Multiple sequence alignment - TraesCS2A01G579000

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G579000 chr2A 100.000 2417 0 0 1 2417 771933092 771935508 0.000000e+00 4464
1 TraesCS2A01G579000 chr2A 94.461 686 18 3 1 685 771922408 771923074 0.000000e+00 1038
2 TraesCS2A01G579000 chr2A 97.909 526 10 1 1 526 771892509 771893033 0.000000e+00 909
3 TraesCS2A01G579000 chr2A 94.340 159 4 2 528 685 771906574 771906728 3.110000e-59 239
4 TraesCS2A01G579000 chr2D 95.474 2077 81 13 1 2069 650584447 650586518 0.000000e+00 3302
5 TraesCS2A01G579000 chr2D 97.759 357 6 2 2061 2417 438530207 438530561 4.420000e-172 614
6 TraesCS2A01G579000 chr2D 98.006 351 7 0 2067 2417 579330207 579330557 5.710000e-171 610
7 TraesCS2A01G579000 chr2D 97.465 355 8 1 2063 2417 438517244 438517597 2.660000e-169 604
8 TraesCS2A01G579000 chr2D 80.282 781 122 18 905 1656 650565430 650566207 5.840000e-156 560
9 TraesCS2A01G579000 chr2B 93.418 790 51 1 1281 2069 787050510 787049721 0.000000e+00 1170
10 TraesCS2A01G579000 chr2B 81.141 806 105 27 905 1666 787098259 787099061 9.560000e-169 603
11 TraesCS2A01G579000 chr2B 81.260 603 92 10 905 1491 787154314 787154911 3.640000e-128 468
12 TraesCS2A01G579000 chr2B 78.901 564 95 18 934 1491 787233274 787233819 6.350000e-96 361
13 TraesCS2A01G579000 chr2B 85.859 99 9 3 796 891 787098176 787098272 1.530000e-17 100
14 TraesCS2A01G579000 chr1D 97.759 357 4 2 2061 2417 147924913 147924561 1.590000e-171 612
15 TraesCS2A01G579000 chr5D 97.479 357 8 1 2061 2417 491428843 491429198 2.050000e-170 608
16 TraesCS2A01G579000 chr5D 97.479 357 5 2 2061 2417 198084319 198084671 7.390000e-170 606
17 TraesCS2A01G579000 chr4D 97.479 357 5 2 2061 2417 403538098 403537746 7.390000e-170 606
18 TraesCS2A01G579000 chr3D 97.479 357 5 2 2061 2417 264326909 264326557 7.390000e-170 606
19 TraesCS2A01G579000 chr7D 96.936 359 11 0 2059 2417 604080223 604079865 9.560000e-169 603


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G579000 chr2A 771933092 771935508 2416 False 4464.0 4464 100.000 1 2417 1 chr2A.!!$F4 2416
1 TraesCS2A01G579000 chr2A 771922408 771923074 666 False 1038.0 1038 94.461 1 685 1 chr2A.!!$F3 684
2 TraesCS2A01G579000 chr2A 771892509 771893033 524 False 909.0 909 97.909 1 526 1 chr2A.!!$F1 525
3 TraesCS2A01G579000 chr2D 650584447 650586518 2071 False 3302.0 3302 95.474 1 2069 1 chr2D.!!$F5 2068
4 TraesCS2A01G579000 chr2D 650565430 650566207 777 False 560.0 560 80.282 905 1656 1 chr2D.!!$F4 751
5 TraesCS2A01G579000 chr2B 787049721 787050510 789 True 1170.0 1170 93.418 1281 2069 1 chr2B.!!$R1 788
6 TraesCS2A01G579000 chr2B 787154314 787154911 597 False 468.0 468 81.260 905 1491 1 chr2B.!!$F1 586
7 TraesCS2A01G579000 chr2B 787233274 787233819 545 False 361.0 361 78.901 934 1491 1 chr2B.!!$F2 557
8 TraesCS2A01G579000 chr2B 787098176 787099061 885 False 351.5 603 83.500 796 1666 2 chr2B.!!$F3 870

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
353 354 0.254747 CGACTCCTATTTTGGGCCCA 59.745 55.0 24.45 24.45 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2177 2233 0.390472 CTTCCACGCCAAGGAGAGTC 60.39 60.0 0.0 0.0 36.33 3.36 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 9.937175 GTATTGCTAGAAAATATCCAGTCAAAC 57.063 33.333 0.00 0.00 0.00 2.93
101 102 6.705825 AGCAATAACGATATGTAAGATGCACA 59.294 34.615 7.31 0.00 31.99 4.57
315 316 7.439108 AGTAGGAATTGCTACATACTTCCTT 57.561 36.000 31.10 10.86 42.29 3.36
353 354 0.254747 CGACTCCTATTTTGGGCCCA 59.745 55.000 24.45 24.45 0.00 5.36
543 545 3.201266 AGGACATAATAAACCTGGGCGAA 59.799 43.478 0.00 0.00 0.00 4.70
673 678 8.453320 GCAGCTTTAATTGGCAGAAATTAATTT 58.547 29.630 13.24 13.24 40.12 1.82
853 862 6.433404 AGATGGGATCATGCAAACATATCTTC 59.567 38.462 0.00 0.00 33.67 2.87
854 863 5.447757 TGGGATCATGCAAACATATCTTCA 58.552 37.500 0.00 0.00 33.67 3.02
928 937 5.164620 TCATCAGTGCCTACAAAAGATCA 57.835 39.130 0.00 0.00 0.00 2.92
975 984 2.674420 TCTATACCCGCTTACTTGGCT 58.326 47.619 0.00 0.00 0.00 4.75
1008 1017 5.604650 AGTTATGACTAAAGAGATGAGGGGG 59.395 44.000 0.00 0.00 33.32 5.40
1047 1056 4.944619 ACTATGCTTGCTACTGCTCATA 57.055 40.909 0.00 0.00 40.48 2.15
1057 1069 0.460987 ACTGCTCATACCGCTCTTGC 60.461 55.000 0.00 0.00 0.00 4.01
1170 1193 5.630121 TCCTTGCCTCATCTTTTTGTCTTA 58.370 37.500 0.00 0.00 0.00 2.10
1305 1330 1.132453 GTTAAGCCTCCCGAATGCAAC 59.868 52.381 0.00 0.00 0.00 4.17
1368 1393 3.347216 CGAAGGGGTCTGTGAAATCATT 58.653 45.455 0.00 0.00 0.00 2.57
1433 1458 6.282930 AGTGCTAAATGAAAAACATGCTTGT 58.717 32.000 0.00 0.00 39.39 3.16
1527 1571 7.875041 TGGAAGAAGTTGAGACTCTAGAAAATG 59.125 37.037 3.68 0.00 34.21 2.32
1694 1749 1.008995 CGTGTTTGTTTCGGGGCAG 60.009 57.895 0.00 0.00 0.00 4.85
1749 1804 9.459640 GGTGTAGGACTTAAATTTTCTTGTTTC 57.540 33.333 0.00 0.00 0.00 2.78
1757 1812 8.966868 ACTTAAATTTTCTTGTTTCACTGGAGA 58.033 29.630 0.00 0.00 0.00 3.71
1785 1840 6.053005 GGGGAATTAATCAATAGTGTCACGA 58.947 40.000 0.00 0.00 0.00 4.35
1917 1973 5.716094 TGTAAGAACACATAAAGAGCGCTA 58.284 37.500 11.50 0.00 0.00 4.26
1922 1978 5.805994 AGAACACATAAAGAGCGCTAAGTAC 59.194 40.000 11.50 0.00 0.00 2.73
2069 2125 6.655003 TGACTTAAGAAAATGAGGGCTAAGTG 59.345 38.462 10.09 0.00 0.00 3.16
2070 2126 6.779860 ACTTAAGAAAATGAGGGCTAAGTGA 58.220 36.000 10.09 0.00 0.00 3.41
2071 2127 6.881602 ACTTAAGAAAATGAGGGCTAAGTGAG 59.118 38.462 10.09 0.00 0.00 3.51
2072 2128 4.227864 AGAAAATGAGGGCTAAGTGAGG 57.772 45.455 0.00 0.00 0.00 3.86
2073 2129 3.054065 AGAAAATGAGGGCTAAGTGAGGG 60.054 47.826 0.00 0.00 0.00 4.30
2074 2130 2.270434 AATGAGGGCTAAGTGAGGGA 57.730 50.000 0.00 0.00 0.00 4.20
2075 2131 1.799933 ATGAGGGCTAAGTGAGGGAG 58.200 55.000 0.00 0.00 0.00 4.30
2076 2132 0.413832 TGAGGGCTAAGTGAGGGAGT 59.586 55.000 0.00 0.00 0.00 3.85
2077 2133 1.116308 GAGGGCTAAGTGAGGGAGTC 58.884 60.000 0.00 0.00 0.00 3.36
2078 2134 0.325765 AGGGCTAAGTGAGGGAGTCC 60.326 60.000 0.00 0.00 35.04 3.85
2080 2136 0.827368 GGCTAAGTGAGGGAGTCCTG 59.173 60.000 9.58 0.00 45.05 3.86
2081 2137 0.827368 GCTAAGTGAGGGAGTCCTGG 59.173 60.000 9.58 0.00 45.05 4.45
2082 2138 1.619977 GCTAAGTGAGGGAGTCCTGGA 60.620 57.143 9.58 0.00 45.05 3.86
2083 2139 2.957312 GCTAAGTGAGGGAGTCCTGGAT 60.957 54.545 9.58 0.00 45.05 3.41
2084 2140 2.350863 AAGTGAGGGAGTCCTGGATT 57.649 50.000 9.58 0.00 45.05 3.01
2085 2141 3.491766 AAGTGAGGGAGTCCTGGATTA 57.508 47.619 9.58 0.00 45.05 1.75
2086 2142 3.039252 AGTGAGGGAGTCCTGGATTAG 57.961 52.381 9.58 0.00 45.05 1.73
2087 2143 2.043227 GTGAGGGAGTCCTGGATTAGG 58.957 57.143 9.58 0.00 45.05 2.69
2095 2151 2.855669 CCTGGATTAGGGGGTCCTC 58.144 63.158 0.00 0.00 43.66 3.71
2096 2152 1.122019 CCTGGATTAGGGGGTCCTCG 61.122 65.000 0.00 0.00 43.66 4.63
2097 2153 1.074775 TGGATTAGGGGGTCCTCGG 60.075 63.158 0.00 0.00 43.66 4.63
2098 2154 1.235112 GGATTAGGGGGTCCTCGGA 59.765 63.158 0.00 0.00 43.66 4.55
2099 2155 1.120184 GGATTAGGGGGTCCTCGGAC 61.120 65.000 7.57 7.57 43.66 4.79
2100 2156 0.398098 GATTAGGGGGTCCTCGGACA 60.398 60.000 17.21 0.00 46.20 4.02
2101 2157 0.398664 ATTAGGGGGTCCTCGGACAG 60.399 60.000 17.21 0.00 46.20 3.51
2102 2158 3.674050 TAGGGGGTCCTCGGACAGC 62.674 68.421 17.21 1.56 46.20 4.40
2117 2173 4.868314 GGACAGCCGGACTATATACTTT 57.132 45.455 5.05 0.00 0.00 2.66
2118 2174 5.972107 GGACAGCCGGACTATATACTTTA 57.028 43.478 5.05 0.00 0.00 1.85
2119 2175 5.952033 GGACAGCCGGACTATATACTTTAG 58.048 45.833 5.05 0.00 0.00 1.85
2120 2176 5.388408 ACAGCCGGACTATATACTTTAGC 57.612 43.478 5.05 0.00 0.00 3.09
2121 2177 4.220163 ACAGCCGGACTATATACTTTAGCC 59.780 45.833 5.05 0.00 0.00 3.93
2122 2178 3.442977 AGCCGGACTATATACTTTAGCCG 59.557 47.826 5.05 0.00 36.74 5.52
2123 2179 4.367386 CCGGACTATATACTTTAGCCGG 57.633 50.000 0.00 14.10 43.40 6.13
2125 2181 4.979388 CGGACTATATACTTTAGCCGGAC 58.021 47.826 5.05 0.00 35.05 4.79
2126 2182 4.699257 CGGACTATATACTTTAGCCGGACT 59.301 45.833 5.05 4.30 35.05 3.85
2127 2183 5.877012 CGGACTATATACTTTAGCCGGACTA 59.123 44.000 5.05 3.09 35.05 2.59
2128 2184 6.541641 CGGACTATATACTTTAGCCGGACTAT 59.458 42.308 5.05 0.00 35.05 2.12
2129 2185 7.066766 CGGACTATATACTTTAGCCGGACTATT 59.933 40.741 5.05 0.00 35.05 1.73
2130 2186 8.189460 GGACTATATACTTTAGCCGGACTATTG 58.811 40.741 5.05 5.06 0.00 1.90
2131 2187 8.064336 ACTATATACTTTAGCCGGACTATTGG 57.936 38.462 5.05 2.71 0.00 3.16
2132 2188 7.892241 ACTATATACTTTAGCCGGACTATTGGA 59.108 37.037 5.05 0.00 0.00 3.53
2133 2189 3.538634 ACTTTAGCCGGACTATTGGAC 57.461 47.619 5.05 0.00 0.00 4.02
2134 2190 3.105283 ACTTTAGCCGGACTATTGGACT 58.895 45.455 5.05 0.00 0.00 3.85
2135 2191 4.284178 ACTTTAGCCGGACTATTGGACTA 58.716 43.478 5.05 0.00 0.00 2.59
2136 2192 4.900054 ACTTTAGCCGGACTATTGGACTAT 59.100 41.667 5.05 0.00 0.00 2.12
2137 2193 4.866508 TTAGCCGGACTATTGGACTATG 57.133 45.455 5.05 0.00 0.00 2.23
2138 2194 2.958818 AGCCGGACTATTGGACTATGA 58.041 47.619 5.05 0.00 0.00 2.15
2139 2195 3.305720 AGCCGGACTATTGGACTATGAA 58.694 45.455 5.05 0.00 0.00 2.57
2140 2196 3.322254 AGCCGGACTATTGGACTATGAAG 59.678 47.826 5.05 0.00 0.00 3.02
2141 2197 3.321111 GCCGGACTATTGGACTATGAAGA 59.679 47.826 5.05 0.00 0.00 2.87
2142 2198 4.021016 GCCGGACTATTGGACTATGAAGAT 60.021 45.833 5.05 0.00 0.00 2.40
2143 2199 5.185249 GCCGGACTATTGGACTATGAAGATA 59.815 44.000 5.05 0.00 0.00 1.98
2144 2200 6.622549 CCGGACTATTGGACTATGAAGATAC 58.377 44.000 0.00 0.00 0.00 2.24
2145 2201 6.208797 CCGGACTATTGGACTATGAAGATACA 59.791 42.308 0.00 0.00 0.00 2.29
2146 2202 7.255836 CCGGACTATTGGACTATGAAGATACAA 60.256 40.741 0.00 0.00 0.00 2.41
2147 2203 7.810282 CGGACTATTGGACTATGAAGATACAAG 59.190 40.741 0.00 0.00 0.00 3.16
2148 2204 8.861086 GGACTATTGGACTATGAAGATACAAGA 58.139 37.037 0.00 0.00 0.00 3.02
2154 2210 9.605275 TTGGACTATGAAGATACAAGATTGAAG 57.395 33.333 0.00 0.00 0.00 3.02
2155 2211 8.981659 TGGACTATGAAGATACAAGATTGAAGA 58.018 33.333 0.00 0.00 0.00 2.87
2156 2212 9.255304 GGACTATGAAGATACAAGATTGAAGAC 57.745 37.037 0.00 0.00 0.00 3.01
2160 2216 7.818493 TGAAGATACAAGATTGAAGACTTCG 57.182 36.000 10.56 0.00 34.37 3.79
2161 2217 7.378966 TGAAGATACAAGATTGAAGACTTCGT 58.621 34.615 10.56 1.87 34.37 3.85
2162 2218 7.542477 TGAAGATACAAGATTGAAGACTTCGTC 59.458 37.037 10.56 10.67 34.37 4.20
2163 2219 6.334202 AGATACAAGATTGAAGACTTCGTCC 58.666 40.000 10.56 2.18 32.18 4.79
2164 2220 3.665190 ACAAGATTGAAGACTTCGTCCC 58.335 45.455 10.56 0.53 32.18 4.46
2165 2221 2.656560 AGATTGAAGACTTCGTCCCG 57.343 50.000 10.56 0.00 32.18 5.14
2166 2222 1.893801 AGATTGAAGACTTCGTCCCGT 59.106 47.619 10.56 0.00 32.18 5.28
2167 2223 1.993370 GATTGAAGACTTCGTCCCGTG 59.007 52.381 10.56 0.00 32.18 4.94
2168 2224 0.748450 TTGAAGACTTCGTCCCGTGT 59.252 50.000 10.56 0.00 32.18 4.49
2169 2225 0.313043 TGAAGACTTCGTCCCGTGTC 59.687 55.000 10.56 0.00 32.18 3.67
2170 2226 0.388263 GAAGACTTCGTCCCGTGTCC 60.388 60.000 0.00 0.00 34.39 4.02
2171 2227 2.126580 GACTTCGTCCCGTGTCCG 60.127 66.667 0.00 0.00 0.00 4.79
2185 2241 3.440023 TCCGGATGGGACTCTCCT 58.560 61.111 0.00 0.00 40.94 3.69
2186 2242 1.704082 TCCGGATGGGACTCTCCTT 59.296 57.895 0.00 0.00 40.94 3.36
2187 2243 0.687757 TCCGGATGGGACTCTCCTTG 60.688 60.000 0.00 0.00 40.94 3.61
2188 2244 1.690219 CCGGATGGGACTCTCCTTGG 61.690 65.000 0.00 0.00 38.47 3.61
2189 2245 1.529309 GGATGGGACTCTCCTTGGC 59.471 63.158 0.00 0.00 36.57 4.52
2190 2246 1.144936 GATGGGACTCTCCTTGGCG 59.855 63.158 0.00 0.00 36.57 5.69
2191 2247 1.613630 ATGGGACTCTCCTTGGCGT 60.614 57.895 0.00 0.00 36.57 5.68
2192 2248 1.903877 ATGGGACTCTCCTTGGCGTG 61.904 60.000 0.00 0.00 36.57 5.34
2193 2249 2.266055 GGACTCTCCTTGGCGTGG 59.734 66.667 0.00 0.00 32.53 4.94
2194 2250 2.283529 GGACTCTCCTTGGCGTGGA 61.284 63.158 0.00 0.00 32.53 4.02
2195 2251 1.671742 GACTCTCCTTGGCGTGGAA 59.328 57.895 0.17 0.00 32.61 3.53
2196 2252 0.390472 GACTCTCCTTGGCGTGGAAG 60.390 60.000 0.17 3.93 32.61 3.46
2197 2253 1.078848 CTCTCCTTGGCGTGGAAGG 60.079 63.158 0.00 0.00 41.36 3.46
2206 2262 2.956987 CGTGGAAGGCAAGCTTGG 59.043 61.111 27.10 9.80 0.00 3.61
2214 2270 4.792106 GCAAGCTTGGCAATACGG 57.208 55.556 27.10 0.00 0.00 4.02
2215 2271 2.179764 GCAAGCTTGGCAATACGGA 58.820 52.632 27.10 0.00 0.00 4.69
2216 2272 0.740737 GCAAGCTTGGCAATACGGAT 59.259 50.000 27.10 0.00 0.00 4.18
2217 2273 1.946768 GCAAGCTTGGCAATACGGATA 59.053 47.619 27.10 0.00 0.00 2.59
2218 2274 2.554032 GCAAGCTTGGCAATACGGATAT 59.446 45.455 27.10 0.00 0.00 1.63
2219 2275 3.610114 GCAAGCTTGGCAATACGGATATG 60.610 47.826 27.10 0.00 0.00 1.78
2220 2276 3.492102 AGCTTGGCAATACGGATATGT 57.508 42.857 0.00 0.00 0.00 2.29
2221 2277 4.617253 AGCTTGGCAATACGGATATGTA 57.383 40.909 0.00 0.00 0.00 2.29
2222 2278 4.569943 AGCTTGGCAATACGGATATGTAG 58.430 43.478 0.00 0.00 0.00 2.74
2223 2279 4.283467 AGCTTGGCAATACGGATATGTAGA 59.717 41.667 0.00 0.00 0.00 2.59
2224 2280 5.046304 AGCTTGGCAATACGGATATGTAGAT 60.046 40.000 0.00 0.00 0.00 1.98
2225 2281 5.292101 GCTTGGCAATACGGATATGTAGATC 59.708 44.000 0.00 0.00 0.00 2.75
2226 2282 6.605471 TTGGCAATACGGATATGTAGATCT 57.395 37.500 0.00 0.00 0.00 2.75
2227 2283 6.208988 TGGCAATACGGATATGTAGATCTC 57.791 41.667 0.00 0.00 0.00 2.75
2228 2284 5.127194 TGGCAATACGGATATGTAGATCTCC 59.873 44.000 0.00 0.00 0.00 3.71
2229 2285 5.361285 GGCAATACGGATATGTAGATCTCCT 59.639 44.000 0.00 0.00 0.00 3.69
2230 2286 6.460399 GGCAATACGGATATGTAGATCTCCTC 60.460 46.154 0.00 0.00 0.00 3.71
2231 2287 6.460399 GCAATACGGATATGTAGATCTCCTCC 60.460 46.154 0.00 0.00 0.00 4.30
2232 2288 3.970842 ACGGATATGTAGATCTCCTCCC 58.029 50.000 0.00 0.00 0.00 4.30
2233 2289 3.594232 ACGGATATGTAGATCTCCTCCCT 59.406 47.826 0.00 0.00 0.00 4.20
2234 2290 4.044825 ACGGATATGTAGATCTCCTCCCTT 59.955 45.833 0.00 0.00 0.00 3.95
2235 2291 4.400884 CGGATATGTAGATCTCCTCCCTTG 59.599 50.000 0.00 0.00 0.00 3.61
2236 2292 5.337788 GGATATGTAGATCTCCTCCCTTGT 58.662 45.833 0.00 0.00 0.00 3.16
2237 2293 6.494952 GGATATGTAGATCTCCTCCCTTGTA 58.505 44.000 0.00 0.00 0.00 2.41
2238 2294 6.954684 GGATATGTAGATCTCCTCCCTTGTAA 59.045 42.308 0.00 0.00 0.00 2.41
2239 2295 7.093684 GGATATGTAGATCTCCTCCCTTGTAAC 60.094 44.444 0.00 0.00 0.00 2.50
2240 2296 4.287552 TGTAGATCTCCTCCCTTGTAACC 58.712 47.826 0.00 0.00 0.00 2.85
2241 2297 2.389715 AGATCTCCTCCCTTGTAACCG 58.610 52.381 0.00 0.00 0.00 4.44
2242 2298 2.024273 AGATCTCCTCCCTTGTAACCGA 60.024 50.000 0.00 0.00 0.00 4.69
2243 2299 1.553706 TCTCCTCCCTTGTAACCGAC 58.446 55.000 0.00 0.00 0.00 4.79
2244 2300 1.076677 TCTCCTCCCTTGTAACCGACT 59.923 52.381 0.00 0.00 0.00 4.18
2245 2301 1.477295 CTCCTCCCTTGTAACCGACTC 59.523 57.143 0.00 0.00 0.00 3.36
2246 2302 1.076677 TCCTCCCTTGTAACCGACTCT 59.923 52.381 0.00 0.00 0.00 3.24
2247 2303 1.204941 CCTCCCTTGTAACCGACTCTG 59.795 57.143 0.00 0.00 0.00 3.35
2248 2304 1.893801 CTCCCTTGTAACCGACTCTGT 59.106 52.381 0.00 0.00 0.00 3.41
2249 2305 1.616865 TCCCTTGTAACCGACTCTGTG 59.383 52.381 0.00 0.00 0.00 3.66
2250 2306 1.343465 CCCTTGTAACCGACTCTGTGT 59.657 52.381 0.00 0.00 0.00 3.72
2251 2307 2.559668 CCCTTGTAACCGACTCTGTGTA 59.440 50.000 0.00 0.00 0.00 2.90
2252 2308 3.006110 CCCTTGTAACCGACTCTGTGTAA 59.994 47.826 0.00 0.00 0.00 2.41
2253 2309 3.985925 CCTTGTAACCGACTCTGTGTAAC 59.014 47.826 0.00 0.00 37.35 2.50
2254 2310 3.648339 TGTAACCGACTCTGTGTAACC 57.352 47.619 0.00 0.00 34.36 2.85
2255 2311 2.297033 TGTAACCGACTCTGTGTAACCC 59.703 50.000 0.00 0.00 34.36 4.11
2256 2312 1.713297 AACCGACTCTGTGTAACCCT 58.287 50.000 0.00 0.00 34.36 4.34
2257 2313 2.592102 ACCGACTCTGTGTAACCCTA 57.408 50.000 0.00 0.00 34.36 3.53
2258 2314 2.444421 ACCGACTCTGTGTAACCCTAG 58.556 52.381 0.00 0.00 34.36 3.02
2259 2315 1.134560 CCGACTCTGTGTAACCCTAGC 59.865 57.143 0.00 0.00 34.36 3.42
2260 2316 1.134560 CGACTCTGTGTAACCCTAGCC 59.865 57.143 0.00 0.00 34.36 3.93
2261 2317 1.481363 GACTCTGTGTAACCCTAGCCC 59.519 57.143 0.00 0.00 34.36 5.19
2262 2318 0.831307 CTCTGTGTAACCCTAGCCCC 59.169 60.000 0.00 0.00 34.36 5.80
2263 2319 0.619543 TCTGTGTAACCCTAGCCCCC 60.620 60.000 0.00 0.00 34.36 5.40
2264 2320 0.620700 CTGTGTAACCCTAGCCCCCT 60.621 60.000 0.00 0.00 34.36 4.79
2265 2321 0.619543 TGTGTAACCCTAGCCCCCTC 60.620 60.000 0.00 0.00 34.36 4.30
2266 2322 1.003835 TGTAACCCTAGCCCCCTCC 59.996 63.158 0.00 0.00 0.00 4.30
2267 2323 2.138831 GTAACCCTAGCCCCCTCCG 61.139 68.421 0.00 0.00 0.00 4.63
2268 2324 3.399911 TAACCCTAGCCCCCTCCGG 62.400 68.421 0.00 0.00 0.00 5.14
2271 2327 4.798682 CCTAGCCCCCTCCGGTGT 62.799 72.222 0.00 0.00 0.00 4.16
2272 2328 3.155167 CTAGCCCCCTCCGGTGTC 61.155 72.222 0.00 0.00 0.00 3.67
2273 2329 3.680196 TAGCCCCCTCCGGTGTCT 61.680 66.667 0.00 0.00 0.00 3.41
2274 2330 2.294170 CTAGCCCCCTCCGGTGTCTA 62.294 65.000 0.00 0.00 0.00 2.59
2275 2331 1.661990 TAGCCCCCTCCGGTGTCTAT 61.662 60.000 0.00 0.00 0.00 1.98
2276 2332 1.152398 GCCCCCTCCGGTGTCTATA 60.152 63.158 0.00 0.00 0.00 1.31
2277 2333 0.544595 GCCCCCTCCGGTGTCTATAT 60.545 60.000 0.00 0.00 0.00 0.86
2278 2334 1.272872 GCCCCCTCCGGTGTCTATATA 60.273 57.143 0.00 0.00 0.00 0.86
2279 2335 2.824303 GCCCCCTCCGGTGTCTATATAA 60.824 54.545 0.00 0.00 0.00 0.98
2280 2336 3.513517 CCCCCTCCGGTGTCTATATAAA 58.486 50.000 0.00 0.00 0.00 1.40
2281 2337 3.260128 CCCCCTCCGGTGTCTATATAAAC 59.740 52.174 0.00 0.00 0.00 2.01
2282 2338 3.260128 CCCCTCCGGTGTCTATATAAACC 59.740 52.174 0.00 0.68 0.00 3.27
2283 2339 3.899360 CCCTCCGGTGTCTATATAAACCA 59.101 47.826 0.00 0.00 32.69 3.67
2284 2340 4.021368 CCCTCCGGTGTCTATATAAACCAG 60.021 50.000 0.00 0.13 32.69 4.00
2285 2341 4.831155 CCTCCGGTGTCTATATAAACCAGA 59.169 45.833 0.00 3.55 32.69 3.86
2286 2342 5.047943 CCTCCGGTGTCTATATAAACCAGAG 60.048 48.000 0.00 11.73 37.10 3.35
2287 2343 4.831155 TCCGGTGTCTATATAAACCAGAGG 59.169 45.833 0.00 0.00 32.69 3.69
2288 2344 4.021368 CCGGTGTCTATATAAACCAGAGGG 60.021 50.000 0.00 0.00 41.29 4.30
2318 2374 5.862924 CGTAGGACAAGAACAACAATCAT 57.137 39.130 0.00 0.00 0.00 2.45
2319 2375 6.961359 CGTAGGACAAGAACAACAATCATA 57.039 37.500 0.00 0.00 0.00 2.15
2320 2376 6.762108 CGTAGGACAAGAACAACAATCATAC 58.238 40.000 0.00 0.00 0.00 2.39
2321 2377 6.183360 CGTAGGACAAGAACAACAATCATACC 60.183 42.308 0.00 0.00 0.00 2.73
2322 2378 5.630121 AGGACAAGAACAACAATCATACCA 58.370 37.500 0.00 0.00 0.00 3.25
2323 2379 6.248433 AGGACAAGAACAACAATCATACCAT 58.752 36.000 0.00 0.00 0.00 3.55
2324 2380 7.402054 AGGACAAGAACAACAATCATACCATA 58.598 34.615 0.00 0.00 0.00 2.74
2325 2381 7.554118 AGGACAAGAACAACAATCATACCATAG 59.446 37.037 0.00 0.00 0.00 2.23
2326 2382 7.201732 GGACAAGAACAACAATCATACCATAGG 60.202 40.741 0.00 0.00 0.00 2.57
2327 2383 6.095440 ACAAGAACAACAATCATACCATAGGC 59.905 38.462 0.00 0.00 0.00 3.93
2328 2384 6.006275 AGAACAACAATCATACCATAGGCT 57.994 37.500 0.00 0.00 0.00 4.58
2329 2385 7.136822 AGAACAACAATCATACCATAGGCTA 57.863 36.000 0.00 0.00 0.00 3.93
2330 2386 7.220030 AGAACAACAATCATACCATAGGCTAG 58.780 38.462 0.00 0.00 0.00 3.42
2331 2387 5.308825 ACAACAATCATACCATAGGCTAGC 58.691 41.667 6.04 6.04 0.00 3.42
2332 2388 5.072329 ACAACAATCATACCATAGGCTAGCT 59.928 40.000 15.72 3.22 0.00 3.32
2333 2389 5.832539 ACAATCATACCATAGGCTAGCTT 57.167 39.130 15.72 10.11 0.00 3.74
2334 2390 6.192970 ACAATCATACCATAGGCTAGCTTT 57.807 37.500 15.72 6.10 0.00 3.51
2335 2391 6.605119 ACAATCATACCATAGGCTAGCTTTT 58.395 36.000 15.72 0.00 0.00 2.27
2336 2392 7.745717 ACAATCATACCATAGGCTAGCTTTTA 58.254 34.615 15.72 5.69 0.00 1.52
2337 2393 7.880195 ACAATCATACCATAGGCTAGCTTTTAG 59.120 37.037 15.72 3.93 0.00 1.85
2338 2394 6.360370 TCATACCATAGGCTAGCTTTTAGG 57.640 41.667 15.72 11.92 0.00 2.69
2339 2395 5.248477 TCATACCATAGGCTAGCTTTTAGGG 59.752 44.000 15.72 16.82 0.00 3.53
2340 2396 3.394645 ACCATAGGCTAGCTTTTAGGGT 58.605 45.455 15.72 17.41 0.00 4.34
2341 2397 3.786450 ACCATAGGCTAGCTTTTAGGGTT 59.214 43.478 15.72 4.99 26.49 4.11
2342 2398 4.229812 ACCATAGGCTAGCTTTTAGGGTTT 59.770 41.667 15.72 0.00 26.49 3.27
2343 2399 5.430745 ACCATAGGCTAGCTTTTAGGGTTTA 59.569 40.000 15.72 0.00 26.49 2.01
2344 2400 5.998363 CCATAGGCTAGCTTTTAGGGTTTAG 59.002 44.000 15.72 0.00 0.00 1.85
2345 2401 3.887352 AGGCTAGCTTTTAGGGTTTAGC 58.113 45.455 15.72 0.00 34.32 3.09
2346 2402 2.950309 GGCTAGCTTTTAGGGTTTAGCC 59.050 50.000 15.72 4.76 44.26 3.93
2347 2403 3.371702 GGCTAGCTTTTAGGGTTTAGCCT 60.372 47.826 15.72 5.72 46.03 4.58
2348 2404 3.878103 GCTAGCTTTTAGGGTTTAGCCTC 59.122 47.826 7.70 0.00 37.43 4.70
2349 2405 4.384318 GCTAGCTTTTAGGGTTTAGCCTCT 60.384 45.833 7.70 0.00 37.43 3.69
2350 2406 5.163332 GCTAGCTTTTAGGGTTTAGCCTCTA 60.163 44.000 7.70 0.00 37.43 2.43
2351 2407 5.100344 AGCTTTTAGGGTTTAGCCTCTAC 57.900 43.478 3.32 0.00 37.43 2.59
2352 2408 3.869832 GCTTTTAGGGTTTAGCCTCTACG 59.130 47.826 3.32 0.00 37.43 3.51
2353 2409 4.382362 GCTTTTAGGGTTTAGCCTCTACGA 60.382 45.833 3.32 0.00 37.43 3.43
2354 2410 5.684291 GCTTTTAGGGTTTAGCCTCTACGAT 60.684 44.000 3.32 0.00 37.43 3.73
2355 2411 5.526506 TTTAGGGTTTAGCCTCTACGATC 57.473 43.478 3.32 0.00 37.43 3.69
2356 2412 3.315880 AGGGTTTAGCCTCTACGATCT 57.684 47.619 0.00 0.00 37.43 2.75
2357 2413 3.644335 AGGGTTTAGCCTCTACGATCTT 58.356 45.455 0.00 0.00 37.43 2.40
2358 2414 3.385111 AGGGTTTAGCCTCTACGATCTTG 59.615 47.826 0.00 0.00 37.43 3.02
2359 2415 3.132467 GGGTTTAGCCTCTACGATCTTGT 59.868 47.826 0.00 0.00 37.43 3.16
2360 2416 4.113354 GGTTTAGCCTCTACGATCTTGTG 58.887 47.826 0.00 0.00 0.00 3.33
2361 2417 4.113354 GTTTAGCCTCTACGATCTTGTGG 58.887 47.826 0.00 0.00 0.00 4.17
2362 2418 1.853963 AGCCTCTACGATCTTGTGGT 58.146 50.000 0.00 0.00 0.00 4.16
2363 2419 3.014304 AGCCTCTACGATCTTGTGGTA 57.986 47.619 0.00 0.00 0.00 3.25
2364 2420 2.952978 AGCCTCTACGATCTTGTGGTAG 59.047 50.000 0.00 0.00 39.64 3.18
2365 2421 2.950309 GCCTCTACGATCTTGTGGTAGA 59.050 50.000 7.08 7.08 43.28 2.59
2366 2422 3.570550 GCCTCTACGATCTTGTGGTAGAT 59.429 47.826 7.58 0.00 44.07 1.98
2367 2423 4.320641 GCCTCTACGATCTTGTGGTAGATC 60.321 50.000 7.58 0.00 44.07 2.75
2375 2431 6.900568 GATCTTGTGGTAGATCAACTCTTG 57.099 41.667 8.37 0.00 46.37 3.02
2376 2432 5.808366 TCTTGTGGTAGATCAACTCTTGT 57.192 39.130 0.00 0.00 35.28 3.16
2377 2433 6.911250 TCTTGTGGTAGATCAACTCTTGTA 57.089 37.500 0.00 0.00 35.28 2.41
2378 2434 7.297936 TCTTGTGGTAGATCAACTCTTGTAA 57.702 36.000 0.00 0.00 35.28 2.41
2379 2435 7.907389 TCTTGTGGTAGATCAACTCTTGTAAT 58.093 34.615 0.00 0.00 35.28 1.89
2380 2436 9.031537 TCTTGTGGTAGATCAACTCTTGTAATA 57.968 33.333 0.00 0.00 35.28 0.98
2381 2437 8.997621 TTGTGGTAGATCAACTCTTGTAATAC 57.002 34.615 0.00 0.00 35.28 1.89
2382 2438 8.362464 TGTGGTAGATCAACTCTTGTAATACT 57.638 34.615 0.00 0.00 35.28 2.12
2383 2439 8.467598 TGTGGTAGATCAACTCTTGTAATACTC 58.532 37.037 0.00 0.00 35.28 2.59
2384 2440 8.467598 GTGGTAGATCAACTCTTGTAATACTCA 58.532 37.037 0.00 0.00 35.28 3.41
2385 2441 9.201989 TGGTAGATCAACTCTTGTAATACTCAT 57.798 33.333 0.00 0.00 35.28 2.90
2405 2461 8.325421 ACTCATATCATCAAGATCAATCAAGC 57.675 34.615 0.00 0.00 38.19 4.01
2406 2462 7.937394 ACTCATATCATCAAGATCAATCAAGCA 59.063 33.333 0.00 0.00 38.19 3.91
2407 2463 8.324163 TCATATCATCAAGATCAATCAAGCAG 57.676 34.615 0.00 0.00 38.19 4.24
2408 2464 7.390718 TCATATCATCAAGATCAATCAAGCAGG 59.609 37.037 0.00 0.00 38.19 4.85
2409 2465 5.106876 TCATCAAGATCAATCAAGCAGGA 57.893 39.130 0.00 0.00 0.00 3.86
2410 2466 5.503002 TCATCAAGATCAATCAAGCAGGAA 58.497 37.500 0.00 0.00 0.00 3.36
2411 2467 5.589050 TCATCAAGATCAATCAAGCAGGAAG 59.411 40.000 0.00 0.00 0.00 3.46
2412 2468 4.914983 TCAAGATCAATCAAGCAGGAAGT 58.085 39.130 0.00 0.00 0.00 3.01
2413 2469 6.053632 TCAAGATCAATCAAGCAGGAAGTA 57.946 37.500 0.00 0.00 0.00 2.24
2414 2470 6.111382 TCAAGATCAATCAAGCAGGAAGTAG 58.889 40.000 0.00 0.00 0.00 2.57
2415 2471 5.033589 AGATCAATCAAGCAGGAAGTAGG 57.966 43.478 0.00 0.00 0.00 3.18
2416 2472 3.634397 TCAATCAAGCAGGAAGTAGGG 57.366 47.619 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 5.825679 AGTCGCTCATGTTACTCTCTTCTAT 59.174 40.000 0.00 0.00 0.00 1.98
315 316 2.967201 TCGGCCTAATAAATCCGGAAGA 59.033 45.455 9.01 0.00 41.98 2.87
526 527 5.112129 ACTTCTTCGCCCAGGTTTATTAT 57.888 39.130 0.00 0.00 0.00 1.28
614 619 8.647796 ACATGTTCGTATGGATTTCCTAAGATA 58.352 33.333 0.00 0.00 36.82 1.98
687 692 9.139734 AGATATGGACAACTTCATTTATGCAAT 57.860 29.630 0.00 0.00 0.00 3.56
690 695 8.844244 AGAAGATATGGACAACTTCATTTATGC 58.156 33.333 0.00 0.00 40.47 3.14
827 833 5.944599 AGATATGTTTGCATGATCCCATCTC 59.055 40.000 0.00 0.00 36.58 2.75
1008 1017 1.002134 TAGGCTTGGCACCTTGAGC 60.002 57.895 1.56 0.46 38.81 4.26
1057 1069 2.936498 CCATACAACGCTTACCAGGAAG 59.064 50.000 0.00 0.00 0.00 3.46
1170 1193 7.038658 GGAGGCTATGGTGTTCTATAGAGAAAT 60.039 40.741 0.38 0.00 43.38 2.17
1356 1381 2.226200 TGTGGCACGAATGATTTCACAG 59.774 45.455 13.77 0.00 31.29 3.66
1368 1393 3.127895 GCATAAAAATAGGTGTGGCACGA 59.872 43.478 13.77 0.00 34.83 4.35
1433 1458 5.539955 TGCATCATACATCCTGAAGTAGCTA 59.460 40.000 0.00 0.00 0.00 3.32
1495 1539 6.836242 AGAGTCTCAACTTCTTCCATTTCTT 58.164 36.000 1.94 0.00 35.28 2.52
1498 1542 7.546250 TCTAGAGTCTCAACTTCTTCCATTT 57.454 36.000 0.00 0.00 35.28 2.32
1527 1571 8.697292 AGTGGAGATCTGTTAGTAATAAGGAAC 58.303 37.037 0.00 0.00 0.00 3.62
1559 1606 3.184382 TCCACTCCACTCCATCAAGTA 57.816 47.619 0.00 0.00 0.00 2.24
1694 1749 7.232737 CCCTAATTCCCATTCCCTAATACAAAC 59.767 40.741 0.00 0.00 0.00 2.93
1723 1778 9.459640 GAAACAAGAAAATTTAAGTCCTACACC 57.540 33.333 0.00 0.00 0.00 4.16
1740 1795 3.470709 CAGCTCTCCAGTGAAACAAGAA 58.529 45.455 0.00 0.00 41.43 2.52
1741 1796 2.224378 CCAGCTCTCCAGTGAAACAAGA 60.224 50.000 0.00 0.00 41.43 3.02
1749 1804 0.622665 AATTCCCCAGCTCTCCAGTG 59.377 55.000 0.00 0.00 0.00 3.66
1751 1806 3.137176 TGATTAATTCCCCAGCTCTCCAG 59.863 47.826 0.00 0.00 0.00 3.86
1757 1812 6.018433 ACACTATTGATTAATTCCCCAGCT 57.982 37.500 0.00 0.00 0.00 4.24
1785 1840 8.692710 TCTCTAATGGTCGTTGTGTTAATCTAT 58.307 33.333 0.00 0.00 0.00 1.98
1896 1952 6.395629 ACTTAGCGCTCTTTATGTGTTCTTA 58.604 36.000 16.34 0.00 0.00 2.10
1898 1954 4.822026 ACTTAGCGCTCTTTATGTGTTCT 58.178 39.130 16.34 0.00 0.00 3.01
1922 1978 7.012894 TCGCTTTATCCATTATTTGGTAACCAG 59.987 37.037 0.00 0.00 46.52 4.00
2077 2133 1.122019 CGAGGACCCCCTAATCCAGG 61.122 65.000 0.00 0.00 44.53 4.45
2078 2134 1.122019 CCGAGGACCCCCTAATCCAG 61.122 65.000 0.00 0.00 44.53 3.86
2079 2135 1.074775 CCGAGGACCCCCTAATCCA 60.075 63.158 0.00 0.00 44.53 3.41
2080 2136 1.120184 GTCCGAGGACCCCCTAATCC 61.120 65.000 11.07 0.00 44.53 3.01
2081 2137 0.398098 TGTCCGAGGACCCCCTAATC 60.398 60.000 18.57 0.00 44.53 1.75
2082 2138 0.398664 CTGTCCGAGGACCCCCTAAT 60.399 60.000 18.57 0.00 44.53 1.73
2083 2139 1.001248 CTGTCCGAGGACCCCCTAA 59.999 63.158 18.57 0.00 44.53 2.69
2084 2140 2.687902 CTGTCCGAGGACCCCCTA 59.312 66.667 18.57 0.00 44.53 3.53
2096 2152 4.868314 AAAGTATATAGTCCGGCTGTCC 57.132 45.455 0.00 0.00 0.00 4.02
2097 2153 5.400703 GCTAAAGTATATAGTCCGGCTGTC 58.599 45.833 0.00 0.00 0.00 3.51
2098 2154 4.220163 GGCTAAAGTATATAGTCCGGCTGT 59.780 45.833 0.00 0.00 0.00 4.40
2099 2155 4.674623 CGGCTAAAGTATATAGTCCGGCTG 60.675 50.000 0.00 5.69 36.89 4.85
2100 2156 3.442977 CGGCTAAAGTATATAGTCCGGCT 59.557 47.826 0.00 0.00 36.89 5.52
2101 2157 3.428589 CCGGCTAAAGTATATAGTCCGGC 60.429 52.174 17.10 9.52 44.83 6.13
2102 2158 4.367386 CCGGCTAAAGTATATAGTCCGG 57.633 50.000 16.09 16.09 45.08 5.14
2103 2159 4.699257 AGTCCGGCTAAAGTATATAGTCCG 59.301 45.833 0.00 7.97 38.56 4.79
2104 2160 7.878547 ATAGTCCGGCTAAAGTATATAGTCC 57.121 40.000 9.24 0.00 32.72 3.85
2105 2161 8.189460 CCAATAGTCCGGCTAAAGTATATAGTC 58.811 40.741 9.24 0.00 32.72 2.59
2106 2162 7.892241 TCCAATAGTCCGGCTAAAGTATATAGT 59.108 37.037 9.24 0.00 32.72 2.12
2107 2163 8.189460 GTCCAATAGTCCGGCTAAAGTATATAG 58.811 40.741 9.24 0.00 32.72 1.31
2108 2164 7.892241 AGTCCAATAGTCCGGCTAAAGTATATA 59.108 37.037 9.24 0.00 32.72 0.86
2109 2165 6.724905 AGTCCAATAGTCCGGCTAAAGTATAT 59.275 38.462 9.24 0.00 32.72 0.86
2110 2166 6.073314 AGTCCAATAGTCCGGCTAAAGTATA 58.927 40.000 9.24 0.00 32.72 1.47
2111 2167 4.900054 AGTCCAATAGTCCGGCTAAAGTAT 59.100 41.667 9.24 0.00 32.72 2.12
2112 2168 4.284178 AGTCCAATAGTCCGGCTAAAGTA 58.716 43.478 9.24 0.00 32.72 2.24
2113 2169 3.105283 AGTCCAATAGTCCGGCTAAAGT 58.895 45.455 9.24 0.00 32.72 2.66
2114 2170 3.821421 AGTCCAATAGTCCGGCTAAAG 57.179 47.619 9.24 5.67 32.72 1.85
2115 2171 4.897076 TCATAGTCCAATAGTCCGGCTAAA 59.103 41.667 9.24 0.00 32.72 1.85
2116 2172 4.476297 TCATAGTCCAATAGTCCGGCTAA 58.524 43.478 9.24 0.00 32.72 3.09
2117 2173 4.108501 TCATAGTCCAATAGTCCGGCTA 57.891 45.455 0.00 1.72 0.00 3.93
2118 2174 2.958818 TCATAGTCCAATAGTCCGGCT 58.041 47.619 0.00 0.00 0.00 5.52
2119 2175 3.321111 TCTTCATAGTCCAATAGTCCGGC 59.679 47.826 0.00 0.00 0.00 6.13
2120 2176 5.730296 ATCTTCATAGTCCAATAGTCCGG 57.270 43.478 0.00 0.00 0.00 5.14
2121 2177 7.215719 TGTATCTTCATAGTCCAATAGTCCG 57.784 40.000 0.00 0.00 0.00 4.79
2122 2178 8.861086 TCTTGTATCTTCATAGTCCAATAGTCC 58.139 37.037 0.00 0.00 0.00 3.85
2128 2184 9.605275 CTTCAATCTTGTATCTTCATAGTCCAA 57.395 33.333 0.00 0.00 0.00 3.53
2129 2185 8.981659 TCTTCAATCTTGTATCTTCATAGTCCA 58.018 33.333 0.00 0.00 0.00 4.02
2130 2186 9.255304 GTCTTCAATCTTGTATCTTCATAGTCC 57.745 37.037 0.00 0.00 0.00 3.85
2134 2190 9.521503 CGAAGTCTTCAATCTTGTATCTTCATA 57.478 33.333 12.99 0.00 32.10 2.15
2135 2191 8.037758 ACGAAGTCTTCAATCTTGTATCTTCAT 58.962 33.333 12.99 0.00 29.74 2.57
2136 2192 7.378966 ACGAAGTCTTCAATCTTGTATCTTCA 58.621 34.615 12.99 0.00 29.74 3.02
2137 2193 7.820044 ACGAAGTCTTCAATCTTGTATCTTC 57.180 36.000 12.99 0.00 29.74 2.87
2168 2224 0.687757 CAAGGAGAGTCCCATCCGGA 60.688 60.000 6.61 6.61 40.73 5.14
2169 2225 1.690219 CCAAGGAGAGTCCCATCCGG 61.690 65.000 0.00 0.00 40.73 5.14
2170 2226 1.826024 CCAAGGAGAGTCCCATCCG 59.174 63.158 1.17 0.00 40.73 4.18
2171 2227 1.529309 GCCAAGGAGAGTCCCATCC 59.471 63.158 0.00 0.00 37.19 3.51
2172 2228 1.144936 CGCCAAGGAGAGTCCCATC 59.855 63.158 0.00 0.00 37.19 3.51
2173 2229 1.613630 ACGCCAAGGAGAGTCCCAT 60.614 57.895 0.00 0.00 37.19 4.00
2174 2230 2.203788 ACGCCAAGGAGAGTCCCA 60.204 61.111 0.00 0.00 37.19 4.37
2175 2231 2.266055 CACGCCAAGGAGAGTCCC 59.734 66.667 0.00 0.00 37.19 4.46
2176 2232 1.827399 TTCCACGCCAAGGAGAGTCC 61.827 60.000 0.00 0.00 36.33 3.85
2177 2233 0.390472 CTTCCACGCCAAGGAGAGTC 60.390 60.000 0.00 0.00 36.33 3.36
2178 2234 1.674057 CTTCCACGCCAAGGAGAGT 59.326 57.895 0.00 0.00 36.33 3.24
2179 2235 1.078848 CCTTCCACGCCAAGGAGAG 60.079 63.158 2.12 0.00 42.94 3.20
2180 2236 3.068881 CCTTCCACGCCAAGGAGA 58.931 61.111 2.12 0.00 42.94 3.71
2181 2237 2.747855 GCCTTCCACGCCAAGGAG 60.748 66.667 10.97 0.00 42.94 3.69
2182 2238 3.126703 TTGCCTTCCACGCCAAGGA 62.127 57.895 10.97 0.00 42.94 3.36
2183 2239 2.597217 TTGCCTTCCACGCCAAGG 60.597 61.111 3.73 3.73 43.13 3.61
2184 2240 2.956987 CTTGCCTTCCACGCCAAG 59.043 61.111 0.00 0.00 0.00 3.61
2185 2241 3.294493 GCTTGCCTTCCACGCCAA 61.294 61.111 0.00 0.00 32.93 4.52
2186 2242 3.790416 AAGCTTGCCTTCCACGCCA 62.790 57.895 0.00 0.00 39.36 5.69
2187 2243 2.985847 AAGCTTGCCTTCCACGCC 60.986 61.111 0.00 0.00 39.36 5.68
2188 2244 2.256461 CAAGCTTGCCTTCCACGC 59.744 61.111 14.65 0.00 38.87 5.34
2189 2245 2.956987 CCAAGCTTGCCTTCCACG 59.043 61.111 21.43 0.62 0.00 4.94
2190 2246 1.747325 TTGCCAAGCTTGCCTTCCAC 61.747 55.000 21.43 4.32 0.00 4.02
2191 2247 0.832983 ATTGCCAAGCTTGCCTTCCA 60.833 50.000 21.43 9.04 0.00 3.53
2192 2248 1.134995 GTATTGCCAAGCTTGCCTTCC 60.135 52.381 21.43 6.63 0.00 3.46
2193 2249 1.468054 CGTATTGCCAAGCTTGCCTTC 60.468 52.381 21.43 9.67 0.00 3.46
2194 2250 0.527565 CGTATTGCCAAGCTTGCCTT 59.472 50.000 21.43 7.68 0.00 4.35
2195 2251 1.315257 CCGTATTGCCAAGCTTGCCT 61.315 55.000 21.43 7.17 0.00 4.75
2196 2252 1.139520 CCGTATTGCCAAGCTTGCC 59.860 57.895 21.43 11.17 0.00 4.52
2197 2253 0.740737 ATCCGTATTGCCAAGCTTGC 59.259 50.000 21.43 16.17 0.00 4.01
2198 2254 3.565482 ACATATCCGTATTGCCAAGCTTG 59.435 43.478 19.93 19.93 0.00 4.01
2199 2255 3.820557 ACATATCCGTATTGCCAAGCTT 58.179 40.909 0.00 0.00 0.00 3.74
2200 2256 3.492102 ACATATCCGTATTGCCAAGCT 57.508 42.857 0.00 0.00 0.00 3.74
2201 2257 4.566004 TCTACATATCCGTATTGCCAAGC 58.434 43.478 0.00 0.00 0.00 4.01
2202 2258 6.634805 AGATCTACATATCCGTATTGCCAAG 58.365 40.000 0.00 0.00 0.00 3.61
2203 2259 6.351033 GGAGATCTACATATCCGTATTGCCAA 60.351 42.308 0.00 0.00 30.60 4.52
2204 2260 5.127194 GGAGATCTACATATCCGTATTGCCA 59.873 44.000 0.00 0.00 30.60 4.92
2205 2261 5.361285 AGGAGATCTACATATCCGTATTGCC 59.639 44.000 7.93 0.00 44.22 4.52
2206 2262 6.458232 AGGAGATCTACATATCCGTATTGC 57.542 41.667 7.93 0.00 44.22 3.56
2207 2263 6.039941 GGGAGGAGATCTACATATCCGTATTG 59.960 46.154 7.93 0.00 44.22 1.90
2208 2264 6.068735 AGGGAGGAGATCTACATATCCGTATT 60.069 42.308 7.93 0.00 44.22 1.89
2209 2265 5.433712 AGGGAGGAGATCTACATATCCGTAT 59.566 44.000 7.93 0.00 44.22 3.06
2210 2266 4.789159 AGGGAGGAGATCTACATATCCGTA 59.211 45.833 7.93 0.00 44.22 4.02
2211 2267 3.594232 AGGGAGGAGATCTACATATCCGT 59.406 47.826 7.93 4.42 44.22 4.69
2212 2268 4.243793 AGGGAGGAGATCTACATATCCG 57.756 50.000 7.93 0.00 44.22 4.18
2213 2269 5.337788 ACAAGGGAGGAGATCTACATATCC 58.662 45.833 7.93 5.41 40.35 2.59
2214 2270 7.093684 GGTTACAAGGGAGGAGATCTACATATC 60.094 44.444 7.93 0.00 0.00 1.63
2215 2271 6.726764 GGTTACAAGGGAGGAGATCTACATAT 59.273 42.308 7.93 0.00 0.00 1.78
2216 2272 6.075984 GGTTACAAGGGAGGAGATCTACATA 58.924 44.000 7.93 0.00 0.00 2.29
2217 2273 4.902448 GGTTACAAGGGAGGAGATCTACAT 59.098 45.833 7.93 0.00 0.00 2.29
2218 2274 4.287552 GGTTACAAGGGAGGAGATCTACA 58.712 47.826 7.93 0.00 0.00 2.74
2219 2275 3.318557 CGGTTACAAGGGAGGAGATCTAC 59.681 52.174 0.00 0.00 0.00 2.59
2220 2276 3.203710 TCGGTTACAAGGGAGGAGATCTA 59.796 47.826 0.00 0.00 0.00 1.98
2221 2277 2.024273 TCGGTTACAAGGGAGGAGATCT 60.024 50.000 0.00 0.00 0.00 2.75
2222 2278 2.101082 GTCGGTTACAAGGGAGGAGATC 59.899 54.545 0.00 0.00 0.00 2.75
2223 2279 2.108970 GTCGGTTACAAGGGAGGAGAT 58.891 52.381 0.00 0.00 0.00 2.75
2224 2280 1.076677 AGTCGGTTACAAGGGAGGAGA 59.923 52.381 0.00 0.00 0.00 3.71
2225 2281 1.477295 GAGTCGGTTACAAGGGAGGAG 59.523 57.143 0.00 0.00 0.00 3.69
2226 2282 1.076677 AGAGTCGGTTACAAGGGAGGA 59.923 52.381 0.00 0.00 0.00 3.71
2227 2283 1.204941 CAGAGTCGGTTACAAGGGAGG 59.795 57.143 0.00 0.00 0.00 4.30
2228 2284 1.893801 ACAGAGTCGGTTACAAGGGAG 59.106 52.381 0.00 0.00 0.00 4.30
2229 2285 1.616865 CACAGAGTCGGTTACAAGGGA 59.383 52.381 0.00 0.00 0.00 4.20
2230 2286 1.343465 ACACAGAGTCGGTTACAAGGG 59.657 52.381 0.00 0.00 0.00 3.95
2231 2287 2.814280 ACACAGAGTCGGTTACAAGG 57.186 50.000 0.00 0.00 0.00 3.61
2232 2288 3.985925 GGTTACACAGAGTCGGTTACAAG 59.014 47.826 0.00 0.00 0.00 3.16
2233 2289 3.243839 GGGTTACACAGAGTCGGTTACAA 60.244 47.826 0.00 0.00 0.00 2.41
2234 2290 2.297033 GGGTTACACAGAGTCGGTTACA 59.703 50.000 0.00 0.00 0.00 2.41
2235 2291 2.560105 AGGGTTACACAGAGTCGGTTAC 59.440 50.000 0.00 0.00 0.00 2.50
2236 2292 2.880443 AGGGTTACACAGAGTCGGTTA 58.120 47.619 0.00 0.00 0.00 2.85
2237 2293 1.713297 AGGGTTACACAGAGTCGGTT 58.287 50.000 0.00 0.00 0.00 4.44
2238 2294 2.444421 CTAGGGTTACACAGAGTCGGT 58.556 52.381 0.00 0.00 0.00 4.69
2239 2295 1.134560 GCTAGGGTTACACAGAGTCGG 59.865 57.143 0.00 0.00 0.00 4.79
2240 2296 1.134560 GGCTAGGGTTACACAGAGTCG 59.865 57.143 0.00 0.00 0.00 4.18
2241 2297 1.481363 GGGCTAGGGTTACACAGAGTC 59.519 57.143 0.00 0.00 0.00 3.36
2242 2298 1.569653 GGGCTAGGGTTACACAGAGT 58.430 55.000 0.00 0.00 0.00 3.24
2243 2299 0.831307 GGGGCTAGGGTTACACAGAG 59.169 60.000 0.00 0.00 0.00 3.35
2244 2300 0.619543 GGGGGCTAGGGTTACACAGA 60.620 60.000 0.00 0.00 0.00 3.41
2245 2301 0.620700 AGGGGGCTAGGGTTACACAG 60.621 60.000 0.00 0.00 0.00 3.66
2246 2302 0.619543 GAGGGGGCTAGGGTTACACA 60.620 60.000 0.00 0.00 0.00 3.72
2247 2303 1.343431 GGAGGGGGCTAGGGTTACAC 61.343 65.000 0.00 0.00 0.00 2.90
2248 2304 1.003835 GGAGGGGGCTAGGGTTACA 59.996 63.158 0.00 0.00 0.00 2.41
2249 2305 2.138831 CGGAGGGGGCTAGGGTTAC 61.139 68.421 0.00 0.00 0.00 2.50
2250 2306 2.284493 CGGAGGGGGCTAGGGTTA 59.716 66.667 0.00 0.00 0.00 2.85
2264 2320 4.831155 CCTCTGGTTTATATAGACACCGGA 59.169 45.833 9.46 12.52 41.56 5.14
2265 2321 4.021368 CCCTCTGGTTTATATAGACACCGG 60.021 50.000 0.00 0.00 37.06 5.28
2266 2322 4.587684 ACCCTCTGGTTTATATAGACACCG 59.412 45.833 5.83 0.00 44.75 4.94
2281 2337 1.755380 CCTACGGACTAAACCCTCTGG 59.245 57.143 0.00 0.00 37.80 3.86
2282 2338 2.731572 TCCTACGGACTAAACCCTCTG 58.268 52.381 0.00 0.00 0.00 3.35
2294 2350 3.823281 TTGTTGTTCTTGTCCTACGGA 57.177 42.857 0.00 0.00 0.00 4.69
2295 2351 4.062293 TGATTGTTGTTCTTGTCCTACGG 58.938 43.478 0.00 0.00 0.00 4.02
2296 2352 5.862924 ATGATTGTTGTTCTTGTCCTACG 57.137 39.130 0.00 0.00 0.00 3.51
2297 2353 6.653320 TGGTATGATTGTTGTTCTTGTCCTAC 59.347 38.462 0.00 0.00 0.00 3.18
2298 2354 6.774673 TGGTATGATTGTTGTTCTTGTCCTA 58.225 36.000 0.00 0.00 0.00 2.94
2299 2355 5.630121 TGGTATGATTGTTGTTCTTGTCCT 58.370 37.500 0.00 0.00 0.00 3.85
2300 2356 5.957842 TGGTATGATTGTTGTTCTTGTCC 57.042 39.130 0.00 0.00 0.00 4.02
2301 2357 7.679638 GCCTATGGTATGATTGTTGTTCTTGTC 60.680 40.741 0.00 0.00 0.00 3.18
2302 2358 6.095440 GCCTATGGTATGATTGTTGTTCTTGT 59.905 38.462 0.00 0.00 0.00 3.16
2303 2359 6.319658 AGCCTATGGTATGATTGTTGTTCTTG 59.680 38.462 0.00 0.00 0.00 3.02
2304 2360 6.426587 AGCCTATGGTATGATTGTTGTTCTT 58.573 36.000 0.00 0.00 0.00 2.52
2305 2361 6.006275 AGCCTATGGTATGATTGTTGTTCT 57.994 37.500 0.00 0.00 0.00 3.01
2306 2362 6.073003 GCTAGCCTATGGTATGATTGTTGTTC 60.073 42.308 2.29 0.00 0.00 3.18
2307 2363 5.765182 GCTAGCCTATGGTATGATTGTTGTT 59.235 40.000 2.29 0.00 0.00 2.83
2308 2364 5.072329 AGCTAGCCTATGGTATGATTGTTGT 59.928 40.000 12.13 0.00 0.00 3.32
2309 2365 5.555017 AGCTAGCCTATGGTATGATTGTTG 58.445 41.667 12.13 0.00 0.00 3.33
2310 2366 5.832539 AGCTAGCCTATGGTATGATTGTT 57.167 39.130 12.13 0.00 0.00 2.83
2311 2367 5.832539 AAGCTAGCCTATGGTATGATTGT 57.167 39.130 12.13 0.00 0.00 2.71
2312 2368 7.335422 CCTAAAAGCTAGCCTATGGTATGATTG 59.665 40.741 12.13 0.00 0.00 2.67
2313 2369 7.398024 CCTAAAAGCTAGCCTATGGTATGATT 58.602 38.462 12.13 0.00 0.00 2.57
2314 2370 6.069963 CCCTAAAAGCTAGCCTATGGTATGAT 60.070 42.308 12.13 0.00 0.00 2.45
2315 2371 5.248477 CCCTAAAAGCTAGCCTATGGTATGA 59.752 44.000 12.13 0.00 0.00 2.15
2316 2372 5.013183 ACCCTAAAAGCTAGCCTATGGTATG 59.987 44.000 12.13 0.00 0.00 2.39
2317 2373 5.163390 ACCCTAAAAGCTAGCCTATGGTAT 58.837 41.667 12.13 0.00 0.00 2.73
2318 2374 4.563782 ACCCTAAAAGCTAGCCTATGGTA 58.436 43.478 12.13 0.00 0.00 3.25
2319 2375 3.394645 ACCCTAAAAGCTAGCCTATGGT 58.605 45.455 12.13 10.17 0.00 3.55
2320 2376 4.439253 AACCCTAAAAGCTAGCCTATGG 57.561 45.455 12.13 9.56 0.00 2.74
2321 2377 5.470437 GCTAAACCCTAAAAGCTAGCCTATG 59.530 44.000 12.13 0.00 32.18 2.23
2322 2378 5.456330 GGCTAAACCCTAAAAGCTAGCCTAT 60.456 44.000 12.13 0.00 45.22 2.57
2323 2379 4.141551 GGCTAAACCCTAAAAGCTAGCCTA 60.142 45.833 12.13 0.00 45.22 3.93
2324 2380 3.371702 GGCTAAACCCTAAAAGCTAGCCT 60.372 47.826 12.13 0.00 45.22 4.58
2325 2381 2.950309 GGCTAAACCCTAAAAGCTAGCC 59.050 50.000 12.13 1.31 43.27 3.93
2326 2382 3.878103 GAGGCTAAACCCTAAAAGCTAGC 59.122 47.826 6.62 6.62 40.58 3.42
2327 2383 5.360649 AGAGGCTAAACCCTAAAAGCTAG 57.639 43.478 0.00 0.00 40.58 3.42
2328 2384 5.163478 CGTAGAGGCTAAACCCTAAAAGCTA 60.163 44.000 0.00 0.00 40.58 3.32
2329 2385 4.382793 CGTAGAGGCTAAACCCTAAAAGCT 60.383 45.833 0.00 0.00 40.58 3.74
2330 2386 3.869832 CGTAGAGGCTAAACCCTAAAAGC 59.130 47.826 0.00 0.00 40.58 3.51
2331 2387 5.334724 TCGTAGAGGCTAAACCCTAAAAG 57.665 43.478 0.00 0.00 40.58 2.27
2332 2388 5.659971 AGATCGTAGAGGCTAAACCCTAAAA 59.340 40.000 0.00 0.00 43.63 1.52
2333 2389 5.206587 AGATCGTAGAGGCTAAACCCTAAA 58.793 41.667 0.00 0.00 43.63 1.85
2334 2390 4.801164 AGATCGTAGAGGCTAAACCCTAA 58.199 43.478 0.00 0.00 43.63 2.69
2335 2391 4.450305 AGATCGTAGAGGCTAAACCCTA 57.550 45.455 0.00 0.00 43.63 3.53
2336 2392 3.315880 AGATCGTAGAGGCTAAACCCT 57.684 47.619 0.00 0.00 43.63 4.34
2337 2393 3.132467 ACAAGATCGTAGAGGCTAAACCC 59.868 47.826 0.00 0.00 43.63 4.11
2338 2394 4.113354 CACAAGATCGTAGAGGCTAAACC 58.887 47.826 0.00 0.00 43.63 3.27
2339 2395 4.113354 CCACAAGATCGTAGAGGCTAAAC 58.887 47.826 0.00 0.00 43.63 2.01
2340 2396 3.767673 ACCACAAGATCGTAGAGGCTAAA 59.232 43.478 0.00 0.00 43.63 1.85
2341 2397 3.362706 ACCACAAGATCGTAGAGGCTAA 58.637 45.455 0.00 0.00 43.63 3.09
2342 2398 3.014304 ACCACAAGATCGTAGAGGCTA 57.986 47.619 0.00 0.00 43.63 3.93
2343 2399 1.853963 ACCACAAGATCGTAGAGGCT 58.146 50.000 0.00 0.00 43.63 4.58
2344 2400 2.950309 TCTACCACAAGATCGTAGAGGC 59.050 50.000 3.99 0.00 43.63 4.70
2345 2401 5.365403 GATCTACCACAAGATCGTAGAGG 57.635 47.826 11.47 5.63 43.63 3.69
2353 2409 6.365970 ACAAGAGTTGATCTACCACAAGAT 57.634 37.500 3.54 0.00 37.23 2.40
2354 2410 5.808366 ACAAGAGTTGATCTACCACAAGA 57.192 39.130 3.54 0.00 37.23 3.02
2355 2411 9.088512 GTATTACAAGAGTTGATCTACCACAAG 57.911 37.037 3.54 0.00 37.23 3.16
2356 2412 8.812972 AGTATTACAAGAGTTGATCTACCACAA 58.187 33.333 3.54 0.00 37.23 3.33
2357 2413 8.362464 AGTATTACAAGAGTTGATCTACCACA 57.638 34.615 3.54 0.00 37.23 4.17
2358 2414 8.467598 TGAGTATTACAAGAGTTGATCTACCAC 58.532 37.037 3.54 0.00 37.23 4.16
2359 2415 8.589701 TGAGTATTACAAGAGTTGATCTACCA 57.410 34.615 3.54 0.00 37.23 3.25
2379 2435 9.433153 GCTTGATTGATCTTGATGATATGAGTA 57.567 33.333 0.00 0.00 35.14 2.59
2380 2436 7.937394 TGCTTGATTGATCTTGATGATATGAGT 59.063 33.333 0.00 0.00 35.14 3.41
2381 2437 8.324163 TGCTTGATTGATCTTGATGATATGAG 57.676 34.615 0.00 0.00 35.14 2.90
2382 2438 7.390718 CCTGCTTGATTGATCTTGATGATATGA 59.609 37.037 0.00 0.00 35.14 2.15
2383 2439 7.390718 TCCTGCTTGATTGATCTTGATGATATG 59.609 37.037 0.00 0.00 35.14 1.78
2384 2440 7.459234 TCCTGCTTGATTGATCTTGATGATAT 58.541 34.615 0.00 0.00 35.14 1.63
2385 2441 6.834107 TCCTGCTTGATTGATCTTGATGATA 58.166 36.000 0.00 0.00 35.14 2.15
2386 2442 5.691896 TCCTGCTTGATTGATCTTGATGAT 58.308 37.500 0.00 0.00 38.27 2.45
2387 2443 5.106876 TCCTGCTTGATTGATCTTGATGA 57.893 39.130 0.00 0.00 0.00 2.92
2388 2444 5.357314 ACTTCCTGCTTGATTGATCTTGATG 59.643 40.000 0.00 0.00 0.00 3.07
2389 2445 5.507637 ACTTCCTGCTTGATTGATCTTGAT 58.492 37.500 0.00 0.00 0.00 2.57
2390 2446 4.914983 ACTTCCTGCTTGATTGATCTTGA 58.085 39.130 0.00 0.00 0.00 3.02
2391 2447 5.296283 CCTACTTCCTGCTTGATTGATCTTG 59.704 44.000 0.00 0.00 0.00 3.02
2392 2448 5.435291 CCTACTTCCTGCTTGATTGATCTT 58.565 41.667 0.00 0.00 0.00 2.40
2393 2449 4.141528 CCCTACTTCCTGCTTGATTGATCT 60.142 45.833 0.00 0.00 0.00 2.75
2394 2450 4.133078 CCCTACTTCCTGCTTGATTGATC 58.867 47.826 0.00 0.00 0.00 2.92
2395 2451 4.162040 CCCTACTTCCTGCTTGATTGAT 57.838 45.455 0.00 0.00 0.00 2.57
2396 2452 3.634397 CCCTACTTCCTGCTTGATTGA 57.366 47.619 0.00 0.00 0.00 2.57


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.