 pabB 166 para-aminobenzoate synthase (subunit A) #11 cwlJ 300 alternate gene name: ycbQ #12 ycbR 105 similar to toxic cation resistance protein #13 phoD 278 phosphodiesterase/alkaline phosphatase D #14 phoB 300 alkaline phosphatase III #15 yerE 264 similar to hypothetical proteins #16 yerF 61 similar to ATP-dependent DNA helicase #17 phoA 300 alkaline phosphatase A #18 yhfI 151 similar to hypothetical proteins #19 yloB 115 similar to calcium-transporting ATPase #20 thyA 300 thymidylate synthase A #21 thyB 83 thymidylate synthase B #22 ypjP 259 ypjP #23 ypiP 296 ypiP #24 yphP 106 similar to hypothetical proteins from B. subtilis #25 ilvD 288 dihydroxy-acid dehydratase #26 ypgR 59 similar to hypothetical proteins #27 bsaA 300 glutathione peroxidase #28 mtrA 187 GTP cyclohydrolase I #29 hbs 300 non-specific DNA-binding protein HBsu #30 ypbB 265 ypbB #31 folC 59 folyl-polyglutamate synthetase #32 valS 300 valyl-tRNA synthetase #33 yvgX 80 similar to heavy metal-transporting ATPase #34 yvgY 73 similar to mercuric transport protein #35 yvgZ 127 similar to hypothetical proteins #36 dnaC 169 replicative DNA helicase Motif number 1 TGCTTTCAGCCCCTTTTCTCAAATTAAAAAC 8 23 0 CCTTTTCTCA 0.667526 -24 AAGAGAAATTCACTTTTTTCACTAACAACAT 10 97 1 CCTTTTTTCA 0.942757 -70 TATTTTGCATTGCATCTTTTCAAAGAAAAAC 12 39 0 TCATCTTTTC 0.375445 -67 TCTCCGTCAGCTCTTTTTTCTTTGATTATCT 12 78 0 CCTTTTTTCT 0.748569 -28 TCAAGATCCCCTCTCTCCTCATTGATCG 13 261 0 CCCTCTCTCC 0.57554 -18 ACAATACCTCTTTCCAACGTAATAC 14 5 1 TCCTCTTTCC 0.813884 -296 GGCAGGAGCACACATTTTTCACCAGATTCCT 15 73 0 CCATTTTTCA 0.914123 -192 GCCATATGCTCTCTTTTTTTATGAAAAAAGA 15 130 1 CCTTTTTTTA 0.849725 -135 GGTGTTTTGATTCTTTTTTCATAAAAAAAGA 15 141 0 TCTTTTTTCA 0.866223 -124 AGAATCAAAACACCTTTTTCAGTGAATAACG 15 158 1 CCCTTTTTCA 0.963749 -107 AACGGCTTTTTCCGTTTTTCCGCGCTATGTG 15 194 1 TCGTTTTTCC 0.598867 -71 TACTTTATCACTCATTTTTCCGATATATGAG 17 49 0 CCATTTTTCC 0.885954 -252 ATGTAAAGCATTCATTTTTCAGAAAAATCTT 17 152 0 TCATTTTTCA 0.807139 -149 TCCCTCTTTCCCCTTTGTAGT 18 1 1 TCCTCTTTCC 0.813884 -151 GTTTAAAACATGCTTTTTTCAAGAAAAATGG 18 85 1 TCTTTTTTCA 0.866223 -67 CTTCAATATACCCATTTTTCTTGAAAAAAGC 18 96 0 CCATTTTTCT 0.658035 -56 GGAGTTAATCCCCCTCTTTTACACCTGTATT 20 153 0 CCCTCTTTTA 0.839553 -148 ACTATTCATATCCTTCTTTCATTTTCAGTTG 20 279 0 TCTTCTTTCA 0.787772 -22 AGGTGCCAAATTCTTTTTTCATCCGAATACA 23 231 1 TCTTTTTTCA 0.866223 -66 GCATGATCTGCACCTTTTTTATCT 25 4 0 CCCTTTTTTA 0.901262 -285 GCAGATCATGCACCTTTTTTATGTGAATTCA 25 24 1 CCCTTTTTTA 0.901262 -265 ATTCATATGGCTCGTTTTTTATCTTATCATT 27 159 0 CCGTTTTTTA 0.641115 -142 CTGATTATTTTACCTTTTTTAAATCGCAATT 27 255 0 TCCTTTTTTA 0.782075 -46 TTCCTTTTTTTCCTTTTTTCATCC 29 4 0 TCTTTTTTCA 0.866223 -297 CTTACTTGCTCTCATTTTTTTCTGAGACAGG 29 205 1 CCATTTTTTT 0.397834 -96 TGATAATCCCCTCTTTTATAAGACAAGG 31 42 0 CCCTCTTTTA 0.839553 -18 TCTCTGCATGCGCCTTTTTTGTACTCTTCCC 32 44 0 CCCTTTTTTG 0.640453 -257 AATTTCTCTACTCTTCTTTCAAGAAATTATG 32 132 0 CCTTCTTTCA 0.904225 -169 TTCGCGGTACCACCTTTTTTCATGAACTCAA 32 202 0 CCCTTTTTTC 0.869477 -99 GGATGAAGAGCTCTTTTTTCGTTCTCAGCCA 32 255 1 CCTTTTTTCG 0.762692 -46 TATGTTTTATTGCATTTTTCCCGCCTTGTTA 36 26 1 TCATTTTTCC 0.753346 -144 * ********* Masking position 5 Map Score: 32.6015 Number of sites scoring better than the average of aligned sites = 1682 Number in coding regions = 1355 Number in noncoding regions = 327 Number of orfs with sites within 600 bp upstream = 350 Fraction of orfs with sites within 600 bp upstream = 0.0562159 Motif number 2 CGGGCCAAACAAATATGGTAGCGGCGGAGGGGATC 1 9 0 AAATAGGCGG 0.927632 -292 ATGACAGGCAACGAATATAACAGGTGGGAGATGAGAG 1 272 1 AGAAAGGTGG 0.777066 -29 CTGAGAATCCTCGTATTCTCCAGGAGGAATGAAT 2 61 1 TGATCGGAGG 0.582486 -24 GAACATAGTTGTGCTTACTGTGGGAGGAGGTAAGGA 5 72 1 GGTTGGGAGG 0.779542 -26 GAAACCGCGTAGGAAGTGTATAGGAGGTTTAGTA 7 62 1 AGATAGGAGG 0.973366 -24 TCATTACTTCAGAAGTGATGACGGAGGGACAGGAGAA 11 239 0 AAGTGGGAGG 0.846619 -62 ATATGATGAAAAGAGATCAAGGGGAGGTGACGTG 11 277 1 AGGAAGGAGG 0.901222 -24 GTGAAGAAAAATAGGCCGAATGGGCGGCTTGCAAACG 13 75 1 AAGAAGGCGG 0.761909 -204 GATAGTACTAAAGAAATAAATTGGAGGAATAGATACT 14 109 0 AGAAAGGAGG 0.958509 -192 GTGGAAATGGTTACATAAAAAGGGAGGCTGAGAG 15 8 0 TAAAAGGAGG 0.595044 -257 GATAGAACGTATGTTTTGTATAGGCGGGTGAACAAAT 16 34 1 AGTTAGGCGG 0.880887 -28 ATGATAAACGGAATACATTAAAGGAGGC 17 283 1 GAATAGGAGG 0.894971 -18 CAAGAAAAATGGGTATATTGAAGGAGGACCAATTTTT 18 104 1 GGATGGGAGG 0.920172 -48 TCAACGGTGTATGTACCAAACTGGCGGTAACTATGAG 20 90 1 AGAAAGGCGG 0.938421 -211 GGAGAAATACAGGTGTAAAAGAGGGGGATTAACTCCT 20 148 1 AGGAAGGGGG 0.756196 -153 TCAGAGCCAAACGCTTCTTACAGGGGGAGAAAGAACC 23 269 1 AGTTAGGGGG 0.792151 -28 ACTTCAGATGAAGGATACTAGAGGGGGCTTTTTTT 24 82 1 AGATAGGGGG 0.925507 -25 GTAAGTAACAATATTAATAGTTGGAGGGTTCAAATCG 25 110 1 AATAGGGAGG 0.730469 -179 CGAAAGAACAAAACAAGGTGAGGGCGGCCTGTATTTA 25 174 1 AAATGGGCGG 0.902149 -115 AATAAGTCACAGATATGCTATAGGAGGACGATC 26 37 1 AAATAGGAGG 0.951056 -23 GAAATTAAATGTATTCATTGGTGGAGGACATAGAAC 28 162 1 GATTGGGAGG 0.65279 -26 TTGTTCCACCAAGAACAATCTGGGAGGTTTTATTC 30 9 0 AGATCGGAGG 0.921025 -257 GATTTTTGTCAGGAAGAATGTAGGTGGATAGG 30 244 1 AGATGGGTGG 0.798633 -22 ATGAAAATAGAAAGAATAAACAGGAGGAATTGAT 34 50 1 AAAAAGGAGG 0.924717 -24 GAAAAATGCAATAAAACATAAGGGAGGAATGAAAG 36 9 0 AAATAGGAGG 0.951056 -161 GGATCGTTTCGGACAGTAACAAGGCGGGAAAAATGCA 36 36 0 GAAACGGCGG 0.531374 -134 * * * ** ***** Masking position 13 Map Score: 27.2383 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 232 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 GTTGTCTAAAAATGAAAAAAATCGGCTTCTGCAAGA 1 130 0 AAAAAATCGC 0.715465 -171 TTCGCTTTCTTTCTAAAAAAACTGCCGGCTGACGC 6 10 1 TAAAAAACGC 0.97625 -185 GCCAATCATTTACATAAAAAAACTGCCAGCGTCAGC 6 38 0 TAAAAAACGC 0.97625 -157 CAGAATTGGATGATTGTAAAAGCCGCAGCTGAGCCA 6 70 0 TGAAAAGCGC 0.852261 -125 TGGAATTGATTTATGAAAGAAACCGCGTAGGAAGTG 7 44 1 TAAGAAACGC 0.857991 -42 CGGGTTTTTAATTTGAGAAAAGGGGCTGAAAGCAGG 8 20 1 AAAAAAGGGC 0.60697 -27 TGATGCACGAAATATAAAAAAACTCCCGGCGAACCG 10 27 0 AAAAAAACCC 0.89228 -140 AATGGGCTGTTGGGCATCAAAGCAGCGTCCGGTGCA 11 168 0 TACAAAGCGC 0.670365 -133 TTTAAATTTATTCATCTAAAAACAGCAAACATAATG 11 200 0 TCAAAAACGC 0.797142 -101 ATTGCATCTTTTCAAAGAAAAACACCGTTCAATTTG 12 26 0 TAAAAAACCC 0.939029 -80 TGTGAGATAATCAAAGAAAAAAGAGCTGACGGAGAT 12 74 1 TGAAAAAGGC 0.780541 -32 TGATCTTAAAAAGAAGCAAAAACACCGAGCCATTTC 13 38 0 AGAAAAACCC 0.775462 -241 TTTTATGAAAAAAGAATCAAAACACCTTTTTCAGTG 15 146 1 AACAAAACCC 0.549044 -119 TATGTTTGTTTAAATAAAAAAACTGCGGATAACCAC 17 95 0 TAAAAAACGC 0.97625 -206 CCGTCTGAACACACCATAAAAACTGCAAAGCAGCTT 23 73 1 AAAAAAACGC 0.956725 -224 GAAAGCTATATAAATATAAAAACACGAAAGAACAAA 25 150 1 TAAAAAACCG 0.582344 -139 GTATTTATCTTATTTGCAAAAACAGCCCATAAATAA 25 204 1 TGAAAAACGC 0.944868 -85 ACTTTATTTCTTCACAGAAAAGCCCCTTTCTAAGGG 28 49 1 TAAAAAGCCC 0.838292 -139 TTAAACGGCTTTTTAAGAAAAACTGCACTCTGAGGA 29 159 0 TAAAAAACGC 0.97625 -142 TTGAAATCTGTTAAAATAAAAAGAGCAAATCAACGA 30 210 1 TAAAAAAGGC 0.895074 -56 GCCGGGGCGGTTTCTAGAGAAACCGCCTTGTCTTAT 31 17 1 TAAGAAACGC 0.857991 -43 TAGAACGGGAAGAGTACAAAAAAGGCGCATGCAGAG 32 38 1 AAAAAAAAGC 0.607891 -263 AAAATGGCTGAGAACGAAAAAAGAGCTCTTCATCCC 32 254 0 AGAAAAAGGC 0.656701 -47 CCGTAGGGTATTACAATAAAAAACGCT 34 2 0 TAAAAAAAGC 0.742433 -72 CCAATCTGCTAACTGAAAAAAACAGGAAACAGACAA 36 71 1 AAAAAAACGG 0.666835 -99 CACCGTCCTCTCATTAAAAAATCTCCAACCTCCATT 36 138 0 TAAAAATCCC 0.636585 -32 * * ****** ** Masking position 10 Map Score: 26.0624 Number of sites scoring better than the average of aligned sites = 1428 Number in coding regions = 1220 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 4 TGTAAAAAGTAAAGTAGAGAAACTATTCAAAA 6 160 1 AAATAAGAAA 0.63627 -35 GTTGTTAGTGAAAAAAGTGAATTTCTCTTCCA 10 94 0 AAAAATGAAT 0.461288 -73 AACATAAAGGAAATAAATGAAAAACTTTCGGG 17 12 1 AAAAATGAAA 0.914244 -289 AAAGCCTTGTAAGGAAATGAAAAAACGCTTTT 17 202 0 AAGAATGAAA 0.81843 -99 GGATGTGCTAAAATAAGAGAAACATGACAATA 22 216 1 AAAAAAGAAA 0.95027 -44 TCACGCCTTAAAATAAAAGAAAGTGTCCCCAG 24 15 0 AAAAAAGAAA 0.95027 -92 GGAGGGTTCAAATCGAAAGAAAGCTATATAAA 25 132 1 AATGAAGAAA 0.472396 -157 CTGTTTTTGCAAATAAGATAAATACAGGCCGC 25 197 0 AAAAAATAAA 0.48656 -92 ACAGCCCATAAATAAACTGAAAATTGTCAAAA 25 225 1 AATAATGAAA 0.666729 -64 AAATCCAATCAAACAATTGAAAGAATTTAGGA 25 259 1 AAAAATGAAA 0.914244 -30 GTTGAGGGGGAAACAACAGAAAACTCTTTAAA 27 48 1 AAAAAAGAAA 0.95027 -253 AAATGAGAGCAAGTAAGAGAAAGACAATTAAA 29 190 0 AAGAAAGAAA 0.889859 -111 CCTGTCTCAGAAAAAAATGAGAGCAAGTAAGA 29 204 0 AAAAATGAGA 0.559298 -97 TCATTACAATAAGTAAGAGGAATAGGTGTTAA 30 73 0 AAGAAAGGAA 0.653451 -193 GGGTATATAAAAATGAAAGAAATATCGCGCCT 33 34 0 AAAGAAGAAA 0.826731 -47 TGCTAACTGAAAAAAACAGGAAACAGACAATT 36 77 1 AAAAAAGGAA 0.816841 -93 TTCTACAGAAAAAAAATAGAAAAATTGTCTGT 36 99 0 AAAAAAGAAA 0.95027 -71 *** ** ***** Masking position 6 Map Score: 10.0091 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 509 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 5 CCGGAAATTCTTTTCATAAACGAATATCAAG 1 169 1 TTTTCATAAC 0.667495 -132 GAGCCAATCATTTACATAAAAAAACTGCCAG 6 45 0 TTTACATAAA 0.784071 -150 GCATTGCATCTTTTCAAAGAAAAACACCGTT 12 33 0 TTTTCAAGAA 0.481263 -73 CTTCTAAAACTTCTCATAAAAGAATAACCAT 14 154 1 TTCTCATAAA 0.853318 -147 TTTGATTCTTTTTTCATAAAAAAAGAGAGCA 15 136 0 TTTTCATAAA 0.90029 -129 CAAAACACCTTTTTCAGTGAATAACGAGATT 15 163 1 TTTTCAGGAA 0.624943 -102 AAGCATTCATTTTTCAGAAAAATCTTTACCT 17 147 0 TTTTCAGAAA 0.795891 -154 AAATGAATGCTTTACATCAAATAAGGCAAGA 17 166 1 TTTACATAAA 0.785198 -135 AAACATGCTTTTTTCAAGAAAAATGGGTATA 18 90 1 TTTTCAAAAA 0.809223 -62 TCCTCCTATCTTTTCAAAAAAATTGGTCCTC 18 127 0 TTTTCAAAAA 0.808062 -25 GGAAAGCCTCCTTTCATGAAATATTGTAAGC 22 108 1 CTTTCATAAA 0.814057 -152 AAAAAGTGAATTCACATAAAAAAGGTGCATG 25 30 0 TTCACATAAA 0.699111 -259 GCCTTTTGGTTTCACAGTAAAATGATTTTCA 27 96 1 TTCACAGAAA 0.670907 -205 ACTTTATTTCTTCACAGAAAAGCCCCTTTCT 28 49 1 TTCACAGAAA 0.659531 -139 CATAAGAAGCCTTTCAGCAAACGGCTTCTCT 32 74 0 CTTTCAGAAA 0.799227 -227 CTCTACTCTTCTTTCAAGAAATTATGCTCCC 32 127 0 CTTTCAAAAA 0.669613 -174 GTACCACCTTTTTTCATGAACTCAATCAGTT 32 196 0 TTTTCATAAC 0.667515 -105 AAGCACCGTCCTCTCATTAAAAAATCTCCAA 36 146 0 CTCTCATAAA 0.735819 -24 ******* *** Masking position 2 Map Score: 11.2923 Number of sites scoring better than the average of aligned sites = 672 Number in coding regions = 506 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 6 TATTCTCCAGGAGGAATGAAT 2 74 1 GAGGAATGAA 0.954106 -11 TCAAAGGCAAGTGGAATGGAAACACTTATA 3 31 1 GTGGAATGGA 0.875744 -58 AAAGAAAATAGAGGAATGATACAA 10 153 1 GAGGAATGAT 0.90397 -14 TTTTACATTTGAGGAATTATACATAACAAA 11 23 0 GAGGAATTAT 0.619382 -278 AAATAAATTGGAGGAATAGATACTGGCCGT 14 103 0 GAGGAATAGA 0.885942 -198 TCGAATGCAGGAAGAATGAGAGGGTGTA 19 9 0 GAAGAATGAG 0.778995 -107 CACACAGTGAGTGGAATAAGATCCTCACTT 20 192 1 GTGGAATAAG 0.647297 -109 ATAAAATAGAGAGGAATAAGCAGTC 22 245 1 GAGGAATAAG 0.862465 -15 ACTGCACTCTGAGGAATGTTTGTCCAACAA 29 144 0 GAGGAATGTT 0.748409 -157 CAATAAGTAAGAGGAATAGGTGTTAAATTG 30 69 0 GAGGAATAGG 0.878996 -197 TTTTTGTCAGGAAGAATGTAGGTGGATAGG 30 246 1 GAAGAATGTA 0.543594 -20 GAATAAACAGGAGGAATTGAT 34 63 1 GAGGAATTGA 0.806318 -11 AAACATAAGGGAGGAATGAAAG 36 3 0 GAGGAATGAA 0.954106 -167 TGTAGAAATGGTAGAATGGAGGTTGGAGAT 36 124 1 GTAGAATGGA 0.560973 -46 ********** Masking position 5 Map Score: 8.39749 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 226 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 7 ATTTTTTTCATTTTTAGACAACATTCCGGAAATTCT 1 144 1 TTTTAAATTC 0.951394 -157 ATTGTTACCTTCTTTTGACAAAATCCTATCTGTGCT 1 227 1 TTTTAAATCC 0.820572 -74 AATGAGCAGGTATTTTAAAGATATTCATATCCTAAC 4 64 0 TTTTAGATTC 0.803229 -40 CTTCTGCTATTGTTTGGAAAGTGTTCTACTGTGGAA 15 39 0 TTTTAAGTTC 0.954968 -226 ATTGTAAGCGTTTTTACACAAAGTGCATAGCAACGA 22 130 1 TTTTAAATGC 0.820572 -130 TTTTCGGATATTTTTCAACAATATTCGAAATAATTT 25 65 0 TTTTAAATTC 0.951394 -224 CGTGTTTTTATATTTATATAGCTTTCTTTCGATTTG 25 140 0 TTTTAAGTTC 0.954968 -149 GATTGGATTTTATTTTGACAATTTTCAGTTTATTTA 25 233 0 TTTTAAATTC 0.951394 -56 CAGTGCGTTTTATTTAAAGAGTTTTCTGTTGTTTCC 27 56 0 TTTTAAGTTC 0.954968 -245 TTGCTCTTTTTATTTTAACAGATTTCAAACAGAAAT 30 202 0 TTTTAAGTTC 0.954968 -64 * *** * ** *** Masking position 8 Map Score: 5.90876 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 64 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 CGTGTTACCGCCGTGAAAGGGCGGTGTCTTAA 1 58 0 CCGAAAGGGC 0.98887 -243 CCATTCTTAACCCTAAAAGGGCTGGAATTGAT 7 22 1 CCCAAAGGGC 0.954898 -64 AATTAAAAACCCGCTAAAGAGC 8 1 0 CCGAAAGAGC 0.979041 -46 CTGATAAAGAGCACTGAGTCAT 13 1 1 CTGAAAGAGC 0.94494 -278 CTGAGTCATTCTGCGAAATGGCTCGGTGTTTT 13 24 1 CTGAAATGGC 0.834129 -255 TGTGCTCCTGCCGATACAGGACTCACCATGCA 15 92 1 CCGACAGGAC 0.895537 -173 ATAACATAGTCTGTCACATAGCTCATAGTTAC 20 116 0 CTGACATAGC 0.623491 -185 TTGCTTGTGGTCGGCAAAGAGCGGTTTGAGCT 23 187 1 TCGAAAGAGC 0.877996 -110 AGCATGGGCTTCCTGACAGGGCATTCACTTTG 28 102 1 TCCACAGGGC 0.671367 -86 AAAGGTGGTACCGCGAAAGAGCTTTTCGTCCT 32 216 1 CCGAAAGAGC 0.979041 -85 CTCTTCATCCCTGTAAAAGGACGAAAAGCTCT 32 233 0 CTGAAAGGAC 0.834129 -68 *** ******* Masking position 6 Map Score: 7.43947 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 353 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 9 TAAGAATGGATCAACGATGT 7 1 0 TCAACGATGT 0.973778 -85 TGGGGAGAGGTCAATGATGTGAATCCAGGA 11 94 1 TCAATGATGT 0.805955 -207 CCGTTCAATTTGAACGGTGTCCTGTCT 12 8 0 TGAACGGTGT 0.947164 -98 CCGTTCAAATTGAACGGTGTTTTTCTTTGA 12 21 1 TGAACGGTGT 0.947164 -85 GCTTACATCTTGAACAATTTAAAGTATTAC 14 29 0 TGAACAATTT 0.551188 -272 AGGAATCTGGTGAAAAATGTGTGCTCCTGC 15 73 1 TGAAAAATGT 0.583145 -192 CGTATAATCCTCAACAATGTTATCAACGGT 20 68 1 TCAACAATGT 0.913003 -233 AACAATGTTATCAACGGTGTATGTACCAAA 20 80 1 TCAACGGTGT 0.963574 -221 AAAATGATTTTCAAAGATGTAAGAGGGAAT 27 114 1 TCAAAGATGT 0.879871 -187 AAAGAGCAAATCAACGATTTTTGTCAGGAA 30 229 1 TCAACGATTT 0.865412 -37 ********** Masking position 4 Map Score: 4.63098 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 78 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 10 AATGAAAAAAATCGGCTTCTGCAAGAGAAA 1 126 0 ATCGGCTTCT 0.811775 -175 TTGGCTCAGCTGCGGCTTTTACAATCATCC 6 69 1 TGCGGCTTTT 0.903219 -126 GCTCTTTAGCGGGTTTTTAATTTGAGA 8 8 1 AGCGGGTTTT 0.890735 -39 AGCAAACATAATGGGCTGTTGGGCATCAAA 11 183 0 ATGGGCTGTT 0.863986 -118 TAACGAGATTAACGGCTTTTTCCGTTTTTC 15 184 1 AACGGCTTTT 0.946644 -81 CTTTGTTAAATGCGGCTGTTGATCATGTAA 17 243 0 TGCGGCTGTT 0.872632 -58 GGATACTAGAGGGGGCTTTTTTT 24 94 1 GGGGGCTTTT 0.832521 -13 CAGTTTATTTATGGGCTGTTTTTGCAAATA 25 214 0 ATGGGCTGTT 0.863986 -75 CCCCTTAGAAAGGGGCTTTTCTGTGAAGAA 28 56 0 AGGGGCTTTT 0.963497 -132 CCCCTTTCTAAGGGGCTTTTCATATTTCAA 28 71 1 AGGGGCTTTT 0.963497 -117 AAGACAATTAAACGGCTTTTTAAGAAAAAC 29 172 0 AACGGCTTTT 0.946644 -129 CCTTTCAGCAAACGGCTTCTCTCTCTGCAT 32 66 0 AACGGCTTCT 0.848648 -235 TATAACGGATAACGGGTGTTTCCCGAATTT 32 158 0 AACGGGTGTT 0.718628 -143 ********** Masking position 7 Map Score: 11.5641 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 522 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 11 TCCTCTCATCTCCCACCTGTTAT 1 288 0 CTCTCACTCC 0.97197 -13 TATCCTAACACTTTCAACCCCTCCAAGCAAA 4 42 0 CTTTCACCCC 0.988557 -62 ACCTGCTTTCAGCCCCTTTTCTCAAA 8 31 0 CTTTCACCCC 0.988557 -16 TCTGTCATCTCCGTCAGCTCTT 12 94 0 CTGTCACTCC 0.949603 -12 CTCTCAGCCTCCCTTTTTATG 15 1 1 CTCTCACCTC 0.902815 -264 AGGTTCTTTCTCCCCCTGTAAGAAGC 23 281 0 CTTTCTCCCC 0.947187 -16 GCCTTTCACCTCCTCCCAAAAGG 29 288 0 CTTTCACTCC 0.97665 -13 ****** **** Masking position 4 Map Score: 6.25638 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 29 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 TCGGCAGCCTGCTTCCGAGATGGT 5 5 1 CAGCCTGCTT 0.950582 -93 GACCTCTCCCCAGCAGATTTGCACCCGCCT 11 76 0 CAGCAGATTT 0.500217 -225 GCCGCCCATTCGGCCTATTTTTCTTCACAT 13 73 0 CGGCCTATTT 0.814751 -206 ACGCGTCATTCAGCCAGCTTTCGGCATGTT 13 128 1 CAGCCAGCTT 0.924536 -151 AGCCAGCTTTCGGCATGTTTCAGCAGCAGG 13 139 1 CGGCATGTTT 0.951857 -140 CATGTTTCAGCAGCAGGCTTGTGAGGGAAG 13 152 1 CAGCAGGCTT 0.853077 -127 CGCCTATCCACGGCCAGTATCTATTCCTCC 14 94 1 CGGCCAGTAT 0.762553 -207 GAGTCAGAATAAGCATGCTTATAGAGTGAT 19 61 1 AAGCATGCTT 0.398997 -55 CTCATAGTTACCGCCAGTTTGGTACATACA 20 97 0 CCGCCAGTTT 0.766707 -204 AAGGTGAGGGCGGCCTGTATTTATCTTATT 25 188 1 CGGCCTGTAT 0.876427 -101 CATAACCCTCCAGCATGTTTAAAAATGGCT 32 281 0 CAGCATGTTT 0.936008 -20 TTTTTTGCGTCGGCATGCTTAGACAACCGT 35 58 1 CGGCATGCTT 0.95729 -70 ********** Masking position 10 Map Score: 3.93495 Number of sites scoring better than the average of aligned sites = 1230 Number in coding regions = 1140 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 13 GCCAATCATTTACATAAAAAAACTGCCAGC 6 44 0 TACATAAAAA 0.840438 -151 GTAAGCGCTGAACATTAAAAACAGGTCTTC 13 178 0 AACATTAAAA 0.360745 -101 TGGAAATGGTTACATAAAAAGGGAGGCTGA 15 14 0 TACATAAAAA 0.840438 -251 TGATTCTTTTTTCATAAAAAAAGAGAGCAT 15 135 0 TTCATAAAAA 0.687684 -130 TCTCGTTATTCACTGAAAAAGGTGTTTTGA 15 162 0 CACTGAAAAA 0.571102 -103 GCATTCATTTTTCAGAAAAATCTTTACCTC 17 146 0 TTCAGAAAAA 0.779424 -155 GATATTGCGGTACATAAAAATTCAAATAGT 20 29 0 TACATAAAAA 0.840438 -272 AAAGTGAATTCACATAAAAAAGGTGCATGA 25 29 0 CACATAAAAA 0.89396 -260 CTTTTGGTTTCACAGTAAAATGATTTTCAA 27 98 1 CACAGTAAAA 0.798364 -203 TTTATTTCTTCACAGAAAAGCCCCTTTCTA 28 51 1 CACAGAAAAG 0.663699 -137 CTAAACCTGTCTCAGAAAAAAATGAGAGCA 29 211 0 CTCAGAAAAA 0.849753 -90 GCCACATTTCAACAGAAAAATGATTGAGAA 30 112 1 AACAGAAAAA 0.755765 -154 CTACCATTTCTACAGAAAAAAAATAGAAAA 36 108 0 TACAGAAAAA 0.894211 -62 GCACCGTCCTCTCATTAAAAAATCTCCAAC 36 145 0 CTCATTAAAA 0.507731 -25 ********** Masking position 7 Map Score: 6.6865 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 404 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 14 CATAGAAAATCATTCCAATACAAACAATAACC 5 32 0 CATTCAATAA 0.688826 -66 TCACTAACAACATTGCTTTACAATTAAAAACA 10 115 1 CATTCTTTAA 0.821634 -52 CATCATATTTCATTACTTCAGAAGTGATGACG 11 253 0 CATTCTTCAA 0.940612 -48 CCCTTGATCTCTTTTCATCATATTTCATTACT 11 268 0 CTTTCATCAA 0.755659 -33 AATCAGTTCACACTTCTTCACAGTCGTTTAAC 13 208 1 CACTCTTCAA 0.798175 -71 ACCATTTAAACATTATAACAAATTCACATAGC 15 217 0 CATTTAACAA 0.62255 -48 AAAATGAATGCTTTACATCAAATAAGGCAAGA 17 165 1 CTTTCATCAA 0.755659 -136 GTAGTGATTTCATTGTAATATAACAGATTACA 18 27 1 CATTTAATAA 0.324188 -125 ATGTTTTAAACATTGTATCAAAACAGTTATTG 18 64 0 CATTTATCAA 0.729357 -88 CTATAGTATCCTTTACTTCAGATGAAGGATAC 24 68 1 CTTTCTTCAA 0.797521 -39 ACATACACTTTATTTCTTCACAGAAAAGCCCC 28 43 1 TATTCTTCAA 0.455686 -145 CGTTTATTATCATTTCTTCACAGTTCAGTCTG 29 244 0 CATTCTTCAA 0.940612 -57 GTTGCTGCCACATTTCAACAGAAAAATGATTG 30 106 1 CATTCAACAA 0.883871 -160 ATATTTCTTTCATTTTTATATACCCCCCAGGT 33 41 1 CATTTTATAA 0.379247 -40 ACTCACTCCTTTATATACACCTGGG 33 66 0 CACTCTTTAA 0.534931 -15 TCCATTCTACCATTTCTACAGAAAAAAAATAG 36 112 0 CATTCTACAA 0.906485 -58 **** ***** * Masking position 4 Map Score: 6.91558 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 405 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 15 TTTCATAAATCAATTCCAGCCCTTTTAGGG 7 32 0 CAATTCCAGC 0.65834 -54 GCGTCCGGTGCAGTACAAGCTTCACGTTTC 11 150 0 CAGTACAAGC 0.859545 -151 GAGCATATGGCAGTACCTGCATGGTGAGTC 15 111 0 CAGTACCTGC 0.850802 -154 TTTAAACAAACATATCATGCAAAGACAGAG 17 117 1 CATATCATGC 0.897333 -184 TGACTCGTCCCATTTCATGCTATAATTATC 19 37 0 CATTTCATGC 0.915025 -79 TTAGCACATCCAAAACATGCAAGTCATGTA 22 197 0 CAAAACATGC 0.761886 -63 AAAAAAGGTGCAGATCATGCACCTTTTTTA 25 15 1 CAGATCATGC 0.947511 -274 TATAAAAAGCCATATCAAGCATTTTAAAGC 29 83 0 CATATCAAGC 0.820943 -218 TGAACTCAATCAGTTCATGCACTTATAACG 32 181 0 CAGTTCATGC 0.956971 -120 ********** Masking position 2 Map Score: 3.35615 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 167 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665