AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_mpneu_reg_300.orf -o00030_mpneu_300.ace -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: K04_orf430 21 pgi; glucose-6-phosphate isomerase (GPI) (phosphoglucose isomerase) Input sequences: #1 R02_orf1386V 236 hypothetical protein. #2 R02_orf694 50 fruA; PTS system, fructose-specific IIABC component (EIIABC-Fru) #3 MPNtRNA-Ser01 300 mptgsb; tRNA-Ser. #4 D09_orf127a 167 hypothetical protein. #5 D09_orf238 55 deoD; purine nucleoside phosphorylase (inosine phosphorylase) (PNP). #6 D09_orf450 287 ffh; signal recognition particle protein (fifty-four homolog). #7 D09_orf560L 300 potA; spermidine/putrescine transport ATP-binding protein potA #8 D12_orf390o 45 dnaJ; dnaJ protein. [SP:DNAJ_MYCPN] #9 D12_orf623 133 pmd1; transport ATP-binding protein. #10 MPNtRNA-Ala 44 tRNA-Ala. #11 D12_orf212 101 dnaE; [EC:2.7.7.-] [SP:PRIM_MYCPN] #12 D12_orf257 300 hypothetical protein. #13 D02_orf122a 225 hypothetical protein. #14 D02_orf122b 100 hypothetical protein. #15 D02_orf521 300 hypothetical protein. #16 H10_orf149 206 hypothetical protein. #17 H10_orf220L 48 hypothetical protein. #18 H10_orf206 38 hypothetical protein. #19 H10_orf145L 138 hypothetical protein. #20 H10_orf187V 89 hsdS1B; #21 A65_orf787o 300 hypothetical protein. #22 K04_orf726 273 vacB; vacB protein homolog. [SP:VACB_MYCPN] #23 G07_orf479 197 hypothetical protein. #24 G07_orf240 24 ung; uracil-DNA glycosylase. [EC:3.2.2.-] [SP:UNG_MYCPN] #25 G07_orf417 300 hypothetical protein. Motif number 1 CAACTAAAGAACTAGCCAAACAGCCAAAGGTCAATCA 1 22 1 ACAAACAGAA 0.975433 -215 AAAGAAGAGCATACTGAAAACAGCTAGCAAAACGGGT 1 80 0 AAAAACAGAG 0.83476 -157 CTAAAGCACCATTTTTTAAAAAGAAAACACCACCAGT 6 17 1 ATAAAAAGAA 0.806244 -271 CAAGAAAACCAAAATTAAAAAAGTAAAGGAAGCAGGG 6 96 1 AAAAAAAGAA 0.948907 -192 AAGGACACTAAAACAGCAAACAGGTAAGGGTGTTTTT 6 170 0 ACAAACAGAA 0.975433 -118 CAAATTCCTTAAGCTGCAAAAAGATAAAAAAGCAAGG 6 256 1 ACAAAAAGAA 0.964298 -32 GGAATCTTTTAACAAGAAAAAAGAGAAGTTGTAGGCT 7 32 0 AAAAAAAGAA 0.948907 -269 TTCAAAATTTAGTCCAAAAACAGTCAAATTTTTAGCA 7 127 1 AAAAACAGAA 0.964665 -174 CGCCAAAATAAAAATACCAACAGATAACCTATAAGGG 11 43 0 ACCAACAGAA 0.880197 -59 ATTGACCAGAATTTCAAAAACTGCCAATAAAATTGCT 12 143 0 AAAAACTGAA 0.933093 -158 TGCTGTAGTTTTGAATAAAAATGCCAACCCGAATGAT 13 117 1 TAAAAATGAA 0.531598 -109 AAGAAGGATAATTCTGCAAACTGCAAAAGAGTTATAA 13 186 1 ACAAACTGAA 0.953013 -40 AGTGTGCTTTAATTTTAAAAAAGAAAGTTTGAAAGGT 14 11 1 AAAAAAAGAG 0.774602 -90 GTACCAGGATAATTGTTAAAAAGGAAATACCTTTTCA 15 94 1 ATAAAAAGAA 0.806244 -207 TACACGAAATACCAATAAAACAGCGAAGCTAATTTAA 15 195 1 AAAAACAGAA 0.964665 -106 TGATGAGCTTAATTTTAAAAATGTAAAATAACGGCC 18 13 1 AAAAAATGAA 0.904645 -26 GTTAGATTTTAAAGCGCAAAATGAAAAACTAACCCTA 22 245 0 ACAAAATGAA 0.932421 -29 CATAAGAAAAATAATGAAAAATGCTAAAGCTTTGTTT 23 43 0 AAAAAATGAA 0.904645 -155 TTATTCCGCTTGTACTCAAACAGAAAAGCACAGCGAG 23 84 1 TCAAACAGAA 0.82608 -114 TACTTGAAACAATTCCCCAACTGCAAAAGGAAATAAA 25 21 1 ACCAACTGAA 0.789611 -280 GGAAAAAGCCACTGCCCAAAAAGTCAAATAAGCGTGC 25 113 0 ACAAAAAGAA 0.964298 -188 * ******* ** Masking position 9 Map Score: 28.4004 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 99 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 TGCTACTGTTAGCTTTAGTGTTGTTGTACGCT 1 118 1 AGTTTAGGTT 0.944623 -119 AATTTATAAAAATTTTTGCGTTTTCTTTTATT 3 150 0 AATTTTGGTT 0.876956 -151 TTTACTTTTTTAATTTTGGTTTTCTTGAGTTC 6 91 0 TATTTTGTTT 0.871026 -197 CTCTTAAGTTGTTGTTTTTTGTCAAGCT 10 7 1 AGTGTTGTTT 0.843312 -38 CAACTGCTGGTATTTTTGCTTTGATTGTTAT 11 10 0 TATTTTGTTT 0.871026 -92 GGATCGCTCTTGATGTTGTTTTGTTTGAAGTC 12 84 1 TGTGTTGTTT 0.829354 -217 CAAAGTTGCACGTTTTAGTTTTCTAAACCTTG 12 257 1 CGTTTAGTTT 0.771214 -44 AGAAGGTTGTTGCTGTAGTTTTGAATAAAAAT 13 107 1 TGTGTAGTTT 0.829354 -119 TTAAAAACGATGATTTAGAGTTAGCTTTAAAA 16 26 1 TGTTTAGGTT 0.939037 -181 AACATTTTTAAGGTTTTGTTTTAACCTGAAAT 20 40 0 AGTTTTGTTT 0.94709 -50 TTCAACACAGAATTTTCGTTTTCCTGCTCCCA 21 38 1 AATTTCGTTT 0.741628 -263 ATAAATAAATTGATTTAGTTTTTTAAATGTGA 21 70 1 TGTTTAGTTT 0.941738 -231 TTTTGGTTTGAAATTTTGATTTTTATTGAAAT 21 108 0 AATTTTGTTT 0.882044 -193 GGTGTGTTATAGTTTTTGGTTTGAAATTTTGA 21 121 0 AGTTTTGTTT 0.94709 -180 TTGTTTTTAATAGTTTCGATTTTATGTCTTCT 21 205 1 TATTTCGTTT 0.721603 -96 AGATTTCTCCAAATTTTGGGTTTTAGTGC 21 282 1 AATTTTGGTT 0.876956 -19 TGCTTTTTCTTATTTTAGGGTTAGTTTTTCAT 22 230 1 TATTTAGGTT 0.865517 -44 CAACAAACAAAGCTTTAGCATTTTTCATTATT 23 39 1 AGTTTAGATT 0.655749 -159 TTTGCAAGCTTGTTTTAGAGTTGCAAAGCAAA 23 169 1 TGTTTAGGTT 0.939037 -29 TGAACCCGAAAGGTTTAGGGTTAGCGGACAAC 25 156 1 AGTTTAGGTT 0.944623 -145 ** ***** *** Masking position 6 Map Score: 19.804 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 134 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 TGCAAACAATTTATAAAAATTTTTGCGTTTTC 3 157 0 TTAAAAATTT 0.835917 -144 AAGCGAGCTCTTCTAAAAATTCCGTTTCTTTC 3 207 1 TTAAAAATTC 0.708776 -94 ACTGATGGTCTGCTTACAATTTATATTGAGAA 3 272 1 TTTACAATTT 0.89121 -29 TTTATTCTTTTAATTGCACTTTTAGGCTGATT 6 205 1 TTTGCACTTT 0.7863 -83 TTAGGCTGATTATTTGCAATTCCGATTTCGCA 6 226 1 TTTGCAATTC 0.889134 -62 GTTAAATTTGTGCTAAAAATTTGACTGTTTTT 7 142 0 TTAAAAATTT 0.835917 -159 TGCAAAAAAATGATTGCAATTTTGTGAGATTT 7 191 0 TTTGCAATTT 0.943732 -110 ACGGTATTTATTGTAGCAATTTTTGACCCCGC 7 252 0 TTAGCAATTT 0.931242 -49 TTCTAAATACTCTTAAAAATTTATTTGGGTGA 12 49 1 TTAAAAATTT 0.835917 -252 TTGCTAAAAATTTTTGCAATTTAAAGTAAAGA 12 116 0 TTTGCAATTT 0.943829 -185 TTGCAAAAATTTTTAGCAATTTTATTGGCAGT 12 129 1 TTAGCAATTT 0.931242 -172 TTATTGGCAGTTTTTGAAATTCTGGTCAATTT 12 150 1 TTTGAAATTC 0.860988 -151 TTTAATGTCTTAGTTTCAATTTTAGTTGATGT 13 19 1 TTTTCAATTT 0.721291 -207 CTTACATAGCTTATTTAAATTTAAAGAAGGTT 13 83 1 TTTTAAATTT 0.666362 -143 TTTAAGTATTTGTTTGAAATTTGTCCTAACTG 15 161 0 TTTGAAATTT 0.928391 -140 TTTCACCACCTACTAAAACTTTTTGAGCTATT 19 37 0 TTAAAACTTT 0.527429 -102 ATTTTGATTTTTATTGAAATTTGACGTCACAT 21 96 0 TTTGAAATTT 0.928376 -205 CAAGTTTAATTCCTAAAAATTCAGTGATTAAA 21 236 0 TTAAAAATTC 0.708776 -65 * ********* Masking position 4 Map Score: 16.5281 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 64 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 AAAGGTCAATCAAGAGAGGGAATCGATTTTGTTA 1 47 1 CAAGAGAATC 0.847278 -190 CCTAAAGTCAGAAAATCCAATATTTAT 2 34 0 AAAGAAAATC 0.93932 -17 TGTTAACAAGAAAGAAACGGAATTTTTAGAAGAG 3 214 0 AAAGAGAATT 0.85574 -87 CAAAATTAAAAAAGTAAAGGAAGCAGGGGATACC 6 105 1 AAAGAGAAGC 0.972772 -183 AGATTAAAGCAAAGGTAAAAAAACACCCTTACCT 6 152 1 AAAGAAAAAC 0.709326 -136 TAAGCTGCAAAAAGATAAAAAAGCAAGGTTCGC 6 265 1 AAAGAAAAGC 0.961378 -23 TTGTAGGCTAAAAGAAGGGGAATTAACAAA 7 7 0 AAAGGGAATT 0.752889 -294 TTCTTGATAAAAAGAAAGGGAATCTTTTAACAAG 7 53 0 AAAGAGAATC 0.956931 -248 AACCTTCTTTAAATTTAAATAAGCTATGTAAGTT 13 81 0 AAATAAAAGC 0.552465 -145 GGAGCCTAAAAAAGAAGGATAATTCTGCAAACTG 13 175 1 AAAGGAAATT 0.679768 -51 AGTTCAACCAAAAGACAAGCAAGCA 15 2 0 AAAGAGAAGC 0.972772 -299 AACCGGAGCACAAGCAGTAAAAGCAGTCTGTACC 15 65 1 CAAGGAAAGC 0.761473 -236 TAACAGCAGTAAAGCTGAGGAATTT 19 124 1 AAAGGGAATT 0.752889 -15 AGTGATTAAAGAAGACATAAAATCGAAACTATTA 21 212 0 GAAGAAAATC 0.677452 -89 TCTTGACCTGAAAGCGAAGCAAGTCCGCCAGTAG 22 122 0 AAAGAGAAGT 0.905111 -152 CCAACTGCAAAAGGAAATAAAAGCTGCTAATGAC 25 37 1 AAGGAAAAGC 0.747679 -264 CACTGCCCAAAAAGTCAAATAAGCGTGCTTCTAC 25 107 0 AAAGAAAAGC 0.961378 -194 **** * * **** Masking position 11 Map Score: 14.2592 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 112 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TTCAGTAATAAAAGAAAACGCAAAAATTTTT 3 144 1 AAAGAAAAGC 0.876175 -157 TCTTTCTTGTTAACAAAAAGCGCAATAAAAA 3 233 1 TAACAAAAGC 0.712431 -68 CAAGCACTGCAACCAAAAAACCAAGCACCTC 4 28 0 AACCAAAAAC 0.818784 -140 CATTTTTTAAAAAGAAAACACCACCAGTACC 6 26 1 AAAGAAAAAC 0.947631 -262 CTTAATTTTTAAAGAAAAAACGGTATTTATT 7 272 0 AAAGAAAAAC 0.947631 -29 TTGTTTAGCTTGACAAAAAACAACAACTTAA 10 14 0 TGACAAAAAC 0.612696 -31 TTGTCAAGCTAAACAAAAAACGCCTA 10 29 1 AAACAAAAAC 0.947631 -16 AAGAGACTTCAAACAAAACAACATCAAGAGC 12 89 0 AAACAAAAAA 0.488873 -212 AGTGCAGTTCAACCAAAAGACAAGCAAGCA 15 10 0 AACCAAAAAC 0.818784 -291 TAATTGTTAAAAAGGAAATACCTTTTCACCT 15 103 1 AAAGGAAAAC 0.725244 -198 TCAAAATTTCAAACCAAAAACTATAACACAC 21 121 1 AAACCAAAAC 0.829286 -180 CCTTTTTAAATGAGAAAAAACTGGAGATTAA 21 166 0 TGAGAAAAAC 0.612696 -135 ATTTTTCGCAAAACCAAAGACCGCGGAATTG 22 163 1 AAACCAAAAC 0.829286 -111 AACCCTAAAATAAGAAAAAGCACTACTAAAA 22 221 0 TAAGAAAAGC 0.712431 -53 TTGTTGAATTAAAGACAAAACTTTACCAAAA 23 14 0 AAAGACAAAC 0.696489 -184 TTTACATTGTAAAGAAAAGACTGCTCGCTGT 23 113 0 AAAGAAAAAC 0.947631 -85 ******** ** Masking position 7 Map Score: 14.1268 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 106 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 GGAATCTAAATTTATTATAAATATTGGATT 2 18 1 TTTATTATAA 0.529707 -33 GCAATACTTATTAATTATAAGACGATTAAG 4 58 1 TTAATTATAA 0.887948 -110 TTTAACTACTTAATTTTTAAAGAAAAAAC 7 282 0 TTAATTTTTA 0.774817 -19 CATTCGAGTGTTAATTATAAAACTGCTTTG 8 13 0 TTAATTATAA 0.887948 -33 ACTACTTGCTTTAATTATAAGACCGCTTAA 9 110 0 TTAATTATAA 0.887948 -24 CATAGCTTATTTAAATTTAAAGAAGGTTGT 13 87 1 TTAAATTTAA 0.435662 -139 AGTGTGCTTTAATTTTAAAAAAGAAAGT 14 9 1 TTAATTTTAA 0.900468 -92 AGCGCGTTAGGTAATTTTAAATTGTTGGTT 17 11 0 GTAATTTTAA 0.72518 -38 CTTGATGAGCTTAATTTTAAAAATGTAAAA 18 11 1 TTAATTTTAA 0.900468 -28 GTTTGAAATTTTGATTTTTATTGAAATTTG 21 105 0 TTGATTTTTA 0.570291 -196 ACCAAGCTCATTGATTTTAATCTCCAGTTT 21 150 1 TTGATTTTAA 0.854602 -151 TTAATGTGTGTTAATTTTAAACTAATGCT 22 10 0 TTAATTTTAA 0.900468 -264 ********** Masking position 4 Map Score: 10.0671 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 21 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 CTTGGTTTTTTTACAGAATTTTGCACTTCAGT 3 118 1 TTAAAATTTT 0.421711 -183 TGCAAACAATTTATAAAAATTTTTGCGTTTTC 3 157 0 TTAAAAATTT 0.562538 -144 TGTGAGATTTTTTGAACAGTTTTTGCAGTTAA 7 169 0 TTTACAGTTT 0.929966 -132 GCAAGAAAATTTATCCCAGTTTTAGGGGGCAA 7 220 1 TTACCAGTTT 0.808532 -81 ATCAAAGCAGTTTTATAATTAAC 8 2 1 TCAACAGTTT 0.682005 -44 TTGCAAAAATTTTTAGCAATTTTATTGGCAGT 12 129 1 TTTACAATTT 0.587685 -172 TTATTTAAATTTAAAGAAGGTTGTTGCTGTAG 13 93 1 TTAAAAGGTT 0.619109 -133 AACTCCACTCTTTTCCAAGTTTAGGTGAAAAG 15 124 0 TTTCAAGTTT 0.701379 -177 CAGTGCCCAATTATATAAGTTTGGCATAAATG 15 232 1 TTAAAAGTTT 0.922958 -69 AGAGTTAGCTTTAAAAAAGTTTAAACGGGTTT 16 42 1 TTAAAAGTTT 0.922958 -165 AAACAAAACCTTAAAAATGTTTAATGAAAGAA 20 51 1 TTAAATGTTT 0.506187 -39 CAAAATTTGTTTTTAATAGTTTCGATTTTATG 21 199 1 TTTATAGTTT 0.597233 -102 TTAATAAAGATTAAACAAGTTTAATTCCTAAA 21 251 0 TTAAAAGTTT 0.922958 -50 GCAAAGACAGTTTAAGCAGCTTTGCAGTTCTT 23 142 0 TTTACAGCTT 0.643068 -56 TGCTAGTTTGTTTGAACAGTTTCAGCTAGCAT 25 190 1 TTTACAGTTT 0.929966 -111 TGTCATGCGTTTTAATCAGTTTGACTTCAAAA 25 238 0 TTTACAGTTT 0.929966 -63 *** * ****** Masking position 11 Map Score: 7.83589 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 124 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GAAGCTTAAAAGGAATCGAGGT 4 3 1 AGCTTAAAAG 0.886651 -165 GCAAATAATCAGCCTAAAAGTGCAATTAAA 6 213 0 AGCCTAAAAG 0.830493 -75 ATTATAAGACCGCTTAAAAACTAGCTTTGG 9 97 0 CGCTTAAAAA 0.95015 -37 TTTCTAAATACTCTTAAAAATTTATTTGGG 12 48 1 CTCTTAAAAA 0.624804 -253 TTACCGCTAAAGCCTAAACACAAACTTACA 13 59 1 AGCCTAAACA 0.706232 -167 TAAAAGAAGGAGCCTAAAAAAGAAGGATAA 13 167 1 AGCCTAAAAA 0.927356 -59 ATTTAGAGTTAGCTTTAAAAAAGTTTAAAC 16 38 1 AGCTTTAAAA 0.834908 -169 AACGCGCTTGCGCTTAAAAAATCGCT 17 33 1 CGCTTAAAAA 0.95015 -16 TGGGAGAAATAGCTCAAAAAGTTTTAGTAG 19 30 1 AGCTCAAAAA 0.793318 -109 TTAAAACAAAACCTTAAAAATGTTTAATGA 20 48 1 ACCTTAAAAA 0.725218 -42 TTTCATTTTGCGCTTTAAAATCTAACAG 22 256 1 CGCTTTAAAA 0.825465 -18 ********** Masking position 7 Map Score: 6.00886 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 64 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 CTTTTTGTTAACAAGAAAGAAACGGAATTT 3 223 0 ACAAGAAAGA 0.677123 -78 AAATAATAAAAAAATAAATAATTAAAGCAC 5 12 0 AAAATAAATA 0.635976 -44 CAAAATTAAAAAAGTAAAGGAAGCAGGGGA 6 105 1 AAAGTAAAGG 0.730186 -183 GTTGTAGGCTAAAAGAAGGGGAATTAACAA 7 12 0 AAAAGAAGGG 0.834602 -289 TTTCTTGATAAAAAGAAAGGGAATCTTTTA 7 58 0 AAAAGAAAGG 0.909055 -243 ATTTTGAACCAAAATAAAGACCACTTTTAA 7 105 0 AAAATAAAGA 0.88965 -196 TTTGCAATTTAAAGTAAAGAGACTTCAAAC 12 106 0 AAAGTAAAGA 0.817426 -195 TTTTCATACTAAAAGAAGGAGCCTAAAAAA 13 158 1 AAAAGAAGGA 0.893027 -68 AGGAGCCTAAAAAAGAAGGATAATTCTGCA 13 174 1 AAAAGAAGGA 0.893027 -52 TTAATTTTAAAAAAGAAAGTTTGAAAGGTG 14 19 1 AAAAGAAAGT 0.656994 -82 TAATTGTTAAAAAGGAAATACCTTTTCACC 15 103 1 AAAGGAAATA 0.665566 -198 TTAAAAATGTAAAATAACGGCC 18 27 1 AAAATAACGG 0.628097 -12 GAAAATAAATATTACAAGCTG 19 2 1 AAAATAAATA 0.635976 -137 TTTAGTAAGAAAAAGAACGAAGTTTATAAA 19 80 1 AAAAGAACGA 0.851438 -59 AATCATAAGAAAAATAATGAAAAATGCTAA 23 53 0 AAAATAATGA 0.506019 -145 CCCAACTGCAAAAGGAAATAAAAGCTGCTA 25 36 1 AAAGGAAATA 0.665566 -265 ********** Masking position 6 Map Score: 8.8922 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 143 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 GTTCCTACTTAAACAGTCTTGGCAAACAAA 4 115 1 AAACAGTCTT 0.866959 -53 GAAACTAGCTTTATCTATACG 5 45 0 AAACTAGCTT 0.887449 -11 GACCGCTTAAAAACTAGCTTTGGCTAAATT 9 90 0 AAACTAGCTT 0.887449 -44 TTCACCTTTCAAACTTTCTTTTTTAAAATT 14 21 0 AAACTTTCTT 0.667855 -80 GGGCACTGTTAAATTAGCTTCGCTGTTTTA 15 210 0 AAATTAGCTT 0.708217 -91 GGGAACAGAAAATCAGGCTTTCAACACAGA 21 19 1 AATCAGGCTT 0.757932 -282 AATAAAGATTAAACAAGTTTAATTCCTAAA 21 251 0 AAACAAGTTT 0.505364 -50 AAAGCTGCTTAAACTGTCTTTGCAAGCTTG 23 151 1 AAACTGTCTT 0.889151 -47 TGCAACTCTAAAACAAGCTTGCAAAGACAG 23 164 0 AAACAAGCTT 0.932485 -34 ********** Masking position 2 Map Score: 2.50336 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 51 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 Motif number 11 AAGTGCAAAATTCTGTAAAAAAACCAAGCGAC 3 114 0 TTCTGAAAAA 0.730232 -187 TTCCGTTTCTTTCTTGTTAACAAAAAGCGCAA 3 226 1 TTCTTTAACA 0.916157 -75 TGGTGGTGTTTTCTTTTTAAAAAATGGTGCTT 6 20 0 TTCTTTAAAA 0.965964 -268 CTTCTCTTTTTTCTTGTTAAAAGATTCCCTTT 7 41 1 TTCTTTAAAA 0.965964 -260 AAAAGAGATTTTCTTGATAAAAAGAAAGGGAA 7 65 0 TTCTTTAAAA 0.965964 -236 GGGATAAATTTTCTTGCAAAAAAATGATTGCA 7 205 0 TTCTTAAAAA 0.873139 -96 TGATGGCCTTTTCATACTAAAAGAAGGAGCCT 13 150 1 TTCATTAAAA 0.875987 -76 CTTTCAAACTTTCTTTTTTAAAATTAAAGCAC 14 14 0 TTCTTTTAAA 0.783419 -87 TTCGTTCTTTTTCTTACTAAAATCAGCAGGTT 19 69 0 TTCTTTAAAA 0.965964 -70 AAATATCCAATTCTTTCTAACAGCAGTAAAGC 19 107 1 TTCTTTAACA 0.916157 -32 TCACAATAATTTCAGGTTAAAACAAAACCTTA 20 32 1 TTCAGTAAAA 0.730553 -58 ***** ***** Masking position 10 Map Score: 10.7562 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 9 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 TTACAATTTATATTGAGAAATTTTTA 3 285 1 TATGGAAATT 0.620309 -16 TGGTCTTTATTTTGGTTCAAAATTTAGTCCAAAA 7 112 1 TTTGTCAATT 0.922297 -189 CAGTCAAATTTTTAGCACAAATTTAACTGCAAAA 7 147 1 TTTGACAATT 0.745435 -154 ATGATTGCAATTTTGTGAGATTTTTTGAACAGTT 7 180 0 TTTGGAGATT 0.830173 -121 ATTGCAAAAATTTTTAGCAATTTTATTGGCAGTT 12 128 1 TTTTGCAATT 0.618297 -173 AATTCCTCCTTTCTGCTCAAGGTTTAGAAAACTA 12 272 0 TTCGTCAATT 0.869035 -29 TTTAAACGGGTTTCGCTAGAAATTCGCCGTTTAG 16 61 1 TTTGTAGATT 0.7199 -146 ACGGCGTTTCTTCTGCGCAATCTTTCGCTTTTCA 16 138 0 TTCGGCAATT 0.926583 -69 AAACCCAAAATTTGGAGAAATCTTAATAAAGATT 21 271 0 TTTGGAAATT 0.933796 -30 TTGCTTCGCTTTCAGGTCAAGATTTGGAAATTTT 22 134 1 TTCGTCAATT 0.869035 -140 CGGTCTTTGGTTTTGCGAAAAATTTCCAAATCTT 22 152 0 TTTGGAAATT 0.933796 -122 CTGTTTTGGTAAAGTTTTGTCTTTAAT 23 4 1 TTTGTAAATT 0.881178 -194 *** * **** ** Masking position 10 Map Score: 3.78967 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 64 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 AAAGGGAAGCCGCACTACCT 3 1 1 AAAGGGAAGC 0.865891 -300 CAAAATTAAAAAAGTAAAGGAAGCAGGGGA 6 105 1 AAAGTAAAGG 0.584682 -183 GGATAAGATTAAAGCAAAGGTAAAAAAACA 6 147 1 AAAGCAAAGG 0.915636 -141 TAACAAGAAAAAAGAGAAGTTGTAGGCTAA 7 30 0 AAAGAGAAGT 0.715717 -271 AGTTCAACCAAAAGACAAGCAAGCA 15 6 0 AAAGACAAGC 0.716216 -295 TACCAATAAAACAGCGAAGCTAATTTAACA 15 204 1 ACAGCGAAGC 0.954618 -97 GCTTGCGTGAAAAGCGAAAGATTGCGCAGA 16 131 1 AAAGCGAAAG 0.576944 -76 TCTTGACCTGAAAGCGAAGCAAGTCCGCCA 22 126 0 AAAGCGAAGC 0.971086 -148 TTGTACTCAAACAGAAAAGCACAGCGAGCA 23 93 1 ACAGAAAAGC 0.812139 -105 AATGTAAAGAACTGCAAAGCTGCTTAAACT 23 136 1 ACTGCAAAGC 0.626309 -62 TTAGAGTTGCAAAGCAAAGTCCAAA 23 183 1 AAAGCAAAGT 0.828091 -15 ********** Masking position 7 Map Score: 2.02143 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 85 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 ATTGAATGGTTTGTGATTGACTTCATTAGA 3 30 0 TTGTGATTGA 0.9537 -271 TATGTGTTGTTTGTGATTGAATGGTTTGTG 3 45 0 TTGTGATTGA 0.9537 -256 CTATGTAAGTTTGTGTTTAGGCTTTAGCGG 13 62 0 TTGTGTTTAG 0.833145 -164 ACTAACAACTTTGTGATTGACAGAAGTAAC 15 38 1 TTGTGATTGA 0.9537 -263 CCTGAAATTATTGTGATTAGTTAGCTCACA 20 18 0 TTGTGATTAG 0.919859 -72 TGGTAAAGTTTTGTCTTTAATTCAACAAAC 23 17 1 TTGTCTTTAA 0.757935 -181 ACGCATGACATTGTCATTAAGAGTAAGGTA 25 260 1 TTGTCATTAA 0.878012 -41 ********** Masking position 4 Map Score: 2.51156 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 29 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 15 TATTAACTTTACCTGGAATAGCGTACAACA 1 139 0 ACCTGGAATA 0.756387 -98 GCCCCCTAAAACTGGGATAAATTTTCTTGC 7 220 0 ACTGGGATAA 0.815898 -81 AGCCTAAAAAAGAAGGATAATTCTGCAAAC 13 177 1 AGAAGGATAA 0.592248 -49 AGCAGTCTGTACCAGGATAATTGTTAAAAA 15 86 1 ACCAGGATAA 0.911752 -215 TTTCACCTAAACTTGGAAAAGAGTGGAGTT 15 126 1 ACTTGGAAAA 0.843086 -175 ACTTAGGTTAAGCTGGAAAATTAACCCTAG 15 265 1 AGCTGGAAAA 0.910315 -36 ATTTATTGGGAGCAGGAAAACGAAAATTCT 21 46 0 AGCAGGAAAA 0.910315 -255 TTGTTCATTGACAGGGAAAATGTCATTAGC 25 62 0 ACAGGGAAAA 0.894163 -239 CGGGTTCAATACCGGGAAAAAGCCACTGCC 25 134 0 ACCGGGAAAA 0.968721 -167 ********** Masking position 7 Map Score: 2.10523 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 23 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617