AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -iphoB_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 glpQ 98 glycerophosphoryl diester phosphodiesterase #2 glpT 296 glycerol-3-phosphate permease #3 yczA 300 yczA #4 ycbL 96 similar to two-component response regulator [YcbM] #5 yclJ 212 similar to two-component response regulator [YclK] #6 phoB 300 alkaline phosphatase III #7 yeeG 135 yeeG #8 rapH 161 response regulator aspartate phosphatase #9 yeeI 160 similar to hypothetical proteins #10 yeeK 134 similar to hypothetical proteins #11 yesE 78 alternate gene name: yeeL #12 cotJA 126 cotJA #13 yesJ 124 alternate gene name: yeeN, yfxC, yfxD; similar to hypothetical proteins #14 yesL 114 similar to hypothetical proteins from B. subtilis #15 yesO 148 similar to sugar-binding protein #16 phoA 300 alkaline phosphatase A #17 yhdW 233 similar to glycerophosphodiester phosphodiesterase #18 ykoG 300 similar to two-component response regulator [YkoH] #19 resD 80 two-component response regulator #20 resC 135 essential protein similar to cytochrome c biogenesis protein #21 resA 131 essential protein similar to cytochrome c biogenesis protein #22 ypuL 91 similar to hypothetical proteins #23 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #24 ypuI 54 similar to hypothetical proteins from B. subtilis #25 ypuG 280 similar to hypothetical proteins #26 yqgH 68 alternate gene name: yzmC; similar to phosphate ABC transporter (permease) #27 yqgG 153 alternate gene name: yzmB; similar to phosphate ABC transporter (binding protein) #28 pbpA 113 penicillin-binding protein 2A #29 yqgE 33 similar to hypothetical proteins #30 sodA 178 superoxide dismutase #31 yqgC 109 yqgC #32 yrkP 267 similar to two-component response regulator [YrkQ] #33 araP 35 integral membrane protein #34 araN 30 sugar-binding protein #35 araA 207 L-arabinose isomerase #36 abnA 196 arabinan-endo 1,5-alpha-L-arabinase #37 ysdC 183 similar to endo-1,4-beta-glucanase #38 phoP 211 two-component response regulator #39 citH 43 malate dehydrogenase #40 citC 163 isocitrate dehydrogenase #41 citZ 300 citrate synthase II #42 msmR 217 transcriptional regulator (LacI family) #43 msmE 33 multiple sugar-binding protein #44 yurJ 181 similar to multiple sugar ABC transporter (ATP-binding protein) #45 yurN 57 similar to sugar permease #46 yurO 80 similar to multiple sugar-binding protein #47 yurP 215 similar to opine catabolism #48 yurQ 102 yurQ #49 yurR 300 similar to opine catabolism #50 yvrI 300 yvrI #51 yvcP 300 similar to two-component response regulator [YvcQ] #52 ywnF 242 ywnF #53 msmX 120 multiple sugar-binding transport ATP-binding protein #54 yxkF 183 similar to hypothetical proteins #55 yxdL 143 similar to ABC transporter (ATP-binding protein) #56 yxdJ 108 similar to two-component response regulator [YxdK] #57 iolI 85 alternate gene name: yxdH; myo-inositol catabolism #58 iolG 22 myo-inositol 2-dehydrogenase #59 iolD 203 alternate gene name: yxdD; myo-inositol catabolism #60 iolC 23 alternate gene name: yxdC; myo-inositol catabolism #61 iolB 74 alternate gene name: yxdB; myo-inositol catabolism #62 iolA 300 methylmalonate-semialdehyde dehydrogenase #63 yycF 300 similar to two-component response regulator [YycG] Motif number 1 CATAAAAATCTGGAGGGAGGCTGTTTAAAG 2 11 0 TGGAGGGAGG 0.442689 -286 TTGTTTTTCGGGAAAGGAGGCACGCCACAC 2 243 1 GGAAAGGAGG 0.945389 -54 AGCACAAACAGCAAAGGGGGATAATTATTA 2 277 1 GCAAAGGGGG 0.783151 -20 ATAGCTGTTAATAAAGGTGGTACCGCGAGA 3 170 1 ATAAAGGTGG 0.877638 -131 TTTGTGTTTCTTAAAGGAGGTGACGGCCAA 3 229 1 TTAAAGGAGG 0.906284 -72 CAGATGAGTTAGAAAGGAGGATATCAA 3 284 1 AGAAAGGAGG 0.940958 -17 ATATCTCATAGAGAAGGAGGGAAGCCG 8 145 1 GAGAAGGAGG 0.753373 -17 TGTAACCTATGTGAAGGAGAGAGTAAAT 10 117 1 GTGAAGGAGA 0.762466 -18 ATTGTTTTTGAGAAAGGAGGAGCCGGA 12 110 1 AGAAAGGAGG 0.940958 -17 AGCACTTACATTAAAGGGGGGATTGGTTTG 15 87 1 TTAAAGGGGG 0.882971 -62 ACGGAATACATTAAAGGAGGC 16 290 1 TTAAAGGAGG 0.906284 -11 TATAATAGCAAAAAAGGAGGCGAGATC 17 8 0 AAAAAGGAGG 0.897101 -226 CTGCAATAGGGGGAAGGGGGCA 21 120 1 GGGAAGGGGG 0.813313 -12 CTCTCCCTGAAAAAGGGAGAGTAAACG 23 8 0 AAAAGGGAGA 0.560668 -115 TAAAAGCACATTAAAGGAGGAAGCACC 25 8 0 TTAAAGGAGG 0.906284 -273 TCTGTAAATAGAAAAGGTGATGTT 28 100 1 GAAAAGGTGA 0.514693 -14 CTAAGGGATAGTAAAGGGGAGTCAGTA 29 17 1 GTAAAGGGGA 0.885895 -17 AGTGACTACAATAAAGGGGATACCGAAAAT 36 74 1 ATAAAGGGGA 0.877263 -123 CGATTTGACAGGAAGGGAGGATAAATAATC 36 135 1 GGAAGGGAGG 0.870131 -62 GCTTTCTAAAATAAAGGAGGTTGAACAAAA 36 177 1 ATAAAGGAGG 0.960353 -20 GATCATCACCATAAGGGAGGTGCCTTCACA 37 13 0 ATAAGGGAGG 0.903615 -171 TGCAGGACTGATGAAGGAGGGTTTGGAAC 37 165 1 ATGAAGGAGG 0.886536 -19 AAAACTAGCCATAAAGGAGAAGAGAGAC 39 26 1 ATAAAGGAGA 0.901587 -18 TACAACACTCTTAAAGGGGAAATTTATTGA 41 265 1 TTAAAGGGGA 0.740498 -36 GAAATTTATTGAAAAGGAGATGTTATAT 41 283 1 GAAAAGGAGA 0.781739 -18 AAGCGAATAAGGAAGGGTGATGGG 42 5 0 GGAAGGGTGA 0.428682 -213 TGTTGGAAAAATAAAGGGGAACCCAGATCT 42 53 0 ATAAAGGGGA 0.877263 -165 AATAATAGGTTAAAAGGAGGCTACCCT 44 8 0 TAAAAGGAGG 0.776818 -174 ATCAAAGAAAAGGTGAAGCTTCGCAC 45 7 1 GAAAAGGTGA 0.514693 -51 TTTTCTTTTTATAAAGGAGATGAGATACCC 45 38 1 ATAAAGGAGA 0.901587 -20 CTGCAGAAAAAGAAGGGAGGTATTTTCCTA 50 155 0 AGAAGGGAGG 0.860495 -146 TGATGTACATATAAGGGGGATCAAC 51 286 1 ATAAGGGGGA 0.73449 -15 GAAACATCAAATAAAGGGGGAGGATTAT 52 225 1 ATAAAGGGGG 0.949744 -18 GTTTACAATAACAAAGGGGGATGTTAG 53 104 1 ACAAAGGGGG 0.768775 -17 AAAAGATCGAGTAAAGGTGGGATCGTTTGT 59 15 1 GTAAAGGTGG 0.886247 -189 GTGTTTACTAATGAAGGAGGCAATAAGA 62 283 1 ATGAAGGAGG 0.886536 -18 ACAACTGGCGATAAAGGTGAAACATGTGTT 63 137 1 ATAAAGGTGA 0.730654 -164 ********** Masking position 4 Map Score: 48.7417 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 260 Number in noncoding regions = 328 Number of orfs with sites within 600 bp upstream = 397 Fraction of orfs with sites within 600 bp upstream = 0.0637649 Motif number 2 CTTTTGACAAGGGGTGTTTTCTGGCTCTTTTT 2 213 1 GGGGTTTTCT 0.853833 -84 TTGCATAGGACGGGGGTTTTTTGTGTTTCTTA 3 210 1 CGGGTTTTTT 0.950303 -91 TTGAAAAACGTGTGTGTTTTATAAAAA 4 6 0 TGGGTTTTAT 0.860789 -91 TGTAATTACGTGTGTGTTTTTTGATTTTGTAA 4 48 1 TGGGTTTTTT 0.971594 -49 TCTGATACGCTGAGTGTCTTTTTTTAGTTATA 17 95 1 TGGGTCTTTT 0.857501 -139 GATACAAACTGGTGAATTTTTTCTGCCATATC 17 152 0 GGGATTTTTT 0.887334 -82 TTGACCGAATGGTGTATTTTTTTGTGCGCTTA 18 74 0 GGGATTTTTT 0.887334 -227 AAACGGCGTTTTTTTTAGATTTGGCA 22 5 1 GGGTTTTTTT 0.926657 -87 CCTTTTTCAGGGAGAGTTTTTTTATGTTTGCT 23 22 1 GGGGTTTTTT 0.982171 -101 CTAGAGGCCGGGCGTTCTTTTTTCCTTTTATC 25 53 0 GGGTCTTTTT 0.773009 -228 TAGTATTGGACGAGAGCTTTTTGGTGGCTTAT 25 202 1 CGGGCTTTTT 0.837505 -79 CCACATCATGTGAGCGTTTTTT 27 1 0 TGGGTTTTTT 0.971594 -153 TCACATGATGTGGGCGTTTTTTTTATACAAAA 27 20 1 TGGGTTTTTT 0.971594 -134 TTTGTAAATCAGTGCGTTTTTTTGTATAAAAA 27 39 0 AGGGTTTTTT 0.827968 -115 CACTCTTACTTGAGTGTCTTTTCTTTCTGTAA 28 75 1 TGGGTCTTTT 0.857501 -39 TGAGCCAAATCGTGAGCTTTTTCATTGATTAC 30 74 1 CGGGCTTTTT 0.837505 -105 TTACATACTGGGAGGTTTTTATT 40 151 1 GGGTTTTTAT 0.695495 -13 CGCCTTTATTTGCGGGTTTTTG 41 1 0 TGGGTTTTTG 0.757069 -300 GCTTTTGATTTGGGCATTTTTTCGCATATAGA 47 62 1 TGGATTTTTT 0.830224 -154 TTTATGTCAAGGGGATTTTTATGTTGAACGTC 55 64 1 GGGTTTTTAT 0.695495 -80 CCGCCGAGATGGCGTGTTTTTTTGTGCGGTGT 56 23 1 GGGGTTTTTT 0.982171 -86 AGGTGAAACATGTGTTTTTTTTCTAAACCTTT 63 151 1 TGGTTTTTTT 0.88694 -150 ** * ******* Masking position 9 Map Score: 22.8167 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 168 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 CCTCCCAATCAAAAAGTAAGCTTGCACACA 13 100 0 AAAAAGTAAG 0.914303 -25 ATATTACTTTAAAATGAAAGCGTTTTCCAA 14 83 1 AAAATGAAAG 0.884883 -32 GCTTTAAAATAAAATGTAAGCACTTACATT 15 69 1 AAAATGTAAG 0.884883 -80 ATAAAGGAAATAAATGAAAAACTTTCGGGG 16 15 1 TAAATGAAAA 0.621152 -286 ACGATTTGATAAAATGAAAGTAACAGAAGG 19 45 1 AAAATGAAAG 0.884883 -36 CATAACCTTCAAAAAGTAAGAAATGTGAAA 21 61 1 AAAAAGTAAG 0.914303 -71 TTAAGGTTGAAAAAAGTAAGATAATACTTG 22 61 1 AAAAAGTAAG 0.914303 -31 AAAAACCTTTAAAATGAAAACTGGCACTCT 28 51 1 AAAATGAAAA 0.826318 -63 AATCCCATTCAAAAAGTGAAAGCGGGGAGG 33 11 1 AAAAAGTGAA 0.784593 -25 CGGCTTTTTTTAAAAGAAAAGATTGACAGT 35 62 1 TAAAAGAAAA 0.694721 -146 TTTCTTTTAGAAAAAGTGAAACCTTTTTCT 37 63 0 AAAAAGTGAA 0.784593 -121 TCACTTTTTCTAAAAGAAAGCTGTAAAAAC 37 74 1 TAAAAGAAAG 0.786178 -110 TAAAAAGAGAGAAAGGCTTGC 38 2 1 AAAAAGAGAG 0.854754 -210 CATTTATAGTAAAAAGAGAAAGGCTGTATT 38 34 0 AAAAAGAGAA 0.784593 -178 CTTTTTACTATAAATGAAAGCGCTATCATA 38 48 1 TAAATGAAAG 0.725955 -164 AGCAGCCAGTAAAATGTAAGCATTTTCTTT 41 184 1 AAAATGTAAG 0.884883 -117 TCTCTCCCCCAAAAAGAAAATGCTTACATT 41 196 0 AAAAAGAAAA 0.868481 -105 ATCTGTCTCGTAAATGTGAAGTAAGCGAAT 42 27 0 TAAATGTGAA 0.474891 -191 TATTATCATATAAAAGTAAGCGGTTACAAT 42 141 0 TAAAAGTAAG 0.786178 -77 TCTAAAATAAAAAATGTAAATTTGTATTAT 44 62 0 AAAATGTAAA 0.826318 -120 TCTCCTTTATAAAAAGAAAAGGTGCGAAGC 45 28 0 AAAAAGAAAA 0.868481 -30 GGAAAGCAAAAAAAAGTAAACTACTACTTT 50 255 0 AAAAAGTAAA 0.868481 -46 CTATCATAACAAAAAGAAAAAGACCGATTT 51 205 1 AAAAAGAAAA 0.868481 -96 TTATTCTTTTAAAATGTGAGTGTTATAATT 52 92 0 AAAATGTGAG 0.809157 -151 ********** Masking position 4 Map Score: 23.6547 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 524 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 4 CTTATCATGATAGCGCTTTCTTAAATTATC 2 140 0 TAGCGCTTTC 0.941489 -157 CTGCTTTGGAAAACGCTTTCATTTTAAAGT 14 88 0 AAACGCTTTC 0.981768 -27 CCTTTAATGTAAGTGCTTACATTTTATTTT 15 74 0 AAGTGCTTAC 0.806625 -75 GGAAATGAAAAAACGCTTTTCGTTATCTTG 16 192 0 AAACGCTTTT 0.76558 -109 ACAGCACCCCTAGTGCTTTCCGTATACAAT 18 189 1 TAGTGCTTTC 0.806624 -112 ATCACGGTAAAAACGCTTTCTAAATTTCAC 21 32 1 AAACGCTTTC 0.981768 -100 TCATAAAATAAAACGCTTTCAAATACAAAA 35 172 0 AAACGCTTTC 0.981768 -36 TCTAATTTGTAAGCGCTTTCTAAAATAAAG 36 163 1 AAGCGCTTTC 0.982136 -34 ACGTTTATGATAGCGCTTTCATTTATAGTA 38 53 0 TAGCGCTTTC 0.941489 -159 CCCAAAAAGAAAATGCTTACATTTTACTGG 41 189 0 AAATGCTTAC 0.803671 -112 CAATTATTGTAACCGCTTACTTTTATATGA 42 136 1 AACCGCTTAC 0.786753 -82 TTACCAAATCAAATGCTTTCCTTCGACCTT 49 245 0 AAATGCTTTC 0.933242 -56 TTGTTATTGTAAACGCTTTCTTATATTGAG 53 88 0 AAACGCTTTC 0.981768 -33 GCCAAGAATTAAACGCTTTCAAAAACACCA 62 197 0 AAACGCTTTC 0.981768 -104 ********** Masking position 2 Map Score: 20.9837 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 118 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 ATCATGATAGCGCTTTCTTAAATTATCATA 2 137 0 CGCTTTCTTA 0.948537 -160 ATGTTCCACTCTCTTTCATATATATCAATC 9 140 0 CTCTTTCATA 0.834364 -21 AGATTGGCCTCTCTTTCATACACCCTTTTA 13 16 1 CTCTTTCATA 0.834364 -109 CTTTGGAAAACGCTTTCATTTTAAAGTAAT 14 85 0 CGCTTTCATT 0.809045 -30 CCTATCCGAACGCTTTAAAATAAAATGTAA 15 58 1 CGCTTTAAAA 0.69359 -91 AGAACTGTGTCGCTTTCAAAGGA 19 4 0 CGCTTTCAAA 0.971725 -77 ACGGTAAAAACGCTTTCTAAATTTCACATA 21 35 1 CGCTTTCTAA 0.940863 -97 GGCGAGCATCAGCTTTCATAAATTGGTAAG 32 153 1 AGCTTTCATA 0.723934 -115 TAAAATAAAACGCTTTCAAATACAAAAGAT 35 169 0 CGCTTTCAAA 0.971725 -39 AATTTGTAAGCGCTTTCTAAAATAAAGGAG 36 166 1 CGCTTTCTAA 0.940863 -31 TAAATGAAAGCGCTATCATAAACGTCTTTA 38 58 1 CGCTATCATA 0.809045 -154 TTATTGTAAACGCTTTCTTATATTGAGTGT 53 85 0 CGCTTTCTTA 0.948537 -36 AAGAATTAAACGCTTTCAAAAACACCAAAA 62 194 0 CGCTTTCAAA 0.971725 -107 ********** Masking position 6 Map Score: 15.5606 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 131 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 TTGGATGGAGATGAGGAGAGCCAGGAATCCAA 2 178 1 ATGAGGGACC 0.856219 -119 TTTTCGGGAAAGGAGGCACGCCACACATCCAG 2 247 1 AGGAGGACCC 0.951864 -50 TGAGTTAGAAAGGAGGATATCAA 3 288 1 AGGAGGTACA 0.879335 -13 ATCTATATTTAGGAGGTTATCCAG 6 287 1 AGGAGGTACC 0.99025 -14 CTCATAGAGAAGGAGGGAAGCCG 8 149 1 AGGAGGAACC 0.978718 -13 GCTTGCGTCAATGAGGTTAGCCTCTTGTTCAG 40 28 1 ATGAGGTACC 0.957302 -136 ATAGGTTAAAAGGAGGCTACCCT 44 2 0 AGGAGGTACC 0.990249 -180 TAATGTCCAGAGGAGGCCAACCCT 46 67 1 AGGAGGCACC 0.964254 -14 GCAGGACCAAAGGAGGGTCATCTT 54 3 0 AGGAGGTCTC 0.906019 -181 ATGTAAACGAATGAGGTTTCCCTTTCAGTTTC 54 65 1 ATGAGGTTCC 0.861733 -119 TAAAACCATAAGGAGGATTTTC 55 132 1 AGGAGGTTTC 0.861733 -12 GTCATTCGGCAGGAGGAAAATCAAAATG 63 283 1 AGGAGGAATC 0.910331 -18 ****** ** ** Masking position 4 Map Score: 10.8939 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 45 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 TTACATCCGTTTTTTATTATGAAAGACAGGTAGT 1 51 1 TTTTTATTGA 0.647701 -48 TCCCTCCAGATTTTTATGTTACTAGTAAAAAAAT 2 23 1 TTTTTATGAA 0.840008 -274 CAATTGTTAGTTTTTATTTCATCAACTAGAAATA 5 119 0 TTTTTATTAA 0.939188 -94 AAAGGGTTCTTTTTTATGAAAAAAACAAATTGAC 8 47 1 TTTTTATGAA 0.838994 -115 CATCACCTCATTTTTATTTCTAGACTATTCAGTC 11 51 0 TTTTTATTTA 0.553662 -28 TCCGAAGGTCTTCTTATTGAAAAAGCTAAGTCGT 12 32 1 TTCTTATTAA 0.771782 -95 ATCCGCAGTTTTTTTATTTAAACAAACATATCAT 16 101 1 TTTTTATTAA 0.939099 -200 GATATGCAGTTTTTTATTTTACCAAAAAAACAGG 18 12 0 TTTTTATTAA 0.939188 -289 CGTATACAATTTTTTATTTTAACATCATAATAGA 18 209 1 TTTTTATTAA 0.939186 -92 GATGTGGGCGTTTTTTTTATACAAAAAAACGCAC 27 26 1 TTTTTTTTAA 0.769532 -128 TTTTTTTGCCAAAAAGGGGTTATC 28 1 1 TTTTTTTGAA 0.53164 -113 AGAGTCATCATTTTTTTTAGAAAATGTGACAAAT 32 115 1 TTTTTTTTAA 0.769516 -153 AGAGCCCGGCTTTTTATTCAATAGGACGGCCAGC 35 23 0 TTTTTATTAG 0.634007 -185 CAGTCCTGCATTCTTATTATACAAAACATGGCGC 37 141 0 TTCTTATTAA 0.771869 -43 AAATTTACATTTTTTATTTTAGAAATATAGCAAA 44 69 1 TTTTTATTAA 0.939168 -113 TCACTCCTCGTTTTTATTATATAACGTTATATAA 47 187 0 TTTTTATTAA 0.939188 -29 GATATACTCTTTTTTAGTGGAGAACATGTGTGTT 54 113 1 TTTTTAGTAA 0.634006 -71 TTTTTCATTATTTTTATTATATTAATCTTTTAAT 62 36 0 TTTTTATTAA 0.939188 -265 ******** * * Masking position 5 Map Score: 12.1686 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 57 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 8 ATTGTTCATATTTTTTTCATACCTTTGGAC 5 88 0 TTTTTTTCAT 0.799389 -125 TCTTTGTCATTCTATTTCATATAGTAT 8 8 0 TCTATTTCAT 0.433918 -154 TATGCAAGGGTCTTTGTCATTCTATTTCAT 8 18 0 TCTTTGTCAT 0.508417 -144 TGTCAATTTGTTTTTTTCATAAAAAAGAAC 8 52 0 TTTTTTTCAT 0.799389 -110 GGAAGAAATTGTTTTTTCATCCTGTCAATT 8 74 0 GTTTTTTCAT 0.753285 -88 GGCTTTTTCTTGCTTTACGGA 9 2 1 GCTTTTTCTT 0.597431 -159 GATGTTCCACTCTCTTTCATATATATCAAT 9 141 0 TCTCTTTCAT 0.676458 -20 ACACGACTTAGCTTTTTCAATAAGAAGACC 12 38 0 GCTTTTTCAA 0.670236 -89 CAGATTGGCCTCTCTTTCATACACCCTTTT 13 15 1 TCTCTTTCAT 0.676458 -110 ACGTAACAAATCTTCTTCAAACCAATCCCC 15 104 0 TCTTCTTCAA 0.550911 -45 AACGAAAAGCGTTTTTTCATTTCCTTACAA 16 198 1 GTTTTTTCAT 0.753285 -103 AACGAAATCATTTTTTTCATATAGGGACGG 18 265 1 TTTTTTTCAT 0.799389 -36 TAACAAACAAGCTTTTTCAAATTCCTATGC 22 34 0 GCTTTTTCAA 0.670236 -58 AATGAATCGCGCTTTTTCATCATCATAAGA 24 17 1 GCTTTTTCAT 0.901049 -38 CAAATCGTGAGCTTTTTCATTGATTACAAA 30 79 1 GCTTTTTCAT 0.901049 -100 TTTTACTCTGTCTTCTTCATGTCTTCCTTG 31 74 0 TCTTCTTCAT 0.846061 -36 GTTCACGTCCTCTTTTTCATTAAAGATAAA 48 78 0 TCTTTTTCAT 0.922385 -25 ATCGCGTCTGTTTTCTTCATTTTCATGACG 49 111 1 TTTTCTTCAT 0.64824 -190 AACAGCATGATTTTCTTCATCACGACACCT 51 145 1 TTTTCTTCAT 0.64824 -156 AGTAAATCGGTCTTTTTCTTTTTGTTATGA 51 208 0 TCTTTTTCTT 0.659494 -93 CTTTACTCGATCTTTTTCAA 59 1 0 TCTTTTTCAA 0.726218 -203 TAAACACTACATTTTTTCATTATTTTTATT 62 52 0 ATTTTTTCAT 0.254263 -249 ATCAATGACGTCTTCTTCTTTGAACCGGCC 63 29 0 TCTTCTTCTT 0.472496 -272 ********** Masking position 7 Map Score: 19.2906 Number of sites scoring better than the average of aligned sites = 1114 Number in coding regions = 929 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 9 TTTTATGAGAAGTTTTAGAAGGAAAGAGCGATAGTAC 6 138 0 AGAAGGAAGA 0.895069 -163 GTCTTGCGTTAGAAATAGAAGGAATGCCGCGATGTGG 9 47 0 AGAAGGAAGC 0.977193 -114 AAGCCTTGTAAGGAAATGAAAAAACGCTTTTCGTTAT 16 196 0 AGAAAAAAGC 0.734709 -105 GGCTGAGATAAAGCGCGGAAGAAACGCGCTTTGATCC 18 149 0 AGAAGAAAGC 0.97677 -152 ATAAAATGAAAGTAACAGAAGGAAAGCAGGGGGAAAA 19 53 1 AGAAGGAAGC 0.977193 -28 GACAGCGATTAAATACACAAGAAAGGCCGCATAAAGA 20 53 0 ACAAGAAAGC 0.900364 -83 CTTTTGTTACATTGAATGAAGAAAGGCTCGCTGTGAA 30 114 1 AGAAGAAAGC 0.97677 -65 ATGCGTGTGAATACAAGGAAGACATGAAGAAGACAGA 31 61 1 AGAAGACAGA 0.725626 -49 ATGCTAACACATACAGAAAAGAAAAGCTAGAACAGCT 48 42 0 AAAAGAAAGC 0.768143 -61 CATTAGGGCAAAAGGTCGAAGGAAAGCATTTGATTTG 49 234 1 AGAAGGAAGC 0.977193 -67 TCCCTACTAAATTAAATGAAGGAAAGCAAAAAAAAGT 50 268 0 AGAAGGAAGC 0.977193 -33 CTTCAGCGGAAATAGAAGAAGACATGCAGGACCAAAG 54 23 0 AGAAGACAGC 0.929991 -161 TGCGATTAGAATATAACCAAGAAATGACCAAAAAGTA 62 102 1 ACAAGAAAGA 0.642739 -199 * ******* ** Masking position 9 Map Score: 11.5614 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 134 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GTTAAGCTAGTATTAATCGATTTTAAAGATTGGATTTACA 6 212 0 TTATTTTAGT 0.957183 -89 AAAATGATTCTTATCATCTATTATGATGTTAAAATAAAAA 18 219 0 TTATTTTAGT 0.957183 -82 AGCGACACAGTTCTCAAACTTTCTCACGATTTGATAAAAT 19 20 1 TTAATTTAGT 0.807507 -61 GATAGCTTCTTCCTTATATCTTATGATGATGAAAAAGCGC 24 25 0 TTATTTTAGT 0.957183 -30 TCGGTCTTTATATTTATCCATTGTAAGGCTCAAGTTTTTC 32 58 0 TTATTTTAGT 0.957183 -210 AAATGATGACTCTTCATAAATTGTTAAGATTCGGTCTTTA 32 88 0 TTATTTTAGT 0.957183 -180 ATCATAAACGTCTTTATTTCTTTTAAAAATGATGTAAAAG 38 72 1 TTATTTTAAT 0.576416 -140 AACAAATGTCTGATTATTGTTTATAATGAGAATAGGCTTA 41 84 1 TTATTTTAGG 0.765315 -217 TTAAATAAGCTTATAAAAATTTGTTATGTTCTTTCAAAAG 41 127 1 TTAATTTAGT 0.807507 -174 ATTATTTATATTATAATGTATTATGACGTTATAATACAAA 44 32 1 TTATTTTAGT 0.957183 -150 AACAGCTTTATTATATTTGTTTGTCATGCTCTTACTTA 48 9 0 TTTTTTTAGT 0.704053 -94 CTGTGCCTGATCCTGATCTGTGTTCACGCTGACCACGACT 49 33 1 TTATTGTAGT 0.765315 -268 TATCGCCAGTTGTTTATCTATTGTCATGCTGGTCAACTTT 63 110 0 TTATTTTAGT 0.957183 -191 AAAGAATGGGTCCTTGTCTATTATAACGGTTTAAGGTCAA 63 197 0 TTGTTTTAGT 0.779052 -104 * * ** ** * * * * Masking position 16 Map Score: 9.08827 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 29 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 TTGGATTCCTGGCTCTCCTCATCTCCATCCAAGC 2 176 0 GTCCCTCATT 0.768514 -121 CGGGAAAGGAGGCACGCCACACATCCAGCACAAA 2 251 1 GACCCACACT 0.803628 -46 CCTATGTTTCGATACTCCTCTCTTGGTAACGGGG 3 109 0 GACCCTCTCT 0.980546 -192 TATGCGCTGCATCTCCTCACCTAACCTTTACA 4 75 0 GTCCCTCACT 0.980546 -22 TAGGCAGATTGGCCTCTCTTTCATACACCC 13 7 1 GTGCCTCTCT 0.902075 -118 GTCTCTCTTCTCCTTTATGGCTAG 39 30 0 GTCCTTCTCT 0.849847 -14 GGGTATCCCTCTCATCTATTTAGTA 42 203 0 GATCCTCTCT 0.87505 -15 GGGTATCTCATCTCCTTTATAAAAAG 45 42 0 GTCCATCTCT 0.849847 -16 ACGTTTTATCGGTTTTCCTCACTTACATACATGA 50 185 0 GTTCCTCACT 0.87505 -116 TTTGTAACCCCGCTCATTCATATTTAT 52 4 1 GACCCGCTCT 0.945855 -239 CGAAGAATCTGGATCGCCGCTCTTTATTCTTTTA 52 111 0 GTCCCGCTCT 0.964712 -132 AGAGTCTCCTCTCTTATGTAAGGAT 54 169 0 GTCCCTCTCT 0.987481 -15 CGTAAACAGCCACTCCTCACTTG 60 2 0 GACCCTCACT 0.969887 -22 * ** ****** * Masking position 14 Map Score: 10.8089 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 55 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 ATATTATCCTTTTACTAAATGCAATTATAT 2 55 0 TTTACTAAAT 0.890041 -242 TCACCTAACCTTTACAAAATCAAAAAACAC 4 61 0 TTTACAAAAT 0.834591 -36 TTCTATATTGTTTTCAAAATTTGGGATTGA 8 104 1 TTTTCAAAAT 0.72352 -58 GACGGTTCCATTTTCCACATCGCGGCATTC 9 33 1 TTTTCCACAT 0.751341 -128 CAAAGAATCCTTTACCACATG 11 2 0 TTTACCACAT 0.853498 -77 GATTTCGTTGTTTACAAAATGATTCTTATC 18 244 0 TTTACAAAAT 0.834591 -57 AAATAAAATGTTTTCTAAATATGAATTACA 40 126 1 TTTTCTAAAT 0.807622 -38 AATCACATCATTTACTAAATATTTAGTAAA 42 85 1 TTTACTAAAT 0.890041 -133 TTCCATAATATTTACTAAATATTTAGTAAA 42 95 0 TTTACTAAAT 0.890041 -123 GAGTTAATATTTTACTAAATAGATGAGAGG 42 191 1 TTTACTAAAT 0.890041 -27 ACTTCGCGGTTTTTCCACATTAGGGCAAAA 49 217 1 TTTTCCACAT 0.751341 -84 GTCTATTCATTTTACCAAATCAAATGCTTT 49 256 0 TTTACCAAAT 0.912442 -45 ********** Masking position 7 Map Score: 7.84445 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 44 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 13 TACCGCGAGACCCTCGTCCTTTGCATAGGACG 3 190 1 CCCTCTCTTT 0.95036 -111 ACACAAAAAACCCCCGTCCTATGCAAAGGACG 3 204 0 CCCCCTCTAT 0.920232 -97 TAAAAAAAGACACTCAGCGTATCAGAACACAT 17 89 0 CACTCGCTAT 0.575357 -145 GTTTTCCCCCTGCTTTCCTTCTGTTAC 19 64 0 CCCCCGCTTC 0.944062 -17 GTTGTCCCCGCACTCCTCTTTTTATTAAGA 26 9 0 CACTCTCTTT 0.776331 -60 TTCCTGAATTCCCCCTGCGTATAATGTGTAAT 27 132 0 CCCCCGCTAT 0.937313 -22 ATTAAACCTGCCGCCAGCATTTC 30 2 0 CCGCCGCTTT 0.784897 -177 GAGAACCTCCCCGCTTTCACTTTTTGAA 33 18 0 CTCCCGCTTC 0.799362 -18 CCGGGCTCTGCCCCCGGCTTTTTTTAAAAGAA 35 48 1 CCCCCGCTTT 0.980254 -160 GTCTCTCTTCTCCTTTATGGCTAGTT 39 28 0 CTCTTTCTTT 0.376405 -16 GGAACTAAAACCCTTTGCTTTTGAAAGAACAT 41 152 0 CCCTTGCTTT 0.768194 -149 CAGAAAAGTCCCCCTATCTTTTGACCCGTTAT 44 160 0 CCCCTTCTTT 0.836483 -22 ATCCTTCACTCCTCGTTTTTATTATATA 47 198 0 CACTCTCTTT 0.776331 -18 AGGAAAATACCTCCCTTCTTTTTCTGCAGTCA 50 156 1 CTCCCTCTTT 0.90042 -145 ATAATCCTCCCCCTTTATTTGATGTTTCAA 52 223 0 CCCCCTTTTT 0.641454 -20 TCCTGCCGAACTCCCTTCATATCTAAAACGCA 57 48 1 CTCCCTCTAT 0.731428 -38 CCAGACTCCCCCATCTGCGTTTTAGATATGAA 57 63 0 CCATCGCTTT 0.551681 -23 AGAGAAGCCCTCCTCTTTCTATTGGCAGA 61 56 0 CCCTCTCTTC 0.866816 -19 ***** ** *** Masking position 10 Map Score: 12.2654 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 347 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 14 CTTTAAACAGCCTCCCTCCAGATTTT 2 7 1 ACAGCCTCCC 0.979285 -290 CACACCTGCCACCGACTCTCT 3 2 0 ACCGACTCTC 0.504073 -299 AGGTGTGAACCGATCCTCCCCTGATGCCGA 3 25 1 CGATCCTCCC 0.7179 -276 ATTTGACCATCCTCTCCCGTCCCTAT 18 285 0 CCATCCTCTC 0.874909 -16 CGCTTCACAGCGAGCCTTTCTTCATTCAAT 30 124 0 CGAGCCTTTC 0.577853 -55 AGCTTCCATCCTCCCATTTTACTCT 31 95 0 CCATCCTCCC 0.928587 -15 CTTGCTTAATACAGCCTTTCTCTTTTTACT 38 27 1 ACAGCCTTTC 0.835049 -185 TTGACGCAAGCCAGCCTCCAATGGTTCT 40 9 0 CCAGCCTCCA 0.811388 -155 ACCGCCTCCCTACTAAATTA 50 291 0 ACCGCCTCCC 0.937246 -10 GGATATGGCGACAGCCTTCCTGCCGAACTC 57 31 1 ACAGCCTTCC 0.903954 -55 GCCAGACTCCCCCATCTGCGT 57 75 0 CCAGACTCCC 0.892052 -11 TGACAGCCACTCCTTCTGTTGG 58 11 0 ACAGCCACTC 0.838541 -12 CGTAAACAGCCACTCCTCACTTG 60 9 0 ACAGCCACTC 0.838541 -15 ********** Masking position 6 Map Score: 6.86063 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 250 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 15 TCTAGAAAGACCTTCGGCGCTTCCGAAGGTC 12 7 1 AGTTCGGCCT 0.865483 -120 AATCGCTGTCCCAATCTTCGGCGGGGCCATACGCG 20 80 1 CATTCGGCGG 0.862804 -56 AAGAAAACAGACGCGATGCGGCAGTGGCAAAAGTC 49 93 0 AGTGCGGCGT 0.956547 -208 GCTGAGCATGGAGTTCGGCGGGATATGGCGAC 57 8 1 AGTTCGGCGG 0.990045 -78 TTAGATATGAAGGGAGTTCGGCAGGAAGGCTGTCG 57 39 0 AGTTCGGCGG 0.990045 -47 GCGCACATGGACGCCGTTCGGCTGTTCGTCGT 61 8 0 AGTTCGGCGT 0.974921 -67 AGGGAGAACCGGCCCTGCGGCCGGTTCAAAGAAG 63 10 1 CGTGCGGCGG 0.969587 -291 AGATGAAATGAAGTCATTCGGCAGGAGGAAAATCA 63 271 1 AGTTCGGCGG 0.990045 -30 * * ****** ** Masking position 7 Map Score: 4.87857 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 44 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084