AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -iarcA_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 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 ycgA 300 similar to hypothetical proteins #5 ycgB 115 ycgB #6 amyE 148 alpha-amylase #7 lctE 176 L-lactate dehydrogenase #8 lctP 31 L-lactate permease #9 ycgK 192 similar to transcriptional regulator (LysR family) #10 cah 71 cephalosporin C deacetylase #11 ycgL 83 ycgL #12 ycgM 190 similar to proline oxidase #13 yfmT 249 similar to benzaldehyde dehydrogenase #14 yfjN 300 similar to hypothetical proteins #15 yfjM 195 yfjM #16 yfjL 29 alternate gene name: yztA #17 acoA 231 acetoin dehydrogenase E1 component (TPP-dependent alpha subunit) #18 citA 108 citrate synthase I #19 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #20 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #21 mmgD 33 citrate synthase III #22 mmgC 27 acyl-CoA dehydrogenase #23 mmgB 149 3-hydroxybutyryl-CoA dehydrogenase #24 mmgA 137 acetyl-CoA acetyltransferase #25 yqiK 78 similar to glycerophosphodiester phosphodiesterase #26 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #27 sodA 178 superoxide dismutase #28 yqgC 109 yqgC #29 yrhG 262 similar to formate dehydrogenase #30 yrhF 300 yrhF #31 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #32 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #33 ysfA 118 ysfA #34 ysfB 68 similar to hypothetical proteins #35 ysfC 102 similar to glycolate oxidase subunit #36 citC 163 isocitrate dehydrogenase #37 citZ 300 citrate synthase II #38 gbsA 198 glycine betaine aldehyde dehydrogenase #39 yvfH 300 similar to L-lactate permease #40 rocA 226 pyrroline-5 carboxylate dehydrogenase #41 yweB 176 alternate gene name: ipa-75d; similar to glutamate dehydrogenase #42 yweA 300 alternate gene name: ipa-74d; similar to hypothetical proteins from B. subtilis #43 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter #44 cydA 300 cytochrome bd ubiquinol oxidase (subunit I) Motif number 1 GAAAAATTAATAAAAGCGCTTACAGATAGAGGCC 2 174 1 TAAGCTTACA 0.936787 -53 GAATCATAACAGAAATTGCTAACATAATCCATAT 9 117 0 AAAGCTAACA 0.907721 -76 GTAAATGGACAAAACCAGCGTTCACAATATCCTC 12 118 0 AAAGCGTTCA 0.935575 -73 TGCTTGATTCAAAAAAGGCTAACAAAATAAAGGG 15 17 1 AAAGCTAACA 0.907721 -179 CAGGCTGAGTAAAAGCTGCGTACAAAAAAGACCC 15 100 0 AAAGCGTACA 0.978188 -96 TTCAGAAGATAGACAGCGCTTACAATTTCTAGTT 24 102 0 AACGCTTACA 0.885829 -36 AAGGGCGTCAAGAAAACGCGTACATAAATTATAA 32 155 0 AAAGCGTACA 0.97817 -138 ATAAATCTTAATAAAGTGCTTACAATTGAAAGAA 32 217 1 AAAGCTTACA 0.984891 -76 TCCCCCTGTCAAAAAACGCTTTCAATCTATTGTA 35 71 0 AAAGCTTTCA 0.954762 -32 TTCAGACATCAAAATTGGGTTACACTTTAAATTG 36 55 1 AAAGGTTACA 0.827346 -109 GTTTATAATGAGAATAGGCTTAAACTTAAATAAG 37 102 1 AAAGCTTAAA 0.858688 -199 TCCCCCAAAAAGAAAATGCTTACATTTTACTGGC 37 188 0 AAAGCTTACA 0.984893 -113 TATCATCTATAGAAACCGCTTACATATGGCGCCA 39 251 1 AAAGCTTACA 0.98478 -50 AAACGCAAAATAAATTTGCGTTCAAGATCGGAAA 40 65 1 TAAGCGTTCA 0.770592 -162 GGCTGATTTTTTAAAGCGCTTACATTACAGCCGG 41 128 1 TAAGCTTACA 0.930293 -49 GGCAAGACCTAAAATTTGCGTAAATGAAAAAGGA 43 77 0 AAAGCGTAAA 0.806949 -224 ATTCAGATTAAGAATACGCTTTCATCATAAATCA 43 136 1 AAAGCTTTCA 0.954749 -165 * ** ******* Masking position 3 Map Score: 23.2746 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 63 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 CACAAACAAAAAGACATCAAAGAGAAACATACCCTGC 7 139 1 AAAATAAAAA 0.861099 -38 AAATTTCGACAATATAATACAACAAGAACTGCATATA 13 51 0 AAAAAAAAGA 0.742342 -199 GTTATTATAGTAAATATAATATTTAAAAAATAATCAA 18 59 0 TAAATAAAAA 0.732164 -50 TGAAAACAGATATATAATAGAGGGAAAACGTTCATCT 20 34 0 TAAAAAAAAA 0.888047 -81 TAGACAAAAAACGCAAAAACGGAGGTT 21 1 1 TAAAAAAAAA 0.888047 -33 AGCATACATTCATAGAAGACAACTAGAAATTGTAAGC 24 82 1 CAAAAAAAGA 0.579195 -56 CCATTCTGGTCAAAGATAAAAGCCAAACATCAGGAAG 26 264 1 CAAATAAAAA 0.747579 -37 GGAAGACATGAAGAAGACAGAGTAAAATGGGAGGATG 28 77 1 AAAGAAAAAA 0.742342 -33 TATCAAGCAGTATATAAGATATTGAAAGAGAATATAT 29 102 0 TAAAAAAAAA 0.888047 -161 AGAAACATACAAAAAATGAAACTGAAACTCTCT 35 7 0 AAAATAAAAA 0.861099 -96 AATCTATTGTAAAAGAAAAAAAGCAAAGCCTTCCATG 35 45 0 AAAAAAAAAA 0.947338 -58 TTTTATTTTCTATATAAGAAAAATAAAATGTTTTCTA 36 106 1 TAAAAAAAAA 0.888047 -58 GAATGGAAAAAAAAAATTATAGGTAAACATTTAACAA 37 52 1 AAAATAAAAA 0.861099 -249 TTCGTTAAGATAAAGAACATAAAGAAATAACTTAACG 38 43 0 TAAAAAAAAA 0.888047 -156 AGGAAAAGTCAAAAAGAAAAATCAAAATGGGACTTTG 38 85 1 AAAGAAAAAA 0.742342 -114 TTGAAATATAAACAGATTAAAACAAAAAAATATATGA 39 47 0 AAAATAAAAA 0.861099 -254 GCTCTTTACGCAAAAAACAAATGCAAAATTATTTTGC 40 25 0 CAAAAAAAAA 0.895767 -202 AAGTTTTTTCAGCAAAAGACAAGAAAATGGCATGATT 40 145 1 AGAAAAAAAA 0.814596 -82 TTGAATCCACAAAAAAAGAGACTGAAAACATCTCAGT 41 32 0 AAAAAAAAAA 0.947338 -145 TTTTTAAAATAGGATAAAAGATATAAAATGTCAGGCA 42 42 1 AGAAAAAAAA 0.814596 -259 AGATGTTACTAGAAAAAGAGAGGGAAATCGTCCATTT 42 78 1 AGAAAAAAAA 0.814596 -223 CTTTTATTTAAACAAAAAAGACCTAAAATTCGCCAAC 43 22 1 AAAAAAAAAA 0.947338 -279 ATAAATAAGCAACAAAATAGACAAAAATCCGTCACAT 44 17 1 AAAAAAAAAA 0.947338 -284 ATCAGTAATTCACAAAATAGACGAAAAAAATATTGCT 44 205 0 CAAAAAAAAA 0.895767 -96 ** * ** * * *** Masking position 9 Map Score: 24.0324 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 296 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 3 AGCCTGGTCAGCCGGCTGTTTGGT 2 5 0 GCCGGCTGTT 0.982872 -222 AGCCGGCTGACCAGGCTGTTTTTTTGCTGC 2 18 1 CCAGGCTGTT 0.826334 -209 ATTGCTGCCCGCCGGCTTGTACGGCGGGCT 5 13 1 GCCGGCTTGT 0.813429 -103 GGCTTGTACGGCGGGCTTTTGAGTTATTCA 5 26 1 GCGGGCTTTT 0.936105 -90 TTGCAGAAGCGCAGGCTGTTATTGTAACAT 5 56 1 GCAGGCTGTT 0.960237 -60 TTCAACCTATGGAGGCTGAA 9 183 1 GGAGGCTGAA 0.415342 -10 GATGATATGCGGCGGCTTTTCACATTTA 11 9 0 GGCGGCTTTT 0.959215 -75 CATATCATCAGGCGGTTTTTTTCTGCAAAC 11 30 1 GGCGGTTTTT 0.824874 -54 TTCTTAGATTGCGGGGTGTTGAGGTTGGAA 12 171 1 GCGGGGTGTT 0.812874 -20 ATTGTCAAAGGCCGGGTGATATCCGGTCTT 17 42 1 GCCGGGTGAT 0.741579 -190 AAGCCGCGTCGGCGGCTGTTTGAGCAATTC 23 84 0 GGCGGCTGTT 0.976744 -66 CAGCCGCCGACGCGGCTTTTATGTGCGGAT 23 96 1 CGCGGCTTTT 0.822507 -54 GTTGTTAGAAGGAGGCTGTTTGACGCAGCC 24 21 1 GGAGGCTGTT 0.946452 -117 GGTGACAGCGCCCGGTTTTTTTCTTATATA 34 23 1 CCCGGTTTTT 0.559088 -46 TTACATACTGGGAGGTTTTTATT 36 151 1 GGAGGTTTTT 0.664675 -13 GCCTTTATTTGCGGGTTTTTG 37 2 0 GCGGGTTTTT 0.745815 -299 TTTACGTCAAGGAGGCTTAT 38 189 1 GGAGGCTTAT 0.748804 -10 AAAGGAATTGGCGGGCTGATTTTTTAAAGC 41 115 1 GCGGGCTGAT 0.887388 -62 TGTTTTTTTGGCCGGCTGTAATGTAAGCGC 41 143 0 GCCGGCTGTA 0.884498 -34 ********** Masking position 7 Map Score: 19.6628 Number of sites scoring better than the average of aligned sites = 915 Number in coding regions = 800 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 4 GGCCTCTATCTGTAAGCGCTTTTATTAATTT 2 177 0 TGTAAGCGTT 0.987668 -50 TATTGTAACATGTAAGCCATAAGCCATTCGT 5 75 1 TGTAAGCCTA 0.79584 -41 TAATTTTAAATGTAAGCGTTAACAAAATTCT 6 25 1 TGTAAGCGTA 0.942389 -124 ATATGGATTATGTTAGCAATTTCTGTTATGA 9 117 1 TGTTAGCATT 0.838037 -76 CCCTTTATTTTGTTAGCCTTTTTTGAATCAA 15 20 0 TGTTAGCCTT 0.848154 -176 AACTAGAAATTGTAAGCGCTGTCTATCTTCT 24 102 1 TGTAAGCGTG 0.932199 -36 TTATAATTTATGTACGCGTTTTCTTGACGCC 32 155 1 TGTACGCGTT 0.921154 -138 TTCTTTCAATTGTAAGCACTTTATTAAGATT 32 220 0 TGTAAGCATT 0.946467 -73 TACAATAGATTGAAAGCGTTTTTTGACAGGG 35 71 1 TGAAAGCGTT 0.959082 -32 GCCAGTAAAATGTAAGCATTTTCTTTTTGGG 37 188 1 TGTAAGCATT 0.946467 -113 TGGCGCCATATGTAAGCGGTTTCTATAGATG 39 254 0 TGTAAGCGTT 0.987668 -47 CCGGCTGTAATGTAAGCGCTTTAAAAAATCA 41 131 0 TGTAAGCGTT 0.987668 -46 TGATTTATGATGAAAGCGTATTCTTAATCTG 43 139 0 TGAAAGCGAT 0.697605 -162 TCATAAATCATGATAGCGTTTTCGTCAACTA 43 160 1 TGATAGCGTT 0.872769 -141 ******** ** Masking position 1 Map Score: 16.0734 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 110 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 AGCCATTCGTAAAAGTGCGGGAGGAAGGTC 5 96 1 AAGGGAGGAA 0.956145 -20 ACAAACAAAAAGACATCAAAGAGAAACATACCCTGC 7 140 1 AAAAGAGAAA 0.425509 -37 ATGAAAAGGTATTTGCCGAGGGGGAAGAT 9 4 0 ATAGGGGGAA 0.958503 -189 ACTAAATCTTATAAAACAAAGGGGAATAATCGGAA 10 47 1 AAAAGGGGAA 0.915434 -25 AGATAGTTAGAAAGTCGGGGGGGGATTCTGTCGAAT 12 39 0 AAGGGGGGAT 0.927667 -152 AATATTTTGAATATTTCTAGGAGGAACTTTTG 13 7 0 AAAGGAGGAA 0.958121 -243 ATAATAACAGAAAAGGATAGGGGGAATACAA 18 88 1 AAAGGGGGAA 0.984189 -21 GAAAACAGATATATAATAGAGGGAAAACGTTCATCT 20 34 0 AAGAGGGAAA 0.657585 -81 TTCAGTACATATATACTAAGGAGGAATTATC 27 158 1 AAAGGAGGAA 0.958121 -21 AAGAAGACAGAGTAAAATGGGAGGATGGAAGCT 28 87 1 ATGGGAGGAT 0.636244 -23 AACCAAGTGAAATGTCCTGAGGGGAACCGGGAAAAG 30 241 1 ATGAGGGGAA 0.792873 -60 TTATAAGGCAATATCGGAAGGGGTAATCAGC 30 280 1 AAAGGGGTAA 0.778864 -21 ATTATAGCTCAAACAGGGGGGAGGATTACAGAATGA 32 37 1 AAGGGAGGAT 0.824981 -256 TATAATAAAAACATGATGAGGGGGAACGCC 34 49 1 AAAGGGGGAA 0.984189 -20 TTTTTACAACACTCTTAAAGGGGAAATTTATTGAAA 37 261 1 ATAGGGGAAA 0.811319 -40 GATATATTTCATAACACGAGGGGGACTACAT 40 206 1 AAAGGGGGAC 0.887566 -21 AGATGTTACTAGAAAAAGAGAGGGAAATCGTCCATT 42 78 1 AAAGAGGGAA 0.733162 -223 AAATTTCAACAATCAATTAGGGGGAAATGTC 42 280 1 ATAGGGGGAA 0.958503 -21 TTTTGTTTAAATAAAAGGGGGAGAAATA 43 3 0 AAGGGAGAAA 0.802323 -298 * * ******** Masking position 15 Map Score: 16.8322 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 226 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 6 CAGTGATTTACCGCTTTTTTATAAAATATCAGA 2 65 1 CCGCTTTTAA 0.909563 -162 CGATCCATCCCCTCTGTTTGAAAATATTAATTA 4 31 0 CCTCTGTTAA 0.959734 -270 ACGCCTATGTCCTCTTATTTATGATTGCTTTCA 4 129 1 CCTCTTTTAG 0.792644 -172 CGATTATTCCCCTTTGTTTTATAAGATTTAGTT 10 46 0 CCTTTGTTAA 0.883888 -26 GATTATCTACCCTATTTTTTATATTCTGGTTAA 14 136 0 CCTATTTTAA 0.673712 -165 TTCTATTCTCCCTCTGATTAATATTTTTAATTA 18 11 1 CCTCTGTTAA 0.959734 -98 GTCACCTCTTCCTTTCTTTTAAACAGTCATTAG 19 273 0 CCTTTCTTAA 0.762593 -28 CCATTCAAATCCCCTTTTTCATCATGTT 23 6 0 CCCCTTTTAC 0.864839 -144 GTAATCCTCCCCCCTGTTTGAGCTATAATATAC 32 33 0 CCCCTGTTAC 0.853369 -260 TACTTTACCCCCTGTTTGATAAGTGCGAAAT 32 272 0 CCCCTGTTAA 0.955906 -21 ATGTGGCGCTCCTTTTTTTAACATGATGTTATT 33 16 1 CCTTTTTTAA 0.89327 -103 ATGAGGTTAGCCTCTTGTTCAGACATCAAAATT 36 38 1 CCTCTTTTAA 0.963242 -126 CCCAAACCCCTCCTTGAAACATAAACTGG 39 282 0 CCCCTCTTAA 0.901456 -19 ACTTTTTTTGCCCTTTTTTAAAATAGGATAAAA 42 28 1 CCCTTTTTAA 0.883888 -273 TATTTCTCCCCCTTTTATTTAAACAAAAAAGAC 43 11 1 CCTTTTTTAA 0.89327 -290 AGTCACAATCCCGCTTATTCAGATTAAGAATAC 43 120 1 CCGCTTTTAA 0.909563 -181 ****** ** * * Masking position 8 Map Score: 13.3872 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 147 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 ACAAAAGGATATATGGGAAGGAGCGGATGTGAA 2 140 1 AATGGGAAGG 0.788804 -87 TACACAAATAACAGGAGGTTATGTTG 2 211 1 AAGGAGGTTG 0.431262 -16 AAAAAACACGAAAGGGGCAATGGGC 3 15 1 AAGGGGCAAG 0.782064 -15 CATCGGTTTGAAAGGAGGAAGCGGAAGAATGAA 6 66 1 AAGGAGGAAG 0.968523 -83 TCATTTACGAAAAGAAGGAGCTGGTTCAAATTA 9 82 0 AAGAAGGAGG 0.747451 -111 TCTGTCGAATAAAGGAGAAAAGGAAGCGACAAA 12 16 0 AAGGAGAAAG 0.861129 -175 TTGCGGTTATAAAGGAGATGCTGACC 13 234 1 AAGGAGATGG 0.547064 -16 GATATCATATAAAGGGGGAGAGGAAA 15 180 1 AAGGGGGAGG 0.987559 -16 CACGTACATATGAGGAAAAGAGTGGGAAC 16 8 1 AATGAGGAAG 0.877805 -22 TGAACCCTAAATAGAAGGAGGCGCACAAA 17 213 1 AAGAAGGAGG 0.747451 -19 AATATTAATCAGAGGGAGAATAGAA 18 3 0 AAGGGAGAAG 0.873241 -106 ACAGAAAAGGATAGGGGGAATACAA 18 94 1 AAGGGGGAAC 0.740042 -15 TGTTTAAAAGAAAGGAAGAGGTGACTTAGT 19 281 1 AAGGAAGAGG 0.834008 -20 GGCGCAGGTCAGATGGGGAGCGGAATTGCTCAA 23 62 1 AATGGGGAGG 0.948804 -88 TAAAAGCCAAACATCAGGAAGAGGTGGTCAT 26 280 1 AATCAGGAAG 0.598524 -21 TTATAAGGCAATATCGGAAGGGGTAATCAGC 30 280 1 AATCGGAAGG 0.436653 -21 CTAGATTACTAGAGGGAGAGGGGCTATC 31 16 1 AAGGGAGAGG 0.904303 -18 AATTGAAAGAAGTGGGGGAAGAGATTTAGCACA 32 240 1 ATGGGGGAAG 0.749698 -53 CACTTATCAAACAGGGGGTAAAGTA 32 278 1 AAGGGGGTAG 0.891508 -15 GCGTTTTTTGACAGGGGGATGGGTGAA 35 86 1 AAGGGGGATG 0.909447 -17 TTAATTTTCTAAAGGAAAAGAGGGTCAGT 38 7 0 AAGGAAAAGG 0.503125 -192 TCTTAACGAAACATGAGGAAAAGTCAAAAAGAA 38 70 1 AATGAGGAAG 0.877805 -129 TTTGCGTTCAAGATCGGAAAAAGAGAAAGGTGA 40 79 1 AATCGGAAAG 0.36105 -148 CAACAATCAATTAGGGGGAAATGTC 42 286 1 TAGGGGGAAG 0.749698 -15 TGTTTAAATAAAAGGGGGAGAAATA 43 3 0 AAGGGGGAGA 0.724873 -298 ATCATGAAAGAAAGCAGGAAAAGACA 43 285 1 AAGCAGGAAG 0.864598 -16 * ******** * Masking position 3 Map Score: 19.9774 Number of sites scoring better than the average of aligned sites = 888 Number in coding regions = 682 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 8 CAGTAAGATTTATAAAAACCTCATGTTCTGGGTCAAA 1 99 1 TTAAAACAGT 0.931395 -202 TTTTATAAAATATCAGAAAATAAAGATATTGACTTAT 2 81 1 TTCAAAAAGT 0.904729 -146 ATGCGATAAGTGTAAAAGAAGCATGGTCAGTTTTTAA 14 222 1 TTAAAGAAGT 0.75293 -79 TCTAATTTATTGTAAGAAAATAATGGTATATTTAGTG 15 141 1 TTAAAAAAGT 0.957375 -55 CTTCATTCAATGTAACAAAAGAATGCTTTGTAATCAA 27 98 0 TTAAAAAAGT 0.957375 -81 AATATCACATTATAATAAAAGCAGTGTTGATGGATTT 30 174 0 TTAAAAAATT 0.722889 -127 GTTCTTGCGATATAATAACATCATGTTAAAAAAAGGA 33 25 0 TTAAAAAAGT 0.957375 -94 TTTTTTCTTATATAATAAAAACATGATGAGGGGGAAC 34 39 1 TTAAAAAAGT 0.957375 -30 TTATTTTCTATATAAGAAAAATAAAATGTTTTCTAAA 36 108 1 TTAAAAAAAT 0.596672 -56 GATTATTGTTTATAATGAGAATAGGCTTAAACTTAAA 37 95 1 TTAAGAAAGT 0.75293 -206 TGTTATGTTCTTTCAAAAGCAAAGGGTTTTAGTTCCA 37 148 1 TTCAAACAGT 0.851634 -153 TTAAGAGTGTTGTAAAAACATGAGGCTTACTTAAAAA 37 242 0 TTAAAAAAGT 0.957375 -59 ACTTTGACAGTTTAAAAACCATATGTTAGATTAAGGT 38 116 1 TTAAAACAGT 0.931395 -83 ATTTAATGTTTTTAACAACCTTAATCTAACATATGGT 38 133 0 TTAAAACATT 0.611923 -66 CTTTGATTTTTTTCAAAATATAATGCTAGGTAACTGG 39 187 1 TTCAAAAAGT 0.904729 -114 * *** ** * * * * Masking position 5 Map Score: 10.8199 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 51 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 AAATTAATAAAAGCGCTTACAGATAGAGGC 2 177 1 AAGCGCTTAC 0.980511 -50 AGAATTTTGTTAACGCTTACATTTAAAATT 6 26 0 TAACGCTTAC 0.879815 -123 GATTGATAAGAAATGCTTTCGCATGCGATA 14 200 1 AAATGCTTTC 0.80891 -101 TATCTGTTTTCAATGCTTACGATGTAAACT 20 59 1 CAATGCTTAC 0.88004 -56 AGAAGATAGACAGCGCTTACAATTTCTAGT 24 103 0 CAGCGCTTAC 0.955817 -35 GGCGTCAAGAAAACGCGTACATAAATTATA 32 156 0 AAACGCGTAC 0.897352 -137 AATCTTAATAAAGTGCTTACAATTGAAAGA 32 220 1 AAGTGCTTAC 0.948677 -73 CCCTGTCAAAAAACGCTTTCAATCTATTGT 35 72 0 AAACGCTTTC 0.920108 -31 CCCAAAAAGAAAATGCTTACATTTTACTGG 37 189 0 AAATGCTTAC 0.944633 -112 CATCTATAGAAACCGCTTACATATGGCGCC 39 254 1 AACCGCTTAC 0.934593 -47 TGATTTTTTAAAGCGCTTACATTACAGCCG 41 131 1 AAGCGCTTAC 0.980511 -46 ********** Masking position 2 Map Score: 9.96097 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 34 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 10 CATTTATATTGTGCAACACTTCACAAACTTTTGCAA 7 93 0 GAATTCACAA 0.981854 -84 CAATATAAATGTGAAATACTTCACAAACAAAAAGAC 7 118 1 GAATTCACAA 0.981854 -59 AACACACATGGCGGAATAGTTCACTAGCAAGTCTTA 30 80 1 GAATTCACTA 0.906514 -221 AAAAATTATAGGTAAACATTTAACAAATGTCTGATT 37 63 1 GAATTAACAA 0.858003 -238 AAAATTAATTGTGAAATACTTCACAATATCGTGCCA 43 238 1 GAATTCACAA 0.981854 -63 AAAAAATATTGCTCAATATTTCACAAATGTGTCAAA 44 182 0 GAATTCACAA 0.981854 -119 CCGAGACTTTGATCAGTAATTCACAAAATAGACGAA 44 217 0 GAATTCACAA 0.981854 -84 CTGTTAATTTGCTCACTACTTCACAAATAGAACCGA 44 249 0 GAATTCACAA 0.981854 -52 * * * ******* Masking position 8 Map Score: 9.53521 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 5 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 TATATCCGTCTTTTTCAATAAACCGTTCCAG 1 199 0 TTTTTCAATA 0.782898 -102 TGACCCGGAATTCTTCATTGAGGGGATAAAA 1 277 0 TTCTTCATTA 0.708706 -24 TTATTGTTTATTTGTCTTACAATTAAACAAA 2 114 1 TTTGTCTTAA 0.749582 -113 CTTTTATTAATTTTTCTTTCACATCCGCTCC 2 159 0 TTTTTCTTTA 0.873171 -68 GCAGCCTTCTTTTTTCATTCATTCATGCCCG 24 45 1 TTTTTCATTA 0.884046 -93 AACGAGCAGATTTGTCTATGAGGATGGCTCT 26 140 0 TTTGTCTATA 0.658863 -161 AATCGTGAGCTTTTTCATTGATTACAAAGCA 27 81 1 TTTTTCATTA 0.884046 -98 CAGCGAGCCTTTCTTCATTCAATGTAACAAA 27 116 0 TTCTTCATTA 0.708706 -63 TATATTTGTCATTGACACAAATTTG 29 5 1 TTTGTCATTA 0.818562 -258 TAAAATAAAATTTTTCAATCAACTAATCAAT 32 116 1 TTTTTCAATA 0.783282 -177 AAAACGCTCCTTTTTCTAAAATGTAATACGT 33 96 0 TTTTTCTAAA 0.705421 -23 GCGCCCGGTTTTTTTCTTATATAATAAAAAC 34 30 1 TTTTTCTTAA 0.834941 -39 GGCTTTGCTTTTTTTCTTTTACAATAGATTG 35 52 1 TTTTTCTTTA 0.873171 -51 AAACATTTTATTTTTCTTATATAGAAAATAA 36 108 0 TTTTTCTTAA 0.834941 -56 CATCCGCTACTTCTTCATATATTTTTTTGTT 39 33 1 TTCTTCATAA 0.641269 -268 TTTTGACTATTTTGTCAAAAAGTCTTGTACT 39 158 1 TTTGTCAAAA 0.610335 -143 CGAACAGAAATTTGTCTAACAGGTGATCACC 40 107 0 TTTGTCTAAA 0.586619 -120 TTACCAGTTCTTTTTCTTAAAAATTAATCTA 42 202 0 TTTTTCTTAA 0.834934 -99 ACAGCGATCCTTTTTCATTTACGCAAATTTT 43 70 1 TTTTTCATTA 0.884046 -231 ********* * Masking position 5 Map Score: 15.1722 Number of sites scoring better than the average of aligned sites = 753 Number in coding regions = 614 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 12 TTTTTATTTTGGGGAATCGGGAGAAAACCT 1 146 0 GGGGAATCGG 0.8339 -155 AAAGGATATATGGGAAGGAGCGGATGTGAA 2 143 1 TGGGAAGGAG 0.564759 -84 GGTTTGAAAGGAGGAAGCGGAAGAATGAAG 6 70 1 GAGGAAGCGG 0.821703 -79 ATCATATAAAGGGGGAGAGGAAA 15 183 1 GGGGGAGAGG 0.977842 -13 TTTGGCAAACTGGGGATCGGCTAAAATATA 19 181 1 TGGGGATCGG 0.723456 -120 GCAGGTCAGATGGGGAGCGGAATTGCTCAA 23 65 1 TGGGGAGCGG 0.93519 -85 AATGTCCTGAGGGGAACCGGGAAAAGCCTT 30 251 1 GGGGAACCGG 0.746508 -50 GATTACTAGAGGGAGAGGGGCTATC 31 19 1 GGGAGAGGGG 0.917356 -15 ATATACGCAGGAGAGAGGGGAGACAGAT 32 9 0 GAGAGAGGGG 0.648792 -284 GCTCAAACAGGGGGGAGGATTACAGAATGA 32 43 1 GGGGGAGGAT 0.636576 -250 ACGCCCTTTTGAGGGAGGAGTAAAATGAAA 32 181 1 GAGGGAGGAG 0.802479 -112 GAAAGAAGTGGGGGAAGAGATTTAGCACAT 32 244 1 GGGGAAGAGA 0.718732 -49 TTTTTTGACAGGGGGATGGGTGAA 35 89 1 GGGGGATGGG 0.949362 -14 TTTTCTTTTTGGGGGAGAGAAATACTTGCA 37 206 1 GGGGGAGAGA 0.888899 -95 TTAAATAAAAGGGGGAGAAATA 43 3 0 GGGGGAGAAA 0.653829 -298 ********** Masking position 6 Map Score: 9.54215 Number of sites scoring better than the average of aligned sites = 459 Number in coding regions = 371 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 13 AATCATACAAAATACGACAAAAACATTTTGAAAAT 1 61 1 AAGACAAAAA 0.861208 -240 ACAAATAAACAATAAGTCAATATCTTTATTTTCTG 2 94 0 AAGTCAATAT 0.716529 -133 ACTCCGAAGTAAGTCTTCAAAAAATCAAATAAGGA 6 115 1 AATTCAAAAT 0.849878 -34 TTTGTTCATAAATCAGACAAAACTTTTCTCTTGCA 7 63 1 AAGACAAAAT 0.885037 -114 AGTTTATTGTAAATGGACAAAACCAGCGTTCACAA 12 125 0 AAGACAAAAA 0.861208 -66 TTCCTCCTAGAAATATTCAAAATATTCTAATCATT 13 17 1 AATTCAAAAT 0.849745 -233 TTTTTATCCAAAAAGTTCAAAAGCAAGGCCACTAA 14 79 1 AATTCAAAAA 0.820267 -222 ATCCCACGTGAAATCTTCAAAATTTACTATAGATT 14 169 1 AATTCAAAAT 0.848678 -132 TAGTAAATATAATATTTAAAAAATAATCAATATTT 18 54 0 AATTAAAAAA 0.459332 -55 TATTATTTCGAAGTTGTAAAAAACTAATACAACAC 19 108 0 AAGTAAAAAT 0.768631 -193 TTGAGGCGCCAATTAGAAAAAATTAGCGGAAAGAA 26 103 0 AAGAAAAAAA 0.535991 -198 TCTTTCTTTCAAGAAGTCAAAAAAAGCCATGTATA 30 13 1 AAGTCAAAAA 0.935001 -288 GAGTAAAATGAAATTGTCAATAAATCTTAATAAAG 32 198 1 AAGTCAATAT 0.716513 -95 TTCCATGGAGAAACATACAAAAAATGAAACTGAAA 35 17 0 AATACAAAAT 0.709507 -86 CTTTTTGACAAAATAGTCAAAATCTTTTGGCGGCC 39 145 0 AAGTCAAAAT 0.946938 -156 CCTATTTTAAAAAAGGGCAAAAAAAGTCGAAGATG 42 20 0 AAGGCAAAAA 0.694082 -281 TGTAGACAAAAATTCGTAAAAATTAATTGTGAAAT 43 220 1 AAGTAAAAAA 0.728106 -81 ATATTTCACAAATGTGTCAAAAAGTCATCCAATAT 44 168 0 AAGTCAAAAT 0.946941 -133 ** ******* * Masking position 9 Map Score: 9.20044 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 354 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 14 ATCACATCCTCGCTTTTTATTTTGGGGAATCGG 1 156 0 CTTTTATTTT 0.777924 -145 CTTGACACTCCTTATTTGATTTTTTGAAGACTT 6 125 0 CATTTATTTT 0.938058 -24 CCATAATGAAAGGATTTGATTTTTGTT 14 284 1 AATTTATTTT 0.869413 -17 TAAATGTATTCGCTTTACATTTTCATCAA 19 7 0 CTTTAATTTT 0.601756 -294 AGCAGTAAGTCGTATTATATTTTAGCCGATCCC 19 193 0 CATTAATTTT 0.867242 -108 TTTCAGCGGACATATTTCACTTTAACCGATAAT 27 41 0 CATTTACTTT 0.657599 -138 AGTTGATTGAAAAATTTTATTTTATCAATATAT 32 107 0 AATTTATTTT 0.82916 -186 AGATTTATTGACAATTTCATTTTACTCCTCCCT 32 192 0 AATTTATTTT 0.868628 -101 TTAGAATATACGTATTACATTTTAGAAAAAGGA 33 87 1 CATTAATTTT 0.867242 -32 GTTAGGAAAAATCATTTTATTTTCTATATAAGA 36 92 1 AATTTATTTT 0.869413 -72 ATATTTAGAAAACATTTTATTTTTCTTATATAG 36 115 0 AATTTATTTT 0.868628 -49 TTTTTATAAGCTTATTTAAGTTTAAGCCTATTC 37 113 0 CATTTAGTTT 0.657599 -188 AATAACTTAACGAATTTAATTTTCTAAAGGAAA 38 22 0 CATTTATTTT 0.937196 -177 TGTCAAAGTCCCATTTTGATTTTTCTTTTTGAC 38 92 0 CTTTTATTTT 0.777924 -107 GGTTGTTAAAAACATTAAATTTTTATTTAACAA 38 150 1 AATTAATTTT 0.672648 -49 CCAGTTACCTAGCATTATATTTTGAAAAAAATC 39 191 0 AATTAATTTT 0.741722 -110 TGAAGTATTTCACAATTAATTTTTACGAATTTT 43 228 0 CAATTATTTT 0.548802 -73 * **** ***** Masking position 6 Map Score: 12.3232 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 130 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 15 ATATTCAATTTTATGCAAGATGAACCGATAG 13 176 1 TATGCAAGAT 0.947196 -74 TCACCATTATAAATGCAAGAAGTGTGCCAGT 17 185 0 AATGCAAGAA 0.913305 -47 TTTCTCACAGTTATGCAAGAAAGGCAATAAA 29 216 0 TATGCAAGAA 0.966416 -47 TTATGAAAAATTAAGCAAGAAATATATATTG 32 84 1 TAAGCAAGAA 0.837581 -209 ATATGAATAAAAATGCAAGAATCATGCCATT 40 170 0 AATGCAAGAA 0.913305 -57 ACCCTTATCATCATGCAAGATCCGTACCAGC 41 71 0 TATGCAAGAT 0.947196 -106 CTATGCTCAATCATGAAAGAAAGCAGGAAAA 43 276 1 TATGAAAGAA 0.762665 -25 TCATCCAATATGATGCAAGATTGCCAGACTG 44 148 0 TATGCAAGAT 0.947196 -153 * ********* Masking position 7 Map Score: 4.80607 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 21 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617