Multiple sequence alignment - TraesCS5B01G008300

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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 TraesCS5B01G008300 chr5B 100.000 2222 0 0 1 2222 9039754 9041975 0.000000e+00 4104
1 TraesCS5B01G008300 chr3A 97.449 1529 37 2 1 1528 675317806 675316279 0.000000e+00 2606
2 TraesCS5B01G008300 chr3A 92.580 849 61 2 681 1528 617439291 617440138 0.000000e+00 1218
3 TraesCS5B01G008300 chr3B 93.868 848 50 2 681 1528 77702593 77703438 0.000000e+00 1277
4 TraesCS5B01G008300 chr3B 93.411 683 44 1 1 682 452906589 452907271 0.000000e+00 1011
5 TraesCS5B01G008300 chr3B 91.789 682 55 1 1 682 77701802 77702482 0.000000e+00 948
6 TraesCS5B01G008300 chr3B 87.092 612 47 4 71 682 572675989 572676568 0.000000e+00 664
7 TraesCS5B01G008300 chr7B 93.302 851 56 1 678 1528 226424074 226424923 0.000000e+00 1254
8 TraesCS5B01G008300 chr7B 92.857 854 50 8 678 1528 290954490 290953645 0.000000e+00 1229
9 TraesCS5B01G008300 chr7B 93.119 683 46 1 1 682 290955275 290954593 0.000000e+00 1000
10 TraesCS5B01G008300 chr7B 92.229 682 52 1 1 682 692793555 692794235 0.000000e+00 965
11 TraesCS5B01G008300 chr7B 92.059 680 51 2 1 679 692826267 692826944 0.000000e+00 953
12 TraesCS5B01G008300 chr5A 92.840 852 59 2 678 1528 33170550 33171400 0.000000e+00 1234
13 TraesCS5B01G008300 chr5A 91.324 680 56 3 1 679 33169763 33170440 0.000000e+00 926
14 TraesCS5B01G008300 chr5A 82.450 547 57 23 1586 2105 7007434 7007968 2.020000e-120 442
15 TraesCS5B01G008300 chr7A 92.479 851 62 2 678 1528 709417338 709418186 0.000000e+00 1216
16 TraesCS5B01G008300 chr4B 92.362 851 62 3 678 1528 622489168 622488321 0.000000e+00 1208
17 TraesCS5B01G008300 chr2B 92.173 856 64 3 674 1528 631331667 631332520 0.000000e+00 1206
18 TraesCS5B01G008300 chrUn 91.104 607 51 2 78 682 278600489 278599884 0.000000e+00 819
19 TraesCS5B01G008300 chrUn 91.139 553 45 3 23 573 278600489 278601039 0.000000e+00 747


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 TraesCS5B01G008300 chr5B 9039754 9041975 2221 False 4104.0 4104 100.0000 1 2222 1 chr5B.!!$F1 2221
1 TraesCS5B01G008300 chr3A 675316279 675317806 1527 True 2606.0 2606 97.4490 1 1528 1 chr3A.!!$R1 1527
2 TraesCS5B01G008300 chr3A 617439291 617440138 847 False 1218.0 1218 92.5800 681 1528 1 chr3A.!!$F1 847
3 TraesCS5B01G008300 chr3B 77701802 77703438 1636 False 1112.5 1277 92.8285 1 1528 2 chr3B.!!$F3 1527
4 TraesCS5B01G008300 chr3B 452906589 452907271 682 False 1011.0 1011 93.4110 1 682 1 chr3B.!!$F1 681
5 TraesCS5B01G008300 chr3B 572675989 572676568 579 False 664.0 664 87.0920 71 682 1 chr3B.!!$F2 611
6 TraesCS5B01G008300 chr7B 226424074 226424923 849 False 1254.0 1254 93.3020 678 1528 1 chr7B.!!$F1 850
7 TraesCS5B01G008300 chr7B 290953645 290955275 1630 True 1114.5 1229 92.9880 1 1528 2 chr7B.!!$R1 1527
8 TraesCS5B01G008300 chr7B 692793555 692794235 680 False 965.0 965 92.2290 1 682 1 chr7B.!!$F2 681
9 TraesCS5B01G008300 chr7B 692826267 692826944 677 False 953.0 953 92.0590 1 679 1 chr7B.!!$F3 678
10 TraesCS5B01G008300 chr5A 33169763 33171400 1637 False 1080.0 1234 92.0820 1 1528 2 chr5A.!!$F2 1527
11 TraesCS5B01G008300 chr5A 7007434 7007968 534 False 442.0 442 82.4500 1586 2105 1 chr5A.!!$F1 519
12 TraesCS5B01G008300 chr7A 709417338 709418186 848 False 1216.0 1216 92.4790 678 1528 1 chr7A.!!$F1 850
13 TraesCS5B01G008300 chr4B 622488321 622489168 847 True 1208.0 1208 92.3620 678 1528 1 chr4B.!!$R1 850
14 TraesCS5B01G008300 chr2B 631331667 631332520 853 False 1206.0 1206 92.1730 674 1528 1 chr2B.!!$F1 854
15 TraesCS5B01G008300 chrUn 278599884 278600489 605 True 819.0 819 91.1040 78 682 1 chrUn.!!$R1 604
16 TraesCS5B01G008300 chrUn 278600489 278601039 550 False 747.0 747 91.1390 23 573 1 chrUn.!!$F1 550

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
87 88 3.270027 CAAGGAAGCCGACATGAACATA 58.73 45.455 0.0 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2012 0.664761 CGCGACCGTTATCCTAGGAA 59.335 55.0 17.3 2.36 0.0 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
87 88 3.270027 CAAGGAAGCCGACATGAACATA 58.730 45.455 0.00 0.00 0.00 2.29
101 102 9.034544 CGACATGAACATAAGAAGTAATCATGA 57.965 33.333 16.96 0.00 43.18 3.07
132 133 4.869297 AGATTCTGCATCTTGACTTCTTCG 59.131 41.667 0.00 0.00 39.47 3.79
515 521 7.349412 AGTCTTCTTAGCTATTCCAATACGT 57.651 36.000 0.00 0.00 0.00 3.57
585 591 6.131264 TCATTTTACTCCCTATGTAGTCCGA 58.869 40.000 0.00 0.00 0.00 4.55
1277 1399 6.460103 AGTTTCCTAATAGGATGGATGCAT 57.540 37.500 10.21 0.00 45.34 3.96
1324 1446 6.897413 AGGATGCACCCTTGATTATTAGTTTT 59.103 34.615 0.00 0.00 40.05 2.43
1396 1519 5.689514 CGGTCAGTCAATGTAAATTGCAAAA 59.310 36.000 1.71 0.00 0.00 2.44
1486 1609 5.109903 GTGGTATTGGATCTGTGTACACTC 58.890 45.833 25.60 15.17 0.00 3.51
1660 1784 0.471591 TGAGGCAAAAGCCCCACAAT 60.472 50.000 2.33 0.00 0.00 2.71
1662 1786 1.194121 AGGCAAAAGCCCCACAATCC 61.194 55.000 2.33 0.00 0.00 3.01
1664 1788 1.194121 GCAAAAGCCCCACAATCCCT 61.194 55.000 0.00 0.00 0.00 4.20
1665 1789 0.897621 CAAAAGCCCCACAATCCCTC 59.102 55.000 0.00 0.00 0.00 4.30
1666 1790 0.252239 AAAAGCCCCACAATCCCTCC 60.252 55.000 0.00 0.00 0.00 4.30
1669 1793 1.078347 GCCCCACAATCCCTCCAAA 59.922 57.895 0.00 0.00 0.00 3.28
1706 1830 1.415659 CCATAAGCACAGGAGGAGGAG 59.584 57.143 0.00 0.00 0.00 3.69
1707 1831 2.392662 CATAAGCACAGGAGGAGGAGA 58.607 52.381 0.00 0.00 0.00 3.71
1708 1832 2.856760 TAAGCACAGGAGGAGGAGAT 57.143 50.000 0.00 0.00 0.00 2.75
1711 1835 1.289231 AGCACAGGAGGAGGAGATACA 59.711 52.381 0.00 0.00 0.00 2.29
1714 1838 3.636679 CACAGGAGGAGGAGATACAGAA 58.363 50.000 0.00 0.00 0.00 3.02
1715 1839 3.636300 CACAGGAGGAGGAGATACAGAAG 59.364 52.174 0.00 0.00 0.00 2.85
1733 1857 3.053395 AGAAGAGAGAGAGAGAGCATGGT 60.053 47.826 0.00 0.00 0.00 3.55
1736 1860 1.287442 AGAGAGAGAGAGCATGGTGGA 59.713 52.381 0.00 0.00 0.00 4.02
1738 1862 1.287442 AGAGAGAGAGCATGGTGGAGA 59.713 52.381 0.00 0.00 0.00 3.71
1758 1882 8.351461 GTGGAGAAAGAGTACATACATACCTAC 58.649 40.741 0.00 0.00 0.00 3.18
1766 1890 4.861102 ACATACATACCTACGGTAAGCC 57.139 45.455 0.00 0.00 41.85 4.35
1770 1894 3.368248 ACATACCTACGGTAAGCCTGAA 58.632 45.455 0.00 0.00 41.85 3.02
1775 1899 3.203716 CCTACGGTAAGCCTGAAATTCC 58.796 50.000 0.00 0.00 0.00 3.01
1783 1927 5.354513 GGTAAGCCTGAAATTCCAAGTAGTC 59.645 44.000 0.00 0.00 0.00 2.59
1787 1931 6.904626 AGCCTGAAATTCCAAGTAGTCATAT 58.095 36.000 0.00 0.00 0.00 1.78
1829 1973 8.206189 ACCTTCAATTTTCAATTCATTGACACT 58.794 29.630 1.52 0.00 45.63 3.55
1837 1981 9.434420 TTTTCAATTCATTGACACTTTCTGTTT 57.566 25.926 1.52 0.00 45.63 2.83
1878 2028 9.420551 CTATAAATGTTTCCTAGGATAACGGTC 57.579 37.037 13.57 0.00 0.00 4.79
1886 2036 2.484062 GGATAACGGTCGCGGAGGA 61.484 63.158 6.13 0.00 0.00 3.71
1910 2060 5.776716 ACCACTCATTGACTTTGATGGAAAT 59.223 36.000 0.00 0.00 31.67 2.17
1919 2069 3.244181 ACTTTGATGGAAATGTTGTGGGC 60.244 43.478 0.00 0.00 0.00 5.36
1928 2078 4.317488 GAAATGTTGTGGGCATGTTCAAT 58.683 39.130 0.00 0.00 0.00 2.57
1936 2086 3.006323 GTGGGCATGTTCAATGGTTGTAA 59.994 43.478 0.00 0.00 0.00 2.41
1937 2087 3.837146 TGGGCATGTTCAATGGTTGTAAT 59.163 39.130 0.00 0.00 0.00 1.89
1947 2097 4.137543 CAATGGTTGTAATAGAGGGCCTC 58.862 47.826 26.42 26.42 0.00 4.70
1990 2140 0.532115 GGGTGCATGGATTTGTGGAC 59.468 55.000 0.00 0.00 36.15 4.02
1991 2141 0.532115 GGTGCATGGATTTGTGGACC 59.468 55.000 0.37 0.37 46.98 4.46
2012 2162 4.696455 CCAATTTTGGGTATGCATTCTCC 58.304 43.478 3.54 5.60 44.70 3.71
2015 2165 3.756082 TTTGGGTATGCATTCTCCCTT 57.244 42.857 24.57 0.00 40.48 3.95
2023 2173 6.262496 GGGTATGCATTCTCCCTTAGTTTTAC 59.738 42.308 20.13 2.73 37.18 2.01
2025 2175 4.258543 TGCATTCTCCCTTAGTTTTACGG 58.741 43.478 0.00 0.00 0.00 4.02
2027 2177 5.123936 GCATTCTCCCTTAGTTTTACGGAT 58.876 41.667 0.00 0.00 0.00 4.18
2028 2178 6.126997 TGCATTCTCCCTTAGTTTTACGGATA 60.127 38.462 0.00 0.00 0.00 2.59
2029 2179 6.764560 GCATTCTCCCTTAGTTTTACGGATAA 59.235 38.462 0.00 0.00 0.00 1.75
2030 2180 7.041984 GCATTCTCCCTTAGTTTTACGGATAAG 60.042 40.741 0.00 0.00 0.00 1.73
2031 2181 7.486407 TTCTCCCTTAGTTTTACGGATAAGT 57.514 36.000 0.00 0.00 0.00 2.24
2032 2182 7.105241 TCTCCCTTAGTTTTACGGATAAGTC 57.895 40.000 0.00 0.00 0.00 3.01
2105 2255 9.853555 GAACTAGACATATGACCTCATCAATAG 57.146 37.037 10.38 1.54 41.93 1.73
2106 2256 9.593565 AACTAGACATATGACCTCATCAATAGA 57.406 33.333 10.38 0.00 41.93 1.98
2107 2257 9.241919 ACTAGACATATGACCTCATCAATAGAG 57.758 37.037 10.38 0.54 41.93 2.43
2108 2258 9.460019 CTAGACATATGACCTCATCAATAGAGA 57.540 37.037 10.38 0.00 41.93 3.10
2109 2259 8.352137 AGACATATGACCTCATCAATAGAGAG 57.648 38.462 10.38 0.00 41.93 3.20
2110 2260 8.169393 AGACATATGACCTCATCAATAGAGAGA 58.831 37.037 10.38 0.00 41.93 3.10
2111 2261 8.718158 ACATATGACCTCATCAATAGAGAGAA 57.282 34.615 10.38 0.00 41.93 2.87
2112 2262 9.152327 ACATATGACCTCATCAATAGAGAGAAA 57.848 33.333 10.38 0.00 41.93 2.52
2113 2263 9.993454 CATATGACCTCATCAATAGAGAGAAAA 57.007 33.333 0.00 0.00 41.93 2.29
2114 2264 9.995003 ATATGACCTCATCAATAGAGAGAAAAC 57.005 33.333 0.00 0.00 41.93 2.43
2115 2265 6.644347 TGACCTCATCAATAGAGAGAAAACC 58.356 40.000 0.00 0.00 35.09 3.27
2116 2266 6.441924 TGACCTCATCAATAGAGAGAAAACCT 59.558 38.462 0.00 0.00 35.09 3.50
2117 2267 6.648192 ACCTCATCAATAGAGAGAAAACCTG 58.352 40.000 0.00 0.00 35.09 4.00
2118 2268 6.441924 ACCTCATCAATAGAGAGAAAACCTGA 59.558 38.462 0.00 0.00 35.09 3.86
2119 2269 6.985645 CCTCATCAATAGAGAGAAAACCTGAG 59.014 42.308 0.00 0.00 35.09 3.35
2120 2270 7.364585 CCTCATCAATAGAGAGAAAACCTGAGT 60.365 40.741 0.00 0.00 35.09 3.41
2121 2271 7.911651 TCATCAATAGAGAGAAAACCTGAGTT 58.088 34.615 0.00 0.00 38.03 3.01
2123 2273 7.969536 TCAATAGAGAGAAAACCTGAGTTTG 57.030 36.000 0.00 0.00 45.54 2.93
2124 2274 7.509546 TCAATAGAGAGAAAACCTGAGTTTGT 58.490 34.615 0.00 0.00 45.54 2.83
2125 2275 7.442364 TCAATAGAGAGAAAACCTGAGTTTGTG 59.558 37.037 0.00 0.00 45.54 3.33
2126 2276 5.104259 AGAGAGAAAACCTGAGTTTGTGT 57.896 39.130 0.00 0.00 45.54 3.72
2127 2277 5.501156 AGAGAGAAAACCTGAGTTTGTGTT 58.499 37.500 0.00 0.00 45.54 3.32
2128 2278 5.355350 AGAGAGAAAACCTGAGTTTGTGTTG 59.645 40.000 0.00 0.00 45.54 3.33
2129 2279 5.010282 AGAGAAAACCTGAGTTTGTGTTGT 58.990 37.500 0.00 0.00 45.54 3.32
2130 2280 5.476945 AGAGAAAACCTGAGTTTGTGTTGTT 59.523 36.000 0.00 0.00 45.54 2.83
2131 2281 5.709966 AGAAAACCTGAGTTTGTGTTGTTC 58.290 37.500 0.00 0.00 45.54 3.18
2132 2282 5.242838 AGAAAACCTGAGTTTGTGTTGTTCA 59.757 36.000 0.00 0.00 45.54 3.18
2133 2283 5.461032 AAACCTGAGTTTGTGTTGTTCAA 57.539 34.783 0.00 0.00 44.57 2.69
2134 2284 5.461032 AACCTGAGTTTGTGTTGTTCAAA 57.539 34.783 0.00 0.00 29.61 2.69
2135 2285 5.461032 ACCTGAGTTTGTGTTGTTCAAAA 57.539 34.783 0.00 0.00 36.71 2.44
2136 2286 5.848406 ACCTGAGTTTGTGTTGTTCAAAAA 58.152 33.333 0.00 0.00 36.71 1.94
2137 2287 6.463360 ACCTGAGTTTGTGTTGTTCAAAAAT 58.537 32.000 0.00 0.00 35.93 1.82
2138 2288 6.368516 ACCTGAGTTTGTGTTGTTCAAAAATG 59.631 34.615 0.00 0.00 35.93 2.32
2139 2289 6.368516 CCTGAGTTTGTGTTGTTCAAAAATGT 59.631 34.615 0.00 0.00 35.93 2.71
2140 2290 7.114882 TGAGTTTGTGTTGTTCAAAAATGTG 57.885 32.000 0.00 0.00 35.93 3.21
2141 2291 5.925907 AGTTTGTGTTGTTCAAAAATGTGC 58.074 33.333 0.00 0.00 35.93 4.57
2142 2292 4.935885 TTGTGTTGTTCAAAAATGTGCC 57.064 36.364 0.00 0.00 0.00 5.01
2143 2293 4.199432 TGTGTTGTTCAAAAATGTGCCT 57.801 36.364 0.00 0.00 0.00 4.75
2144 2294 4.573900 TGTGTTGTTCAAAAATGTGCCTT 58.426 34.783 0.00 0.00 0.00 4.35
2145 2295 4.999950 TGTGTTGTTCAAAAATGTGCCTTT 59.000 33.333 0.00 0.00 0.00 3.11
2146 2296 5.471456 TGTGTTGTTCAAAAATGTGCCTTTT 59.529 32.000 0.00 0.00 0.00 2.27
2147 2297 5.794448 GTGTTGTTCAAAAATGTGCCTTTTG 59.206 36.000 2.37 2.37 42.54 2.44
2148 2298 4.612932 TGTTCAAAAATGTGCCTTTTGC 57.387 36.364 3.69 0.00 41.48 3.68
2149 2299 3.376546 TGTTCAAAAATGTGCCTTTTGCC 59.623 39.130 3.69 0.00 41.48 4.52
2150 2300 3.272574 TCAAAAATGTGCCTTTTGCCA 57.727 38.095 3.69 0.00 41.48 4.92
2151 2301 3.818180 TCAAAAATGTGCCTTTTGCCAT 58.182 36.364 3.69 0.00 41.48 4.40
2152 2302 3.564644 TCAAAAATGTGCCTTTTGCCATG 59.435 39.130 3.69 0.00 41.48 3.66
2153 2303 2.188062 AAATGTGCCTTTTGCCATGG 57.812 45.000 7.63 7.63 40.16 3.66
2154 2304 1.350071 AATGTGCCTTTTGCCATGGA 58.650 45.000 18.40 0.00 40.16 3.41
2155 2305 1.575419 ATGTGCCTTTTGCCATGGAT 58.425 45.000 18.40 0.00 40.16 3.41
2156 2306 2.228545 TGTGCCTTTTGCCATGGATA 57.771 45.000 18.40 0.00 40.16 2.59
2157 2307 2.749600 TGTGCCTTTTGCCATGGATAT 58.250 42.857 18.40 0.00 40.16 1.63
2158 2308 3.106054 TGTGCCTTTTGCCATGGATATT 58.894 40.909 18.40 0.00 40.16 1.28
2159 2309 3.118702 TGTGCCTTTTGCCATGGATATTG 60.119 43.478 18.40 1.49 40.16 1.90
2160 2310 3.106054 TGCCTTTTGCCATGGATATTGT 58.894 40.909 18.40 0.00 40.16 2.71
2161 2311 4.099266 GTGCCTTTTGCCATGGATATTGTA 59.901 41.667 18.40 0.00 40.16 2.41
2162 2312 4.900652 TGCCTTTTGCCATGGATATTGTAT 59.099 37.500 18.40 0.00 40.16 2.29
2163 2313 5.366186 TGCCTTTTGCCATGGATATTGTATT 59.634 36.000 18.40 0.00 40.16 1.89
2164 2314 6.126825 TGCCTTTTGCCATGGATATTGTATTT 60.127 34.615 18.40 0.00 40.16 1.40
2165 2315 7.070447 TGCCTTTTGCCATGGATATTGTATTTA 59.930 33.333 18.40 0.00 40.16 1.40
2166 2316 7.384932 GCCTTTTGCCATGGATATTGTATTTAC 59.615 37.037 18.40 0.00 0.00 2.01
2167 2317 8.641541 CCTTTTGCCATGGATATTGTATTTACT 58.358 33.333 18.40 0.00 0.00 2.24
2170 2320 9.814899 TTTGCCATGGATATTGTATTTACTTTG 57.185 29.630 18.40 0.00 0.00 2.77
2171 2321 7.432869 TGCCATGGATATTGTATTTACTTTGC 58.567 34.615 18.40 0.00 0.00 3.68
2172 2322 7.069208 TGCCATGGATATTGTATTTACTTTGCA 59.931 33.333 18.40 0.00 0.00 4.08
2173 2323 7.925483 GCCATGGATATTGTATTTACTTTGCAA 59.075 33.333 18.40 0.00 0.00 4.08
2174 2324 9.814899 CCATGGATATTGTATTTACTTTGCAAA 57.185 29.630 5.56 12.14 0.00 3.68
2183 2333 9.539825 TTGTATTTACTTTGCAAAATCATGTGT 57.460 25.926 13.84 8.15 0.00 3.72
2184 2334 8.976471 TGTATTTACTTTGCAAAATCATGTGTG 58.024 29.630 13.84 0.54 0.00 3.82
2185 2335 9.190858 GTATTTACTTTGCAAAATCATGTGTGA 57.809 29.630 13.84 0.00 39.04 3.58
2186 2336 7.697352 TTTACTTTGCAAAATCATGTGTGAG 57.303 32.000 13.84 0.00 37.87 3.51
2187 2337 5.266733 ACTTTGCAAAATCATGTGTGAGT 57.733 34.783 13.84 0.00 37.87 3.41
2188 2338 5.045215 ACTTTGCAAAATCATGTGTGAGTG 58.955 37.500 13.84 0.00 37.87 3.51
2189 2339 4.915158 TTGCAAAATCATGTGTGAGTGA 57.085 36.364 0.00 0.00 37.87 3.41
2190 2340 4.227512 TGCAAAATCATGTGTGAGTGAC 57.772 40.909 0.00 0.00 37.87 3.67
2191 2341 3.631227 TGCAAAATCATGTGTGAGTGACA 59.369 39.130 0.00 0.00 37.87 3.58
2192 2342 4.097589 TGCAAAATCATGTGTGAGTGACAA 59.902 37.500 0.00 0.00 37.87 3.18
2193 2343 5.221283 TGCAAAATCATGTGTGAGTGACAAT 60.221 36.000 0.00 0.00 37.87 2.71
2194 2344 6.016443 TGCAAAATCATGTGTGAGTGACAATA 60.016 34.615 0.00 0.00 37.87 1.90
2195 2345 6.525628 GCAAAATCATGTGTGAGTGACAATAG 59.474 38.462 0.00 0.00 37.87 1.73
2196 2346 7.573656 GCAAAATCATGTGTGAGTGACAATAGA 60.574 37.037 0.00 0.00 37.87 1.98
2197 2347 6.974932 AATCATGTGTGAGTGACAATAGAC 57.025 37.500 0.00 0.00 37.87 2.59
2198 2348 5.728637 TCATGTGTGAGTGACAATAGACT 57.271 39.130 0.00 0.00 35.91 3.24
2199 2349 6.834168 TCATGTGTGAGTGACAATAGACTA 57.166 37.500 0.00 0.00 35.91 2.59
2200 2350 7.410120 TCATGTGTGAGTGACAATAGACTAT 57.590 36.000 0.00 0.00 35.91 2.12
2201 2351 7.260603 TCATGTGTGAGTGACAATAGACTATG 58.739 38.462 0.00 0.00 35.91 2.23
2202 2352 5.965922 TGTGTGAGTGACAATAGACTATGG 58.034 41.667 0.00 0.00 35.91 2.74
2203 2353 5.105351 TGTGTGAGTGACAATAGACTATGGG 60.105 44.000 1.87 0.00 35.91 4.00
2204 2354 5.023452 TGTGAGTGACAATAGACTATGGGT 58.977 41.667 1.87 1.33 0.00 4.51
2205 2355 5.105351 TGTGAGTGACAATAGACTATGGGTG 60.105 44.000 1.87 0.00 0.00 4.61
2206 2356 5.127194 GTGAGTGACAATAGACTATGGGTGA 59.873 44.000 1.87 0.00 0.00 4.02
2207 2357 5.719563 TGAGTGACAATAGACTATGGGTGAA 59.280 40.000 1.87 0.00 0.00 3.18
2208 2358 6.212589 TGAGTGACAATAGACTATGGGTGAAA 59.787 38.462 1.87 0.00 0.00 2.69
2209 2359 6.407202 AGTGACAATAGACTATGGGTGAAAC 58.593 40.000 1.87 0.10 0.00 2.78
2210 2360 6.213600 AGTGACAATAGACTATGGGTGAAACT 59.786 38.462 1.87 2.00 36.74 2.66
2211 2361 6.879458 GTGACAATAGACTATGGGTGAAACTT 59.121 38.462 1.87 0.00 36.74 2.66
2212 2362 7.390718 GTGACAATAGACTATGGGTGAAACTTT 59.609 37.037 1.87 0.00 36.74 2.66
2213 2363 7.390440 TGACAATAGACTATGGGTGAAACTTTG 59.610 37.037 1.87 0.00 36.74 2.77
2214 2364 7.458397 ACAATAGACTATGGGTGAAACTTTGA 58.542 34.615 1.87 0.00 36.74 2.69
2215 2365 7.942341 ACAATAGACTATGGGTGAAACTTTGAA 59.058 33.333 1.87 0.00 36.74 2.69
2216 2366 8.454106 CAATAGACTATGGGTGAAACTTTGAAG 58.546 37.037 0.00 0.00 36.74 3.02
2217 2367 5.316987 AGACTATGGGTGAAACTTTGAAGG 58.683 41.667 0.00 0.00 36.74 3.46
2218 2368 4.407365 ACTATGGGTGAAACTTTGAAGGG 58.593 43.478 0.00 0.00 36.74 3.95
2219 2369 2.838637 TGGGTGAAACTTTGAAGGGT 57.161 45.000 0.00 0.00 36.74 4.34
2220 2370 3.108847 TGGGTGAAACTTTGAAGGGTT 57.891 42.857 0.00 0.00 36.74 4.11
2221 2371 2.763448 TGGGTGAAACTTTGAAGGGTTG 59.237 45.455 0.00 0.00 36.74 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 7.794041 AGTCAAGATGCAGAATCTCTATTTCT 58.206 34.615 0.00 0.00 45.37 2.52
112 113 3.244215 ACCGAAGAAGTCAAGATGCAGAA 60.244 43.478 0.00 0.00 0.00 3.02
132 133 6.890293 ACAAAGTAGGATCAAGAAGGATACC 58.110 40.000 0.00 0.00 37.17 2.73
345 349 3.445096 GCATAAGTTTGGCTGGTTGAGAT 59.555 43.478 0.00 0.00 0.00 2.75
619 625 9.566331 AAATCATTCTCATATATACTCCCTCCA 57.434 33.333 0.00 0.00 0.00 3.86
1277 1399 8.618240 TCCTATTCTGGGTAACTAAATCAGAA 57.382 34.615 6.54 6.54 44.92 3.02
1324 1446 1.209504 CTCCACGCCTGGGAAATTAGA 59.790 52.381 1.63 0.00 38.25 2.10
1396 1519 4.588528 ACCTAAACCATTTTCTGTGTGCAT 59.411 37.500 0.00 0.00 0.00 3.96
1486 1609 3.181443 ACTTCTTTAAGGACACCCCACAG 60.181 47.826 0.00 0.00 37.01 3.66
1684 1808 1.561542 CCTCCTCCTGTGCTTATGGTT 59.438 52.381 0.00 0.00 0.00 3.67
1685 1809 1.207791 CCTCCTCCTGTGCTTATGGT 58.792 55.000 0.00 0.00 0.00 3.55
1691 1815 1.289231 TGTATCTCCTCCTCCTGTGCT 59.711 52.381 0.00 0.00 0.00 4.40
1706 1830 5.368145 TGCTCTCTCTCTCTCTTCTGTATC 58.632 45.833 0.00 0.00 0.00 2.24
1707 1831 5.372343 TGCTCTCTCTCTCTCTTCTGTAT 57.628 43.478 0.00 0.00 0.00 2.29
1708 1832 4.835284 TGCTCTCTCTCTCTCTTCTGTA 57.165 45.455 0.00 0.00 0.00 2.74
1711 1835 3.053395 ACCATGCTCTCTCTCTCTCTTCT 60.053 47.826 0.00 0.00 0.00 2.85
1714 1838 2.658285 CACCATGCTCTCTCTCTCTCT 58.342 52.381 0.00 0.00 0.00 3.10
1715 1839 1.682854 CCACCATGCTCTCTCTCTCTC 59.317 57.143 0.00 0.00 0.00 3.20
1733 1857 7.228108 CGTAGGTATGTATGTACTCTTTCTCCA 59.772 40.741 0.00 0.00 0.00 3.86
1758 1882 3.081804 ACTTGGAATTTCAGGCTTACCG 58.918 45.455 0.00 0.00 42.76 4.02
1857 2007 4.690122 CGACCGTTATCCTAGGAAACATT 58.310 43.478 17.30 10.34 0.00 2.71
1860 2010 2.467838 GCGACCGTTATCCTAGGAAAC 58.532 52.381 17.30 18.48 0.00 2.78
1861 2011 1.066002 CGCGACCGTTATCCTAGGAAA 59.934 52.381 17.30 8.82 0.00 3.13
1862 2012 0.664761 CGCGACCGTTATCCTAGGAA 59.335 55.000 17.30 2.36 0.00 3.36
1864 2014 1.168407 TCCGCGACCGTTATCCTAGG 61.168 60.000 8.23 0.82 0.00 3.02
1871 2021 3.443045 GGTCCTCCGCGACCGTTA 61.443 66.667 8.23 0.00 42.88 3.18
1886 2036 4.371624 TCCATCAAAGTCAATGAGTGGT 57.628 40.909 0.00 0.00 32.27 4.16
1890 2040 7.115805 CACAACATTTCCATCAAAGTCAATGAG 59.884 37.037 0.00 0.00 0.00 2.90
1892 2042 6.146510 CCACAACATTTCCATCAAAGTCAATG 59.853 38.462 0.00 0.00 0.00 2.82
1910 2060 1.343789 CCATTGAACATGCCCACAACA 59.656 47.619 0.00 0.00 0.00 3.33
1919 2069 6.460123 GCCCTCTATTACAACCATTGAACATG 60.460 42.308 0.00 0.00 0.00 3.21
1928 2078 3.130734 AGAGGCCCTCTATTACAACCA 57.869 47.619 12.79 0.00 39.28 3.67
1936 2086 2.577772 AGGAACAAGAGGCCCTCTAT 57.422 50.000 15.10 2.23 40.28 1.98
1937 2087 2.188817 GAAGGAACAAGAGGCCCTCTA 58.811 52.381 15.10 0.00 40.28 2.43
1947 2097 6.698766 CCATTCAAAACAGAAGAAGGAACAAG 59.301 38.462 0.00 0.00 0.00 3.16
1991 2141 4.406649 AGGGAGAATGCATACCCAAAATTG 59.593 41.667 27.07 0.00 44.25 2.32
2009 2159 7.110043 AGACTTATCCGTAAAACTAAGGGAG 57.890 40.000 0.00 0.00 34.59 4.30
2023 2173 7.787725 AGGCATTAGTTAAAAGACTTATCCG 57.212 36.000 0.00 0.00 0.00 4.18
2027 2177 9.733556 TGATGAAGGCATTAGTTAAAAGACTTA 57.266 29.630 0.00 0.00 34.11 2.24
2028 2178 8.635765 TGATGAAGGCATTAGTTAAAAGACTT 57.364 30.769 0.00 0.00 34.11 3.01
2029 2179 8.814038 ATGATGAAGGCATTAGTTAAAAGACT 57.186 30.769 0.00 0.00 34.11 3.24
2030 2180 9.860898 AAATGATGAAGGCATTAGTTAAAAGAC 57.139 29.630 0.00 0.00 35.06 3.01
2075 2225 9.367160 TGATGAGGTCATATGTCTAGTTCAATA 57.633 33.333 1.90 0.00 36.57 1.90
2076 2226 8.255111 TGATGAGGTCATATGTCTAGTTCAAT 57.745 34.615 1.90 0.00 36.57 2.57
2083 2233 9.460019 CTCTCTATTGATGAGGTCATATGTCTA 57.540 37.037 1.90 0.00 36.54 2.59
2085 2235 8.347004 TCTCTCTATTGATGAGGTCATATGTC 57.653 38.462 1.90 0.00 36.54 3.06
2105 2255 5.123979 ACAACACAAACTCAGGTTTTCTCTC 59.876 40.000 0.00 0.00 42.96 3.20
2106 2256 5.010282 ACAACACAAACTCAGGTTTTCTCT 58.990 37.500 0.00 0.00 42.96 3.10
2107 2257 5.310720 ACAACACAAACTCAGGTTTTCTC 57.689 39.130 0.00 0.00 42.96 2.87
2108 2258 5.242838 TGAACAACACAAACTCAGGTTTTCT 59.757 36.000 0.00 0.00 42.96 2.52
2109 2259 5.465935 TGAACAACACAAACTCAGGTTTTC 58.534 37.500 0.00 0.00 42.96 2.29
2110 2260 5.461032 TGAACAACACAAACTCAGGTTTT 57.539 34.783 0.00 0.00 42.96 2.43
2111 2261 5.461032 TTGAACAACACAAACTCAGGTTT 57.539 34.783 0.00 0.00 45.35 3.27
2112 2262 5.461032 TTTGAACAACACAAACTCAGGTT 57.539 34.783 0.00 0.00 37.24 3.50
2113 2263 5.461032 TTTTGAACAACACAAACTCAGGT 57.539 34.783 0.00 0.00 37.05 4.00
2114 2264 6.368516 ACATTTTTGAACAACACAAACTCAGG 59.631 34.615 0.00 0.00 37.05 3.86
2115 2265 7.228840 CACATTTTTGAACAACACAAACTCAG 58.771 34.615 0.00 0.00 37.05 3.35
2116 2266 6.347240 GCACATTTTTGAACAACACAAACTCA 60.347 34.615 0.00 0.00 37.05 3.41
2117 2267 6.014898 GCACATTTTTGAACAACACAAACTC 58.985 36.000 0.00 0.00 37.05 3.01
2118 2268 5.106752 GGCACATTTTTGAACAACACAAACT 60.107 36.000 0.00 0.00 37.05 2.66
2119 2269 5.085390 GGCACATTTTTGAACAACACAAAC 58.915 37.500 0.00 0.00 37.05 2.93
2120 2270 4.999950 AGGCACATTTTTGAACAACACAAA 59.000 33.333 0.00 0.00 35.81 2.83
2121 2271 4.573900 AGGCACATTTTTGAACAACACAA 58.426 34.783 0.00 0.00 0.00 3.33
2122 2272 4.199432 AGGCACATTTTTGAACAACACA 57.801 36.364 0.00 0.00 0.00 3.72
2123 2273 5.544136 AAAGGCACATTTTTGAACAACAC 57.456 34.783 0.00 0.00 0.00 3.32
2124 2274 5.618640 GCAAAAGGCACATTTTTGAACAACA 60.619 36.000 12.28 0.00 44.37 3.33
2125 2275 4.792702 GCAAAAGGCACATTTTTGAACAAC 59.207 37.500 12.28 0.00 44.37 3.32
2126 2276 4.142513 GGCAAAAGGCACATTTTTGAACAA 60.143 37.500 12.28 0.00 44.37 2.83
2127 2277 3.376546 GGCAAAAGGCACATTTTTGAACA 59.623 39.130 12.28 0.00 44.37 3.18
2128 2278 3.376546 TGGCAAAAGGCACATTTTTGAAC 59.623 39.130 12.28 6.08 44.37 3.18
2129 2279 3.614092 TGGCAAAAGGCACATTTTTGAA 58.386 36.364 12.28 0.00 44.37 2.69
2130 2280 3.272574 TGGCAAAAGGCACATTTTTGA 57.727 38.095 12.28 0.00 44.37 2.69
2140 2290 3.825143 ACAATATCCATGGCAAAAGGC 57.175 42.857 6.96 0.00 43.74 4.35
2141 2291 8.641541 AGTAAATACAATATCCATGGCAAAAGG 58.358 33.333 6.96 0.00 0.00 3.11
2144 2294 9.814899 CAAAGTAAATACAATATCCATGGCAAA 57.185 29.630 6.96 0.00 0.00 3.68
2145 2295 7.925483 GCAAAGTAAATACAATATCCATGGCAA 59.075 33.333 6.96 0.00 0.00 4.52
2146 2296 7.069208 TGCAAAGTAAATACAATATCCATGGCA 59.931 33.333 6.96 0.00 0.00 4.92
2147 2297 7.432869 TGCAAAGTAAATACAATATCCATGGC 58.567 34.615 6.96 0.00 0.00 4.40
2148 2298 9.814899 TTTGCAAAGTAAATACAATATCCATGG 57.185 29.630 8.05 4.97 0.00 3.66
2157 2307 9.539825 ACACATGATTTTGCAAAGTAAATACAA 57.460 25.926 12.41 0.00 0.00 2.41
2158 2308 8.976471 CACACATGATTTTGCAAAGTAAATACA 58.024 29.630 12.41 3.87 0.00 2.29
2159 2309 9.190858 TCACACATGATTTTGCAAAGTAAATAC 57.809 29.630 12.41 0.00 0.00 1.89
2160 2310 9.409312 CTCACACATGATTTTGCAAAGTAAATA 57.591 29.630 12.41 0.00 33.22 1.40
2161 2311 7.927629 ACTCACACATGATTTTGCAAAGTAAAT 59.072 29.630 12.41 2.70 33.22 1.40
2162 2312 7.222417 CACTCACACATGATTTTGCAAAGTAAA 59.778 33.333 12.41 2.12 33.22 2.01
2163 2313 6.696583 CACTCACACATGATTTTGCAAAGTAA 59.303 34.615 12.41 2.71 33.22 2.24
2164 2314 6.039159 TCACTCACACATGATTTTGCAAAGTA 59.961 34.615 12.41 0.00 33.22 2.24
2165 2315 5.045215 CACTCACACATGATTTTGCAAAGT 58.955 37.500 12.41 9.72 33.22 2.66
2166 2316 5.174398 GTCACTCACACATGATTTTGCAAAG 59.826 40.000 12.41 2.86 33.22 2.77
2167 2317 5.042593 GTCACTCACACATGATTTTGCAAA 58.957 37.500 8.05 8.05 33.22 3.68
2168 2318 4.097589 TGTCACTCACACATGATTTTGCAA 59.902 37.500 0.00 0.00 33.22 4.08
2169 2319 3.631227 TGTCACTCACACATGATTTTGCA 59.369 39.130 0.00 0.00 33.22 4.08
2170 2320 4.227512 TGTCACTCACACATGATTTTGC 57.772 40.909 0.00 0.00 33.22 3.68
2171 2321 7.747799 GTCTATTGTCACTCACACATGATTTTG 59.252 37.037 0.00 0.00 33.41 2.44
2172 2322 7.663081 AGTCTATTGTCACTCACACATGATTTT 59.337 33.333 0.00 0.00 33.41 1.82
2173 2323 7.164122 AGTCTATTGTCACTCACACATGATTT 58.836 34.615 0.00 0.00 33.41 2.17
2174 2324 6.705302 AGTCTATTGTCACTCACACATGATT 58.295 36.000 0.00 0.00 33.41 2.57
2175 2325 6.291648 AGTCTATTGTCACTCACACATGAT 57.708 37.500 0.00 0.00 33.41 2.45
2176 2326 5.728637 AGTCTATTGTCACTCACACATGA 57.271 39.130 0.00 0.00 33.41 3.07
2177 2327 6.478016 CCATAGTCTATTGTCACTCACACATG 59.522 42.308 0.00 0.00 33.41 3.21
2178 2328 6.407412 CCCATAGTCTATTGTCACTCACACAT 60.407 42.308 0.00 0.00 33.41 3.21
2179 2329 5.105351 CCCATAGTCTATTGTCACTCACACA 60.105 44.000 0.00 0.00 33.41 3.72
2180 2330 5.105310 ACCCATAGTCTATTGTCACTCACAC 60.105 44.000 0.00 0.00 33.41 3.82
2181 2331 5.023452 ACCCATAGTCTATTGTCACTCACA 58.977 41.667 0.00 0.00 0.00 3.58
2182 2332 5.127194 TCACCCATAGTCTATTGTCACTCAC 59.873 44.000 0.00 0.00 0.00 3.51
2183 2333 5.269189 TCACCCATAGTCTATTGTCACTCA 58.731 41.667 0.00 0.00 0.00 3.41
2184 2334 5.854010 TCACCCATAGTCTATTGTCACTC 57.146 43.478 0.00 0.00 0.00 3.51
2185 2335 6.213600 AGTTTCACCCATAGTCTATTGTCACT 59.786 38.462 0.00 0.00 0.00 3.41
2186 2336 6.407202 AGTTTCACCCATAGTCTATTGTCAC 58.593 40.000 0.00 0.00 0.00 3.67
2187 2337 6.620877 AGTTTCACCCATAGTCTATTGTCA 57.379 37.500 0.00 0.00 0.00 3.58
2188 2338 7.606456 TCAAAGTTTCACCCATAGTCTATTGTC 59.394 37.037 0.00 0.00 0.00 3.18
2189 2339 7.458397 TCAAAGTTTCACCCATAGTCTATTGT 58.542 34.615 0.00 0.00 0.00 2.71
2190 2340 7.921786 TCAAAGTTTCACCCATAGTCTATTG 57.078 36.000 0.00 0.00 0.00 1.90
2191 2341 7.611855 CCTTCAAAGTTTCACCCATAGTCTATT 59.388 37.037 0.00 0.00 0.00 1.73
2192 2342 7.112779 CCTTCAAAGTTTCACCCATAGTCTAT 58.887 38.462 0.00 0.00 0.00 1.98
2193 2343 6.472887 CCTTCAAAGTTTCACCCATAGTCTA 58.527 40.000 0.00 0.00 0.00 2.59
2194 2344 5.316987 CCTTCAAAGTTTCACCCATAGTCT 58.683 41.667 0.00 0.00 0.00 3.24
2195 2345 4.459337 CCCTTCAAAGTTTCACCCATAGTC 59.541 45.833 0.00 0.00 0.00 2.59
2196 2346 4.141018 ACCCTTCAAAGTTTCACCCATAGT 60.141 41.667 0.00 0.00 0.00 2.12
2197 2347 4.407365 ACCCTTCAAAGTTTCACCCATAG 58.593 43.478 0.00 0.00 0.00 2.23
2198 2348 4.463050 ACCCTTCAAAGTTTCACCCATA 57.537 40.909 0.00 0.00 0.00 2.74
2199 2349 3.328535 ACCCTTCAAAGTTTCACCCAT 57.671 42.857 0.00 0.00 0.00 4.00
2200 2350 2.763448 CAACCCTTCAAAGTTTCACCCA 59.237 45.455 0.00 0.00 0.00 4.51
2201 2351 3.452755 CAACCCTTCAAAGTTTCACCC 57.547 47.619 0.00 0.00 0.00 4.61


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

AutoCloner maintained by Alex Coulton.