AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -igalR_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 ydjK 300 similar to sugar transporter #2 glvA 300 6-phospho-alpha-glucosidase #3 yfiA 64 similar to hypothetical proteins #4 yfiB 105 similar to ABC transporter (ATP-binding protein) #5 yfiD 154 similar to hypothetical proteins #6 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #7 yfiG 174 similar to metabolite transport protein #8 yhjM 103 similar to transcriptional regulator (LacI family) #9 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #10 yjlC 300 yjlC #11 yjlD 39 similar to NADH dehydrogenase #12 yjmA 197 similar to glucuronate isomerase #13 yjmB 67 similar to Na+:galactoside symporter #14 yjmC 104 similar to malate dehydrogenase #15 yjmE 24 similar to D-mannonate hydrolase #16 yjmG 47 similar to hexuronate transporter #17 yjmH 87 similar to transcriptional regulator (LacI family) #18 ccpA 274 transcriptional regulator (Lacl family) #19 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #20 ytxJ 23 alternate gene name: csb40; similar to general stress protein #21 ytxH 27 alternate gene name: csb40; similar to general stress protein #22 ytxG 161 alternate gene name: csb40; similar to general stress protein #23 murC 249 UDP-N-acetyl muramate-alanine ligase #24 ytpS 159 ytpS #25 ytpP 234 similar to thioredoxin H1 #26 yufN 300 similar to ABC transporter (lipoprotein) #27 yufO 75 similar to ABC transporter (ATP-binding protein) #28 araE 137 permease #29 ywtG 300 similar to metabolite transport protein #30 rbsR 300 transcriptional regulator (LacI family) #31 galK 80 galactokinase #32 ywcC 300 alternate gene name: ipa-33d #33 galE 114 UDP-glucose 4-epimerase #34 yxkA 129 similar to hypothetical proteins #35 iolR 300 transcriptional regulator (DeoR family) #36 iolS 53 alternate gene name: yxbF; myo-inositol catabolism #37 yxcE 261 yxcE #38 yxcC 238 similar to metabolite transport protein Motif number 1 GTGAGACTTTAAGATTACAAAAAAGGTAAAAAAACCAAATCTC 2 122 1 AAAAAAAAAA 0.946643 -179 AAATGAAATAAAAGTACTATAAAACTGTAACAAAAAAAGACCT 5 28 0 AAAAAAAAAA 0.946643 -127 TTGTCTTATAATCTTTTTAGAAAGCGGTTACAACAAGGGGTAT 7 67 1 ATAAAATAAA 0.387904 -108 CCGATTTCAGAAACTAGGATAAATTTGTAATAAATTTTTAGAT 8 36 0 AAAAAAAAAA 0.946643 -68 TGAAATGTTAACGCTGTCATAAACATAAAAAAAGACATTGCCA 12 62 0 ACAAAAAAAA 0.606919 -136 GATTGATCCCAAAGGAATATAAAGGTAAAATAAAAACAAATCA 12 118 1 AAAAAAAAAA 0.946643 -80 ATATAAAGAATATTTAAAATAATTTGTAAATAAAATGTGTTTG 14 18 1 TAAAATAAAA 0.625157 -87 TTTATAACTAAATAAACGAGAAAGCATAAAAAAAGGCCGCACG 18 32 0 AAAAAAAAAA 0.946643 -243 GGAAATACTGAAATACAAAAAATTTTATAAAAACTCTACTTTA 19 128 0 AAAAATAAAA 0.766377 -108 TATTCTCCGTTATGTAAGAAAATCCTTTAATAAGCTTTCCCAT 22 47 0 TAAAATAAAA 0.625183 -115 AACCTGATACTAAACATAACAAAACATATAAAATACGCCGCTA 23 131 1 TAAAAATAAA 0.625183 -119 ACTCCCATAAATCCGCCAAAAAAAACGAATCATGTGAAAAGC 24 10 1 AAAAAAAACA 0.566961 -150 AATGGACGAGTATCGATAAAAAACATGTAAGAACATAAACAAC 25 188 1 TAAAAAAAAA 0.900209 -47 CCGCTCCTTTATTTCAAAATAAAAGAAAAACAAGGGATAAGGG 27 36 0 ATAAAAAAAA 0.774136 -40 TACATTTAATTAGTACGTACAAATATAGAATAATCTTGTTTGC 28 22 0 TAAAAAAAAA 0.900209 -116 AAAAGGTTTAATGGCCGGAAAAAGAGGCTAAAAGATTTCTAAA 29 216 1 ATAAAATAAA 0.387904 -85 TTAGACCTGTAAATGGGGAGAAACAGAAAAGACTATCATCCCA 30 48 0 AAAAAAAAAC 0.714667 -253 TTTTTTGACAAAGTCTTCACAAATATGGATGAAGATTTCTTGA 30 133 0 AAAAAAATAA 0.469037 -168 AATCCGAAGTTAGCAATAAAAATATCAAAAGAAATCTAATTGT 30 216 0 TAAAATAAAA 0.625183 -85 TATGAAGAAATAAGGGGAATAAAAAATAAAAACCAGAAAGGTG 31 41 1 TAAAAAAAAC 0.560158 -40 GCTAAAAAATATGAAAAAACTATTAATAAACGATTAAAC 33 7 1 AAAAAAAAAA 0.946643 -108 GCGATTAGAATATAACCAAGAAATGACCAAAAAGTAACCTGTT 35 61 0 TAAAAAAAAA 0.900209 -240 TTAAAAGATTAATATAATAAAAATAATGAAAAAATGTAGTGTT 35 127 0 AAAAAAAAAA 0.946643 -174 CTTGAATCTTTACGTAACATAAATATATAATAAAAACCAAAAG 35 254 0 TAAAAAAAAA 0.900209 -47 AACCTTACAAAATGAGCCATAAATCCGATAAAATAAAGGTAGT 37 87 1 AAAAAATAAA 0.766377 -175 AAATAACTTTATGCTCAGAGAAACCATTAAAAAAACCTTACCC 38 40 0 ATAAAAAAAA 0.774136 -199 TGAGCCAATGAAGTATCTAAAAATATGTAACAAAGTTAATAGA 38 185 0 AAAAAAAAAA 0.946643 -54 ** * *** ** ** Masking position 12 Map Score: 29.1261 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 231 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 2 AGAAAATAGTTGTTCATGTTTTTATCCAAT 1 194 0 TGTTCATGTT 0.817413 -107 GCAGGGGGATTTTTTATTTTTGTCCGCCTT 6 36 1 TTTTTATTTT 0.894312 -58 TTTCTATCCCTTTTTATTATAAGGAAATGG 9 59 0 TTTTTATTAT 0.855467 -65 CTTATTCAATTGTTTATTTTTAGATAAAAA 10 111 1 TGTTTATTTT 0.892326 -190 GCAATGTCTTTTTTTATGTTTATGACAGCG 12 64 1 TTTTTATGTT 0.892326 -134 TTTTGATTTGTTTTTATTTTACCTTTATAT 12 134 0 TTTTTATTTT 0.894312 -64 GTGCGGCCTTTTTTTATGCTTTCTCGTTTA 18 33 1 TTTTTATGCT 0.689902 -242 TGTACATTATTTTTCATTATTCATCAAATT 18 134 0 TTTTCATTAT 0.765518 -141 CTACATAAAGTGTTTATGCTATAGATAAGG 18 222 1 TGTTTATGCT 0.685425 -53 GCACATTCATTTTTTATTTTGTAGTTATCA 19 198 0 TTTTTATTTT 0.894312 -38 ATCTCACTGCTTTTTATTTATCTGATGGGA 22 23 1 TTTTTATTTA 0.642307 -139 CCAGTACACATGTTTATGATTGAAGAAAAC 22 103 1 TGTTTATGAT 0.850236 -59 TCCCTCCAGTTGTTTATGTTCTTACATGTT 25 209 0 TGTTTATGTT 0.890307 -26 GAGTAAAGCGTTTTCATTTAAACCTTCAAT 28 97 0 TTTTCATTTA 0.497607 -41 CCATTAAACCTTTTTATTTTTCTGATCATA 29 200 0 TTTTTATTTT 0.894312 -101 AACTTCGGATTGTTCATGATAATCTATCTA 30 248 1 TGTTCATGAT 0.757954 -53 AGCTCCTCCTTGTTTATGTAACCGTTTACA 30 278 0 TGTTTATGTA 0.632674 -23 ACCTTTCTGGTTTTTATTTTTTATTCCCCT 31 53 0 TTTTTATTTT 0.894312 -28 AGTATTTAATTGTTTATTATTATAAATAAG 32 131 0 TGTTTATTAT 0.852871 -170 AAATGATTTATTTTCATTTACATACTATCC 32 165 0 TTTTCATTTA 0.497607 -136 AAATGACCTGTTTTCATTATATAGTGTTTA 33 77 0 TTTTCATTAT 0.765518 -38 AAAAATGTAGTGTTTATGATTGACTTATGG 35 111 0 TGTTTATGAT 0.850236 -190 TTTTTCATTATTTTTATTATATTAATCTTT 35 137 1 TTTTTATTAT 0.855467 -164 TAACTTTTGGTTTTTATTATATATTTATGT 35 251 1 TTTTTATTAT 0.855467 -50 ********** Masking position 4 Map Score: 25.4909 Number of sites scoring better than the average of aligned sites = 698 Number in coding regions = 437 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 286 Fraction of orfs with sites within 600 bp upstream = 0.0459364 Motif number 3 CTCCTTTTCGGGAGGGTTTTCGTTTGCCGT 4 19 1 GGAGGGTTTT 0.974555 -87 AAAGGGGTTTGGAGGCTTTTAC 4 94 1 GGAGGCTTTT 0.966608 -12 CAACTTGTTAGGAGGCGTTTAC 6 82 1 GGAGGCGTTT 0.941803 -12 TAATCGAATTGGAGTTTTTTGTGTTTGCTA 10 55 1 GGAGTTTTTT 0.632353 -246 AAATGTGTTTGTAGGGGTTTCGCTTGGAGA 14 50 1 GTAGGGGTTT 0.66619 -55 TGAAAAGGAAGGAGGCACTTGC 14 93 1 GGAGGCACTT 0.66278 -12 TCCAGTAAAAGGAGTGGTTTTAGG 18 261 1 GGAGTGGTTT 0.795161 -14 GATGATATCTGGACGCTTTTTT 19 3 0 GGACGCTTTT 0.806706 -233 GGGTAATAAAGTAGAGTTTTTATAAAATTT 19 122 1 GTAGAGTTTT 0.39291 -114 CGCCGCTAAGGGAGGCTTTTCAGCCGCCGC 23 166 1 GGAGGCTTTT 0.966608 -84 TAGTTTTCTGGGACGGTTTTTAGTATACCA 24 119 0 GGACGGTTTT 0.846671 -41 ATATACATAAGGAGGGATTTTTATT 25 6 0 GGAGGGATTT 0.956226 -229 ATAAACAACTGGAGGGATATGAA 25 222 1 GGAGGGATAT 0.636964 -13 TCATTTTTTAGGAGGGTTTACATC 33 101 1 GGAGGGTTTA 0.754676 -14 TTGCAGTGAAGGAGATATTTC 34 2 0 GGAGATATTT 0.495207 -128 GATTCAAGAAGGAGTTTTTTAT 35 289 1 GGAGTTTTTT 0.632353 -12 CAACTGAGGAGGAGACATTT 38 229 1 GGAGACATTT 0.749578 -10 ********** Masking position 3 Map Score: 14.8432 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 176 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 4 GGGCTGCTGCCTTCCTCACATTTCGTAAGCAGGC 1 227 0 CTCCTCTTTC 0.977936 -74 ATGAAATTCCCCCATTTTCGAATCTGTAA 3 6 1 ATCCCCTTTC 0.985302 -59 ATCAGATCCCCCCATTTTCTTTCTATTAT 3 46 0 ATCCCCTTTC 0.985302 -19 AGACTGCCCTCCTTTTCGGGAGGGTTT 4 4 1 CTCCCTTTTC 0.968684 -102 GGCTTTCTTCCCCTTCTTTCAAGAATGGCA 7 155 0 CTCCCCTTTC 0.993674 -20 TAAATGTTTACTACCCAGTTTTTCATCTTGCCAT 10 152 0 CTCCCATTTC 0.946068 -149 GCATCCTTCTCTTCCCCGCCTTTCGAAGGAAATA 26 93 1 CTCCCCTTTC 0.993674 -208 TCGAGCCCTTATCCCTTGTTTTTCTTTTATTTTG 27 31 1 ATCCTTTTTC 0.788344 -45 TTTATTTTTTATTCCCCTTATTTCTTCATAGAAA 31 37 0 ATCCCCTTTC 0.985302 -44 ATGAATCCCTCTCTCTATTTTCTCGTTCTATA 34 108 0 CTTCTCTTTC 0.794762 -22 ** **** **** Masking position 11 Map Score: 13.7646 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 43 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 ACCTCATAACCTTCCCTTCTTCTTAGCATG 1 163 0 CTTCCCTTCT 0.633689 -138 TCCAGGGCTGCTGCCTTCCTCACATTTCGT 1 235 0 CTGCCTTCCT 0.939705 -66 AGACTGCCCTCCTTTTCGGGAGG 4 4 1 CTGCCCTCCT 0.904034 -102 TAAGCCAATGCATCCCTCCTTCAGCAATAC 7 106 0 CATCCCTCCT 0.810033 -69 GGCTTTCTTCCCCTTCTTTCAA 7 163 0 CTTTCTTCCC 0.66169 -12 CAAGTGCCTCCTTCCTTTTCAGTTTTTTGG 14 84 0 CTTCCTTTTC 0.830568 -21 CTAATTCCCTTCCTTATCATACCGGCTG 17 70 0 CTTCCTTATC 0.598387 -18 GGCCGCCGTGCGGCCTTTTTTTATGCTTTC 18 26 1 CGGCCTTTTT 0.487269 -249 TTTTTTCATCCTTTCCCTGCACATTC 19 220 0 CATCCTTTCC 0.851322 -16 GACTCAAGCTCTTCCTTCCCTGC 20 4 0 CTTCCTTCCC 0.971884 -20 ACGCCTTCCGCATCCTTCTCTTCCCCGCCT 26 84 1 CATCCTTCTC 0.923565 -217 TTCCCTGCCCTCCCGAATGTTGAG 28 124 0 CTGCCCTCCC 0.967208 -14 CAAGATTGGACGGCCTTCTCTTACTTCTCT 35 177 0 CGGCCTTCTC 0.91986 -124 GAAGAAAACAGCCTTCTCCAATGGAGAA 37 9 1 CAGCCTTCTC 0.944621 -253 CACAAAAAAACAGCCTTCTCCATTGGAGAA 37 24 0 CAGCCTTCTC 0.944621 -238 ********** Masking position 7 Map Score: 12.3534 Number of sites scoring better than the average of aligned sites = 533 Number in coding regions = 443 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 6 TTGGATGTTTTATATAAATGATTATAAATAAT 2 6 1 TTTTTAAAGT 0.824887 -295 AATTTTGTTACATTTTACGAAAATGAAATAAAAGTAC 5 54 0 CTTTTGAAGA 0.739463 -101 CCCCCTGCCGTTATTTCGGCAAGGGGATTGCAG 6 7 0 TATTTGAAGA 0.862877 -87 TGTCTTATAATCTTTTTAGAAAGCGGTTACAACAAGG 7 68 1 TTTTTGAAGT 0.961983 -107 AAATTTATCCTAGTTTCTGAAATCGGTAACATGTCAA 8 53 1 TGTTTGAAGT 0.87168 -51 TGTCAACAACTTTTTTAAGGAAGGGAAAAT 8 84 1 TTTTTGAAGA 0.961983 -20 AACGTTGATTTTATTTACGAAAGGGGTTAGACACG 9 9 0 TATTTGAAGT 0.862877 -115 TATCCCTTTTTATTATAAGGAAATGGAGGTACACTTT 9 48 0 TTTATGAAGA 0.656944 -76 TTGTGTTTGCTATTTTCAGAGAGAGTAAAGGATTTTG 10 73 1 TTTTTGGAGA 0.847178 -228 TAGTAAACATTTATTTTTGTAAATGATTGTGCATGAA 10 173 1 TATTTGAAGT 0.862877 -128 AGTTTGCTGATTTTTTTGGAAAGGGTAGTGCCTCTCC 10 250 0 TTTTTGAAGA 0.961983 -51 GGGATCAATCTCTTTTTTGAAAATGAAATGTTAACGC 12 91 0 TTTTTGAAGA 0.961982 -107 TATAAGTTCTTGTTTTTGAAAATTGATAACGATAATG 29 78 1 TTTTTAAAGT 0.824887 -223 GTCTGTGGGATTTTTTTAGAAATCTTTTAGCCTCTTT 29 236 0 TTTTTGAATT 0.541682 -65 CAGCTCCTCCTTGTTTATGTAACCGTTTACATAGATA 30 272 0 TGTTTGAAGT 0.87168 -29 TATTAGTCATTTTTTTAGGGAATAGGTAGGTGGTTTT 32 82 0 TTTTTGAAGT 0.961983 -219 TCGGTGTATATCTTTTGCAAGATTGGACGGCCTTCTC 35 187 0 TTTTTAGAGA 0.507871 -114 TTGAAACATTTGTTTTGAAAAAACGGAAACTTTATAG 38 125 0 TTTTTAAAGA 0.824887 -114 * **** * ** * * Masking position 6 Map Score: 15.1026 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 232 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 TTAACGAGAAATGAAATCGCTTCCATAGGGATTGA 1 128 1 AGAAACGTCA 0.953768 -173 ATAAATGGAATTGTAAACGTTATCAAGGAGGTCGT 2 273 1 TGTAACGTCA 0.90896 -28 AGCTTACATTAAGTAAGTGATAACATTTATCAAGG 5 122 1 AGTAATGTCA 0.74588 -33 ATAATCTTTTTAGAAAGCGGTTACAACAAGGGGTA 7 74 1 TGAAACGTCA 0.822134 -101 AGTTGTTGACATGTTACCGATTTCAGAAACTAGGA 8 60 0 AGTTACGTCA 0.966073 -44 TGAAAATGAAATGTTAACGCTGTCATAAACATAAA 12 76 0 AGTTACGTCA 0.966073 -122 CTATTTCAAAATGTTAACGTTAACATTTTGATTTG 12 154 0 AGTTACGTCA 0.966073 -44 TATAAAAACCAAGTATACGTTTTCATCATCTATAA 18 69 1 AGTATCGTCA 0.825852 -206 AGTCTTACTTCAGAAAACGATGTCACGGTTTTCCG 26 43 1 CGAAACGTCA 0.795293 -258 CCGAATGTTGAGTAAAGCGTTTTCATTTAAACCTT 28 101 0 ATAAACGTCA 0.596806 -37 GTGATTCAGTACATTATCGTTATCAATTTTCAAAA 29 91 0 AATTACGTCA 0.671392 -210 CTCCTTGTTTATGTAACCGTTTACATAGATAGATT 30 268 0 AGTAACGTCA 0.97805 -33 CCTTCACTGCAAGTTATCCATAACAAATTGTTACG 34 20 1 AGTTACCTCA 0.735433 -110 * **** ** * ** Masking position 15 Map Score: 8.29751 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 94 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 ACATACGCATTTTGAAAAAGACTGGGGGAAA 1 276 1 TTTGAAAAGA 0.744185 -25 ATTTTACGAAAATGAAATAAAAGTACTATAA 5 49 0 AATGAAAAAA 0.635179 -106 ATTTTCGTAAAATGTAACAAAATTACTTGAC 5 67 1 AATGTAAAAA 0.428833 -88 CTAGGATAAATTTGTAATAAATTTTTAGATT 8 35 0 TTTGTAAAAA 0.842284 -69 GATAACACTTTTTGAACAAAATTTGAACGTG 10 14 0 TTTGAACAAA 0.769914 -287 ACGTTAACATTTTGAAATAGAATGAAAGACG 12 169 1 TTTGAAAAGA 0.744185 -29 GGCGCTTTTTTTTGTAAAAAACCCTTGAACA 19 34 1 TTTGTAAAAA 0.842284 -202 TATTCTCCGTTATGTAAGAAAATCCTTTAAT 22 59 0 TATGTAAAAA 0.698715 -103 CATGTTTATGATTGAAGAAAACGGGTAAACA 22 111 1 ATTGAAGAAA 0.520052 -51 CCGGATCAGCTTTGAACCAAATTTTTCTGGG 26 243 1 TTTGAACAAA 0.769814 -58 TTTCTTTTATTTTGAAATAAAGGAGCGGTCA 27 51 1 TTTGAAAAAA 0.925708 -25 TTTCGGCGACATTGAAAAAAATACAAGTAAA 29 156 1 ATTGAAAAAA 0.801438 -145 AACGCATGACTTTGAAACAATTTTAATAAAA 30 90 1 TTTGAAAAAT 0.515725 -211 AATAACTGATTTTGAAGCAAAACCTTACAAA 37 67 1 TTTGAAGAAA 0.769814 -195 ATCTAGCTCATATGAAATAAAGCTGACCCAG 37 182 1 TATGAAAAAA 0.843179 -80 AAACATTTGTTTTGAAAAAACGGAAACTTTA 38 128 0 TTTGAAAAAC 0.612513 -111 TATCTAAAAATATGTAACAAAGTTAATAGAT 38 184 0 TATGTAAAAA 0.697374 -55 ******* *** Masking position 6 Map Score: 8.3879 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 331 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 9 TAAGCAGGCTTCAGAAAATAGTTGTTCATGTT 1 204 0 TCAGAAAAAT 0.884156 -97 AAAGACATTGCCAGAAAGCACTCGGAAAGGAA 12 43 0 CCAGAAAGAT 0.83419 -155 CGGATCACTATCCGAAAATTCTTAAGACACAG 13 37 1 TCCGAAAATT 0.657326 -31 GCTGGTCGGCCCAGAAAAGATTAAGCTATCAG 24 85 0 CCAGAAAAAT 0.935552 -75 AAAAACCGTCCCAGAAAACTATAAGGGAGTTA 24 128 1 CCAGAAAATT 0.955061 -32 AAGTCTTACTTCAGAAAACGATGTCACGGTTT 26 42 1 TCAGAAAAGT 0.863527 -259 TTTGTTATTATCAGAAAATTTTATCGATTCTA 26 177 1 TCAGAAAATT 0.917858 -124 ATATAACCCCCCAGAAAAATTTGGTTCAAAGC 26 251 0 CCAGAAAATT 0.955061 -50 AAACTTATGATCAGAAAAATAAAAAGGTTTAA 29 195 1 TCAGAAAATA 0.714577 -106 GACTATCATCCCAGAAAATGTTTAATTATGTT 30 29 0 CCAGAAAAGT 0.923282 -272 ATGGGGAGAAACAGAAAAGACTATCATCCCAG 30 47 0 ACAGAAAAAT 0.65313 -254 AAAATAAAAACCAGAAAGGTGATTGCAC 31 63 1 CCAGAAAGTA 0.622682 -18 ******** * * Masking position 6 Map Score: 5.33934 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 134 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 ATGGCGGTCTTTTTGACGGCAAACGAAAACCCTCCCGA 4 26 0 TTGAGGAAAA 0.847727 -80 AAACTGCTTATAGTAAAGGAGAATTGGAT 10 282 1 TTAAGGGAAA 0.721612 -19 TCCCAAAGGAATATAAAGGTAAAATAAAAACAAATCAA 12 124 1 ATAAGGAAAA 0.932983 -74 ATCCTACATGATGTGAGGGCAATGTTCAAGGGTTTTTT 19 49 0 ATGAGGAATA 0.847727 -187 CTTTTTATTTATCTGATGGGAAAGCTTATTAAAGGATT 22 32 1 ATGAGGAAAA 0.95724 -130 GGATTTTCTTACATAACGGAGAATAGTATGTATACAGC 22 65 1 ATAAGGGAAA 0.912459 -97 AACATCGTGTACATGAGGGTGAAATTTACAGATGGATA 25 33 0 ATGAGGGAAA 0.943696 -202 AATATGATAATGATAATGGGAAAGCCAATCTTACATAT 25 100 1 TTAAGGAAAA 0.775891 -135 AAATACAAGTAAATGATTGGAAAACTTATGATCAGAAA 29 174 1 ATGATGAAAA 0.829094 -127 ATGTCATTGCAGCTGATGGAGAAAGGGAGTCATCTTT 29 274 1 ATGAGGGAAA 0.943696 -27 TAAATTGTATATATAATTGAAAAATTTAAGGTTTTCAC 30 179 0 ATAATGAAAA 0.75105 -122 ATCAAAAGAAATCTAATTGTAAATTGTATATATAATTG 30 198 0 ATAATGAAAA 0.75105 -103 TTCTATGAAGAAATAAGGGGAATAAAAAATAAAAACCA 31 38 1 ATAAGGAATA 0.775891 -43 GGTGTTCACAAACTGAAGGAAAAACCACCTACCTATTC 32 62 1 ATGAGGAAAC 0.739514 -239 ATCCGGTGTAAGATAAGGGTAATCATTACCGCCAGGAG 32 267 1 ATAAGGAATA 0.775891 -34 CTCAGAAAGAAAGTGATTGAGAAAGCAAAAGTATGAAA 37 134 1 ATGATGGAAA 0.784116 -128 * *** ** *** * Masking position 12 Map Score: 11.8293 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 210 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 AAAGAACAATGGTCATTTCTTTGTGCATAAC 1 98 0 GGTCTTTCTT 0.942799 -203 CTTATGAAAAGGTTCTTTTGTACGATTCGGA 2 53 0 GGTTTTTTGT 0.538075 -248 TTACTATGGCGGTCTTTTTGACGGCAAACGA 4 38 0 GGTCTTTTGA 0.595617 -68 CCTGCACAGAGGTCTTTTTTTGTTACAGTTT 5 19 1 GGTCTTTTTT 0.965342 -136 ATAACGGCAGGGGGATTTTTTATTTTTGTCC 6 30 1 GGGGTTTTTT 0.629318 -64 TAAGCAGTTTGCTGATTTTTTTGGAAAGGGT 10 261 0 GCTGTTTTTT 0.846762 -40 TTTCTGGCAATGTCTTTTTTTATGTTTATGA 12 58 1 TGTCTTTTTT 0.565402 -140 GCCGCCGTGCGGCCTTTTTTTATGCTTTCTC 18 27 1 GGCCTTTTTT 0.757529 -248 ATATCATCTGGCGCTTTTTTTTGTAAAAAAC 19 25 1 GCGCTTTTTT 0.794363 -211 TTTAGTATCAGGTTATTTCTTTCCGATTAAA 23 114 0 GGTTTTTCTT 0.62186 -136 GCATTATCAAGCTCGTTTCGTTTAACATCGT 25 63 0 GCTCTTTCGT 0.822745 -172 TGATTGACCGCTCCTTTATTTCAAAATAAA 27 56 0 GCTCTTTATT 0.631424 -20 TAAGGTTTTCACTCTTTTTTTGACAAAGTCT 30 160 0 ACTCTTTTTT 0.606502 -141 TGGTTATATTAGTCATTTTTTTAGGGAATAG 32 94 0 AGTCTTTTTT 0.696426 -207 GTTTCCCAGGGGTCATTTTTAATAGGCTAAA 32 192 0 GGTCTTTTTA 0.778469 -109 AATGAAAACAGGTCATTTTTTAGGAGGGTTT 33 89 1 GGTCTTTTTT 0.965342 -26 GTTACTTTTTGGTCATTTCTTGGTTATATTC 35 66 1 GGTCTTTCTT 0.942799 -235 ATTGGAGAAGGCTGTTTTCTTC 37 2 0 GCTGTTTCTT 0.7658 -260 AATGGAGAAGGCTGTTTTTTTGTGCGATAAA 37 30 1 GCTGTTTTTT 0.846762 -232 CGGATTTATGGCTCATTTTGTAAGGTTTTGC 37 83 0 GCTCTTTTGT 0.886927 -179 **** ****** Masking position 6 Map Score: 14.5902 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 484 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 12 CTCATGGTATAAATGGAATTGTAAACGTTAT 2 265 1 AAATGGATTG 0.730218 -36 AATCGAGTAAAAAGGGGTTTGGAGGCTTTTA 4 84 1 AAAGGGTTTG 0.912209 -22 CGGTTACAACAAGGGGTATTGCTGAAGGAGG 7 91 1 AAGGGGATTG 0.798013 -84 TTTATTTACGAAAGGGGTTAGACACG 9 6 0 AAAGGGTTAG 0.855624 -118 CAGAGAGAGTAAAGGATTTTGACTTATTCAA 10 89 1 AAAGGATTTG 0.866216 -212 TTATTTTTGTAAATGATTGTGCATGAATTCA 10 183 1 AAATGATGTG 0.785853 -118 ATTTTTTTGGAAAGGGTAGTGCCTCTCCCTG 10 247 0 AAAGGGAGTG 0.798013 -54 TATGATAAGGAAGGGAATTAG 17 77 1 AAGGGATTAG 0.770583 -11 ACAAAATAAAAAATGAATGTGCAGGGAAAGG 19 206 1 AAATGATGTG 0.785853 -30 AGAAAACTATAAGGGAGTTAGAGATAAATT 24 140 1 AAGGGATTAG 0.770583 -20 CGTTGCATATAAGTGGTTTTGCCTCAAGCAG 25 143 1 AAGTGGTTTG 0.854843 -92 AACTTCTTAAAAATGGATGTGGACCGGTTCT 33 47 1 AAATGGTGTG 0.854843 -68 CTCAGAAAGAAAGTGATTGAGAAAGCAAAAG 37 134 1 AAGTGATGAG 0.655612 -128 CAAATGTTTCAAATGAGATAGGAAATGGGTA 38 150 1 AAATGAATAG 0.490311 -89 ****** **** Masking position 2 Map Score: 6.12372 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 201 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 13 GTCATTTCTTTGTGCATAACCTCGTTCATT 1 88 0 TGTGCATAAC 0.883006 -213 AAAAGACCTCTGTGCAGGACAAAGGT 5 7 0 TGTGCAGGAC 0.970939 -148 TGTAAATGATTGTGCATGAATTCACAATCC 10 190 1 TGTGCATGAA 0.958178 -111 AAAAAATGAATGTGCAGGGAAAGGATGAAA 19 213 1 TGTGCAGGGA 0.949025 -23 TTACAGCAGCTGTGCATAGACAAATCTTGA 23 76 1 TGTGCATAGA 0.807903 -174 TCTAAGAAATTGTTCAGGACAGCCCATCAC 26 205 1 TGTTCAGGAC 0.812513 -96 AGTAACCTGTTGTGCATGAAATGGTTGCTT 35 42 0 TGTGCATGAA 0.958178 -259 ********** Masking position 6 Map Score: 1.54456 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 51 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 ATGACGACCTCCTTGATAACGTTTAC 2 285 0 ACCTCCTTGA 0.807333 -16 AGACTGCCCTCCTTTTCGGGAGGGTT 4 7 1 CCCTCCTTTT 0.934597 -99 TTTATCCTCCTTGATAAATGTTAT 5 141 0 TCCTCCTTGA 0.83276 -14 TTTATTTTTGTCCGCCTTGTTATGATGAGA 6 48 1 TCCGCCTTGT 0.930104 -46 TTTAAAGTGTACCTCCATTTCCTTATAATA 9 45 1 ACCTCCATTT 0.732317 -79 TTGAATCATCCTCCTTTTTAAGTCGGAT 9 106 0 TCCTCCTTTT 0.945428 -18 CATCAAACATACCGCCTCTCCCACTATATT 17 17 0 ACCGCCTCTC 0.610694 -71 TATTCCTCCTCTTAGTATTTTTT 21 15 0 TCCTCCTCTT 0.834126 -13 CTCAAACCTCCTTGCTGCAGGATAT 22 147 0 ACCTCCTTGC 0.904227 -15 AATAAAAATCCCTCCTTATGTATATCCAT 25 10 1 CCCTCCTTAT 0.818699 -225 CCTTCTCTTCCCCGCCTTTCGAAGGAAATA 26 97 1 CCCGCCTTTC 0.841198 -204 TAAGGGCTCGACCTCCTTATCCCTGCGATT 27 12 0 ACCTCCTTAT 0.821652 -64 AACAGCTCCTCCTTGTTTATGTAACC 30 285 0 TCCTCCTTGT 0.952536 -16 TAAATATGCATCCGCCATTTATTTTT 35 7 0 TCCGCCATTT 0.683108 -294 ********** Masking position 5 Map Score: 10.1046 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 239 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 15 GTAATAAATTTTTAGATTATAAAATCATTGGAGGT 8 18 0 TTTAATAAAT 0.734888 -86 GTCTAACCCCTTTCGTAAATAAAATCAACGTTTTA 9 14 1 TTTTATAAAT 0.734916 -110 CCCAAACGCTTTTAAGTGATAAAGTAATCTATGAA 19 90 0 TTTGATAAAT 0.955305 -146 CTTAAAAGCGTTTGGGTAATAAAGTAGAGTTTTTA 19 109 1 TTTGATAAAT 0.955305 -127 ATGACTTAGTTTTTCGGGATCAACTAACCAA 26 7 0 TTTGATCAAT 0.850233 -294 AGGCTGTTTTTTTGTGCGATAAATTCCTAAATAAC 37 38 1 TTTGATAAAT 0.955305 -224 AATCACTTTCTTTCTGAGATAAACTACCTTTATTT 37 117 0 TTTGATAAAT 0.955305 -145 TGATCATCTCTTTTGGCTATAAAGTTTCCGTTTTT 38 109 1 TTTGATAAAT 0.955305 -130 *** * ***** * Masking position 9 Map Score: 2.43915 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 25 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493