Multiple sequence alignment - TraesCS1D01G082400

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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 TraesCS1D01G082400 chr1D 100.000 4139 0 0 1 4139 64334457 64338595 0.000000e+00 7644.0
1 TraesCS1D01G082400 chr1D 96.847 4091 97 17 1 4083 96037561 96033495 0.000000e+00 6811.0
2 TraesCS1D01G082400 chr1D 94.282 2116 81 19 1991 4083 439404022 439406120 0.000000e+00 3201.0
3 TraesCS1D01G082400 chr1D 93.919 1480 67 9 151 1623 439402107 439403570 0.000000e+00 2213.0
4 TraesCS1D01G082400 chr1D 84.586 266 24 9 1 261 96032878 96032625 8.890000e-62 248.0
5 TraesCS1D01G082400 chr1D 79.343 213 24 13 1 208 439406763 439406960 9.340000e-27 132.0
6 TraesCS1D01G082400 chr4A 92.571 4038 189 49 69 4083 557665516 557661567 0.000000e+00 5692.0
7 TraesCS1D01G082400 chr4A 91.999 4037 186 60 69 4083 554696832 554700753 0.000000e+00 5539.0
8 TraesCS1D01G082400 chr4A 92.593 54 4 0 4086 4139 557661535 557661482 1.230000e-10 78.7
9 TraesCS1D01G082400 chr7D 93.556 3616 164 25 486 4082 600061961 600065526 0.000000e+00 5323.0
10 TraesCS1D01G082400 chr7D 92.449 490 15 6 1 488 600061452 600061921 0.000000e+00 680.0
11 TraesCS1D01G082400 chr6A 93.136 2899 141 28 1203 4082 121725818 121722959 0.000000e+00 4198.0
12 TraesCS1D01G082400 chr6A 92.986 499 20 10 1 488 121727025 121726531 0.000000e+00 713.0
13 TraesCS1D01G082400 chr7B 94.273 2235 108 10 713 2940 6997819 7000040 0.000000e+00 3400.0
14 TraesCS1D01G082400 chr7B 92.940 1119 66 7 2971 4078 7000041 7001157 0.000000e+00 1616.0
15 TraesCS1D01G082400 chr3B 92.929 2291 108 25 1806 4083 734914114 734911865 0.000000e+00 3284.0
16 TraesCS1D01G082400 chr3B 94.462 1300 60 10 486 1775 774216736 774218033 0.000000e+00 1991.0
17 TraesCS1D01G082400 chr3B 93.776 482 21 6 12 488 734914904 734914427 0.000000e+00 715.0
18 TraesCS1D01G082400 chr3B 93.426 289 18 1 1640 1928 774402735 774403022 1.060000e-115 427.0
19 TraesCS1D01G082400 chr4D 96.077 1810 63 3 1296 3100 42333705 42335511 0.000000e+00 2942.0
20 TraesCS1D01G082400 chr4D 92.963 1279 60 18 33 1303 42331653 42332909 0.000000e+00 1836.0
21 TraesCS1D01G082400 chr3A 90.774 2157 134 25 1949 4083 714788240 714790353 0.000000e+00 2820.0
22 TraesCS1D01G082400 chr3A 91.866 1758 88 19 2343 4083 607845896 607847615 0.000000e+00 2403.0
23 TraesCS1D01G082400 chr3D 93.886 1374 51 8 2319 3677 579688196 579689551 0.000000e+00 2041.0
24 TraesCS1D01G082400 chr3D 93.702 1302 58 9 486 1765 579686711 579688010 0.000000e+00 1929.0
25 TraesCS1D01G082400 chr3D 93.927 494 20 5 1 488 579686182 579686671 0.000000e+00 737.0
26 TraesCS1D01G082400 chr3D 91.061 358 23 4 3711 4059 579689548 579689905 3.740000e-130 475.0
27 TraesCS1D01G082400 chr3D 79.059 425 50 28 3751 4139 579685217 579685638 5.310000e-64 255.0
28 TraesCS1D01G082400 chr3D 81.188 202 21 10 1 197 579690699 579690888 3.330000e-31 147.0
29 TraesCS1D01G082400 chr2B 84.243 2126 230 56 1045 3128 760892561 760890499 0.000000e+00 1973.0
30 TraesCS1D01G082400 chr2B 94.480 942 45 7 486 1424 755328532 755329469 0.000000e+00 1445.0
31 TraesCS1D01G082400 chr2B 80.303 264 35 10 3 261 755332832 755333083 2.540000e-42 183.0
32 TraesCS1D01G082400 chr2A 87.172 1450 119 31 2647 4082 749651367 749652763 0.000000e+00 1585.0
33 TraesCS1D01G082400 chr2A 84.763 991 86 29 1045 2005 752095092 752094137 0.000000e+00 933.0
34 TraesCS1D01G082400 chr2A 81.633 294 42 4 1819 2110 752094487 752094204 2.490000e-57 233.0
35 TraesCS1D01G082400 chr2D 88.571 1155 112 15 1983 3128 620512053 620510910 0.000000e+00 1384.0
36 TraesCS1D01G082400 chr6B 90.922 727 41 18 33 750 144005971 144006681 0.000000e+00 953.0
37 TraesCS1D01G082400 chr6D 89.439 767 48 22 1 750 68973037 68973787 0.000000e+00 937.0
38 TraesCS1D01G082400 chr6D 77.224 281 42 16 3793 4059 68972081 68972353 1.200000e-30 145.0


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 TraesCS1D01G082400 chr1D 64334457 64338595 4138 False 7644.000000 7644 100.000000 1 4139 1 chr1D.!!$F1 4138
1 TraesCS1D01G082400 chr1D 96032625 96037561 4936 True 3529.500000 6811 90.716500 1 4083 2 chr1D.!!$R1 4082
2 TraesCS1D01G082400 chr1D 439402107 439406960 4853 False 1848.666667 3201 89.181333 1 4083 3 chr1D.!!$F2 4082
3 TraesCS1D01G082400 chr4A 554696832 554700753 3921 False 5539.000000 5539 91.999000 69 4083 1 chr4A.!!$F1 4014
4 TraesCS1D01G082400 chr4A 557661482 557665516 4034 True 2885.350000 5692 92.582000 69 4139 2 chr4A.!!$R1 4070
5 TraesCS1D01G082400 chr7D 600061452 600065526 4074 False 3001.500000 5323 93.002500 1 4082 2 chr7D.!!$F1 4081
6 TraesCS1D01G082400 chr6A 121722959 121727025 4066 True 2455.500000 4198 93.061000 1 4082 2 chr6A.!!$R1 4081
7 TraesCS1D01G082400 chr7B 6997819 7001157 3338 False 2508.000000 3400 93.606500 713 4078 2 chr7B.!!$F1 3365
8 TraesCS1D01G082400 chr3B 734911865 734914904 3039 True 1999.500000 3284 93.352500 12 4083 2 chr3B.!!$R1 4071
9 TraesCS1D01G082400 chr3B 774216736 774218033 1297 False 1991.000000 1991 94.462000 486 1775 1 chr3B.!!$F1 1289
10 TraesCS1D01G082400 chr4D 42331653 42335511 3858 False 2389.000000 2942 94.520000 33 3100 2 chr4D.!!$F1 3067
11 TraesCS1D01G082400 chr3A 714788240 714790353 2113 False 2820.000000 2820 90.774000 1949 4083 1 chr3A.!!$F2 2134
12 TraesCS1D01G082400 chr3A 607845896 607847615 1719 False 2403.000000 2403 91.866000 2343 4083 1 chr3A.!!$F1 1740
13 TraesCS1D01G082400 chr3D 579685217 579690888 5671 False 930.666667 2041 88.803833 1 4139 6 chr3D.!!$F1 4138
14 TraesCS1D01G082400 chr2B 760890499 760892561 2062 True 1973.000000 1973 84.243000 1045 3128 1 chr2B.!!$R1 2083
15 TraesCS1D01G082400 chr2B 755328532 755333083 4551 False 814.000000 1445 87.391500 3 1424 2 chr2B.!!$F1 1421
16 TraesCS1D01G082400 chr2A 749651367 749652763 1396 False 1585.000000 1585 87.172000 2647 4082 1 chr2A.!!$F1 1435
17 TraesCS1D01G082400 chr2A 752094137 752095092 955 True 583.000000 933 83.198000 1045 2110 2 chr2A.!!$R1 1065
18 TraesCS1D01G082400 chr2D 620510910 620512053 1143 True 1384.000000 1384 88.571000 1983 3128 1 chr2D.!!$R1 1145
19 TraesCS1D01G082400 chr6B 144005971 144006681 710 False 953.000000 953 90.922000 33 750 1 chr6B.!!$F1 717
20 TraesCS1D01G082400 chr6D 68972081 68973787 1706 False 541.000000 937 83.331500 1 4059 2 chr6D.!!$F1 4058

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
470 1616 0.743688 CGAGCTGATGCCTGTAGTCT 59.256 55.0 0.00 0.0 40.80 3.24 F
1109 2367 0.035056 CCTCTGCCCCGTTTGATTCT 60.035 55.0 0.00 0.0 0.00 2.40 F
1432 3521 1.165270 GTACCACATGGGCAGAACAC 58.835 55.0 2.32 0.0 42.05 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 4778 0.326264 ACATCAAGTCACCCAGGAGC 59.674 55.000 0.00 0.00 0.00 4.70 R
2648 5316 1.075536 AGGACCCCCAAGACATTTGTC 59.924 52.381 2.41 2.41 39.04 3.18 R
3189 5891 0.179103 GGGGGAAATGCATTTCAGCG 60.179 55.000 39.11 0.00 46.03 5.18 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
19 1053 2.573941 GCCTTGAGATGGATTGTTGC 57.426 50.000 0.00 0.00 0.00 4.17
32 1066 4.060205 GGATTGTTGCTTGTTGCTTGATT 58.940 39.130 0.00 0.00 43.37 2.57
33 1067 4.084223 GGATTGTTGCTTGTTGCTTGATTG 60.084 41.667 0.00 0.00 43.37 2.67
34 1068 3.797451 TGTTGCTTGTTGCTTGATTGA 57.203 38.095 0.00 0.00 43.37 2.57
35 1069 4.325028 TGTTGCTTGTTGCTTGATTGAT 57.675 36.364 0.00 0.00 43.37 2.57
215 1349 2.854963 TGCCAGTTCCTGATCATATGC 58.145 47.619 0.00 0.00 32.44 3.14
445 1590 8.068893 ACGCAGGTATATTTACATTCTTTACG 57.931 34.615 0.00 0.00 0.00 3.18
470 1616 0.743688 CGAGCTGATGCCTGTAGTCT 59.256 55.000 0.00 0.00 40.80 3.24
539 1785 6.917477 TGGCTAATTTGATTCATTATCGTTGC 59.083 34.615 0.00 0.00 35.94 4.17
637 1884 3.546670 CCCTCTCGAATTTAACTCGTTCG 59.453 47.826 0.00 0.00 44.31 3.95
818 2068 3.494749 GCAGCTGAGCTCTTTCTGGATAT 60.495 47.826 20.43 0.00 36.40 1.63
1049 2303 3.007182 ACAAAATGGTCTCATTGCAAGGG 59.993 43.478 11.73 2.73 42.29 3.95
1082 2340 3.618780 CTCCCACCTCAGTGCAGGC 62.619 68.421 8.13 0.00 43.09 4.85
1109 2367 0.035056 CCTCTGCCCCGTTTGATTCT 60.035 55.000 0.00 0.00 0.00 2.40
1432 3521 1.165270 GTACCACATGGGCAGAACAC 58.835 55.000 2.32 0.00 42.05 3.32
1615 3862 9.887406 ATTTAAGAAACATAAACAGTACCAACG 57.113 29.630 0.00 0.00 0.00 4.10
1683 3930 3.642938 GTGGCAATGGTCACCTGTA 57.357 52.632 0.00 0.00 43.89 2.74
1707 3956 9.351570 GTATTCCTTAGTCTATTAACGCATACC 57.648 37.037 0.00 0.00 0.00 2.73
1895 4144 9.214957 TGCATACTGGAAGAAATATAATTACGG 57.785 33.333 0.00 0.00 37.43 4.02
1896 4145 9.431887 GCATACTGGAAGAAATATAATTACGGA 57.568 33.333 0.00 0.00 37.43 4.69
1899 4148 8.379457 ACTGGAAGAAATATAATTACGGAAGC 57.621 34.615 0.00 0.00 37.43 3.86
1900 4149 7.990886 ACTGGAAGAAATATAATTACGGAAGCA 59.009 33.333 0.00 0.00 37.43 3.91
1901 4150 8.740123 TGGAAGAAATATAATTACGGAAGCAA 57.260 30.769 0.00 0.00 0.00 3.91
1902 4151 8.617809 TGGAAGAAATATAATTACGGAAGCAAC 58.382 33.333 0.00 0.00 0.00 4.17
1903 4152 8.837389 GGAAGAAATATAATTACGGAAGCAACT 58.163 33.333 0.00 0.00 0.00 3.16
1908 4157 9.946165 AAATATAATTACGGAAGCAACTTTAGC 57.054 29.630 0.00 0.00 0.00 3.09
1909 4158 6.995511 ATAATTACGGAAGCAACTTTAGCA 57.004 33.333 0.00 0.00 0.00 3.49
1910 4159 5.897377 AATTACGGAAGCAACTTTAGCAT 57.103 34.783 0.00 0.00 0.00 3.79
1911 4160 5.897377 ATTACGGAAGCAACTTTAGCATT 57.103 34.783 0.00 0.00 0.00 3.56
1912 4161 3.559238 ACGGAAGCAACTTTAGCATTG 57.441 42.857 0.00 0.00 0.00 2.82
1913 4162 2.884639 ACGGAAGCAACTTTAGCATTGT 59.115 40.909 0.00 0.00 0.00 2.71
1914 4163 4.069304 ACGGAAGCAACTTTAGCATTGTA 58.931 39.130 0.00 0.00 0.00 2.41
1915 4164 4.517453 ACGGAAGCAACTTTAGCATTGTAA 59.483 37.500 0.00 0.00 0.00 2.41
1916 4165 5.009210 ACGGAAGCAACTTTAGCATTGTAAA 59.991 36.000 0.00 0.00 0.00 2.01
1917 4166 6.092748 CGGAAGCAACTTTAGCATTGTAAAT 58.907 36.000 0.00 0.00 0.00 1.40
1918 4167 6.033831 CGGAAGCAACTTTAGCATTGTAAATG 59.966 38.462 0.00 0.00 0.00 2.32
1919 4168 6.868339 GGAAGCAACTTTAGCATTGTAAATGT 59.132 34.615 2.23 0.00 0.00 2.71
1920 4169 7.384932 GGAAGCAACTTTAGCATTGTAAATGTT 59.615 33.333 2.23 0.00 0.00 2.71
1921 4170 7.642071 AGCAACTTTAGCATTGTAAATGTTG 57.358 32.000 17.65 17.65 36.04 3.33
1922 4171 6.146021 AGCAACTTTAGCATTGTAAATGTTGC 59.854 34.615 26.95 26.95 44.58 4.17
1923 4172 6.515882 CAACTTTAGCATTGTAAATGTTGCG 58.484 36.000 13.55 0.00 40.00 4.85
1924 4173 5.768317 ACTTTAGCATTGTAAATGTTGCGT 58.232 33.333 2.23 0.00 40.00 5.24
1925 4174 6.904498 ACTTTAGCATTGTAAATGTTGCGTA 58.096 32.000 2.23 0.00 40.00 4.42
1926 4175 7.364200 ACTTTAGCATTGTAAATGTTGCGTAA 58.636 30.769 2.23 0.00 40.00 3.18
1927 4176 7.863375 ACTTTAGCATTGTAAATGTTGCGTAAA 59.137 29.630 2.23 0.00 40.00 2.01
1928 4177 8.749841 TTTAGCATTGTAAATGTTGCGTAAAT 57.250 26.923 2.23 0.00 40.00 1.40
1929 4178 6.869421 AGCATTGTAAATGTTGCGTAAATC 57.131 33.333 2.23 0.00 40.00 2.17
1930 4179 6.620678 AGCATTGTAAATGTTGCGTAAATCT 58.379 32.000 2.23 0.00 40.00 2.40
1931 4180 6.527722 AGCATTGTAAATGTTGCGTAAATCTG 59.472 34.615 2.23 0.00 40.00 2.90
1932 4181 6.526325 GCATTGTAAATGTTGCGTAAATCTGA 59.474 34.615 2.23 0.00 0.00 3.27
1933 4182 7.220683 GCATTGTAAATGTTGCGTAAATCTGAT 59.779 33.333 2.23 0.00 0.00 2.90
1934 4183 9.075519 CATTGTAAATGTTGCGTAAATCTGATT 57.924 29.630 0.00 0.00 0.00 2.57
1935 4184 9.638239 ATTGTAAATGTTGCGTAAATCTGATTT 57.362 25.926 18.64 18.64 36.29 2.17
1936 4185 8.446489 TGTAAATGTTGCGTAAATCTGATTTG 57.554 30.769 22.47 10.21 33.82 2.32
1937 4186 8.293157 TGTAAATGTTGCGTAAATCTGATTTGA 58.707 29.630 22.47 6.95 33.82 2.69
1938 4187 7.801547 AAATGTTGCGTAAATCTGATTTGAG 57.198 32.000 22.47 16.85 33.82 3.02
1939 4188 6.741992 ATGTTGCGTAAATCTGATTTGAGA 57.258 33.333 22.47 3.27 33.82 3.27
1940 4189 6.552859 TGTTGCGTAAATCTGATTTGAGAA 57.447 33.333 22.47 10.16 33.82 2.87
1941 4190 6.964908 TGTTGCGTAAATCTGATTTGAGAAA 58.035 32.000 22.47 14.63 33.82 2.52
1942 4191 6.855914 TGTTGCGTAAATCTGATTTGAGAAAC 59.144 34.615 22.47 22.64 33.22 2.78
1943 4192 6.552859 TGCGTAAATCTGATTTGAGAAACA 57.447 33.333 22.47 10.86 33.82 2.83
1944 4193 6.964908 TGCGTAAATCTGATTTGAGAAACAA 58.035 32.000 22.47 0.56 36.65 2.83
1945 4194 7.077605 TGCGTAAATCTGATTTGAGAAACAAG 58.922 34.615 22.47 7.02 39.77 3.16
1946 4195 7.041440 TGCGTAAATCTGATTTGAGAAACAAGA 60.041 33.333 22.47 0.00 39.77 3.02
1947 4196 7.803189 GCGTAAATCTGATTTGAGAAACAAGAA 59.197 33.333 22.47 0.00 39.77 2.52
1956 4205 7.502226 TGATTTGAGAAACAAGAACAGTACCAT 59.498 33.333 0.00 0.00 39.77 3.55
1959 4208 5.071788 TGAGAAACAAGAACAGTACCATCCT 59.928 40.000 0.00 0.00 0.00 3.24
1962 4211 6.935208 AGAAACAAGAACAGTACCATCCTAAC 59.065 38.462 0.00 0.00 0.00 2.34
1969 4218 6.901300 AGAACAGTACCATCCTAACCAATAGA 59.099 38.462 0.00 0.00 33.04 1.98
1971 4220 5.602978 ACAGTACCATCCTAACCAATAGAGG 59.397 44.000 0.00 0.00 33.04 3.69
1976 4225 5.310857 ACCATCCTAACCAATAGAGGGAATC 59.689 44.000 0.00 0.00 33.04 2.52
1977 4226 5.310594 CCATCCTAACCAATAGAGGGAATCA 59.689 44.000 0.00 0.00 33.04 2.57
1986 4409 6.846505 ACCAATAGAGGGAATCATCAAGAGTA 59.153 38.462 0.00 0.00 0.00 2.59
1989 4613 4.555689 AGAGGGAATCATCAAGAGTAGCT 58.444 43.478 0.00 0.00 0.00 3.32
2124 4752 4.214971 CCTGATCTGTGTTTTTGTGGAGAG 59.785 45.833 0.00 0.00 0.00 3.20
2146 4774 1.356124 AGTGGCTTCAGTGGATGTCT 58.644 50.000 0.00 0.00 0.00 3.41
2150 4778 1.457346 GCTTCAGTGGATGTCTTGGG 58.543 55.000 0.00 0.00 0.00 4.12
2196 4824 3.508845 ATACAGCAGTTGGTTCCACTT 57.491 42.857 0.00 0.00 0.00 3.16
2380 5028 9.909644 GACTTGTTTCTTACTCATACTTGACTA 57.090 33.333 0.00 0.00 0.00 2.59
2917 5616 5.296780 GCTTGTTGCTGATATAAGCTTGGTA 59.703 40.000 13.45 2.38 43.90 3.25
2942 5643 6.491403 ACCTTCAGCAACTTAATCTCACAAAT 59.509 34.615 0.00 0.00 0.00 2.32
2943 5644 7.014615 ACCTTCAGCAACTTAATCTCACAAATT 59.985 33.333 0.00 0.00 0.00 1.82
2946 5647 9.598517 TTCAGCAACTTAATCTCACAAATTTTT 57.401 25.926 0.00 0.00 0.00 1.94
3095 5796 1.595311 TGGGCCAAGTATGAGTCCAT 58.405 50.000 2.13 0.00 36.81 3.41
3242 5958 5.038033 TGTTTGCTAATTTCGAAACACACC 58.962 37.500 13.81 1.86 34.27 4.16
3265 5981 5.239963 CCGGTTACTTCCATTTGTGTACTTT 59.760 40.000 0.00 0.00 0.00 2.66
3266 5982 6.427547 CCGGTTACTTCCATTTGTGTACTTTA 59.572 38.462 0.00 0.00 0.00 1.85
3302 6020 6.811954 AGTTCTTCTCACCTATAGCTAAAGC 58.188 40.000 0.00 0.00 42.49 3.51
3446 6177 7.254932 CCGAATCCTTGATTCCTTGATAACTTC 60.255 40.741 10.37 0.00 43.70 3.01
3731 6552 8.755696 TGTTGCCAACTTGAAACATATATTTC 57.244 30.769 9.30 0.00 38.77 2.17
3793 6614 0.899720 AGGCAATTCGTCCTCGGTTA 59.100 50.000 0.00 0.00 37.69 2.85
3831 6653 1.742761 CGTCTGGTGAGGCATTCATT 58.257 50.000 0.00 0.00 38.29 2.57
3849 6684 2.182516 TTCCTGATTCCCTCTCCTCC 57.817 55.000 0.00 0.00 0.00 4.30
3984 6820 3.334691 TGATTTTGCTCGTCCTCGATTT 58.665 40.909 0.00 0.00 45.21 2.17
4059 6896 7.194278 GTCACTTTAGAGTCGCTTGTGATATA 58.806 38.462 12.54 0.00 34.83 0.86
4078 6915 6.318648 TGATATAATTTTGCTTGTCCTCGCTT 59.681 34.615 0.00 0.00 0.00 4.68
4083 6920 2.029844 GCTTGTCCTCGCTTTCGCT 61.030 57.895 0.00 0.00 35.26 4.93
4084 6921 1.784062 CTTGTCCTCGCTTTCGCTG 59.216 57.895 0.00 0.00 35.26 5.18
4114 6980 2.750637 TCCGTCCCTGCGACTCTC 60.751 66.667 0.00 0.00 39.56 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 1053 5.163893 GGCAATCAATCAATCAAGCAACAAG 60.164 40.000 0.00 0.00 0.00 3.16
32 1066 4.239428 TCCATCTCAAGGCAATCAATCA 57.761 40.909 0.00 0.00 0.00 2.57
33 1067 5.068723 ACAATCCATCTCAAGGCAATCAATC 59.931 40.000 0.00 0.00 0.00 2.67
34 1068 4.960469 ACAATCCATCTCAAGGCAATCAAT 59.040 37.500 0.00 0.00 0.00 2.57
35 1069 4.346730 ACAATCCATCTCAAGGCAATCAA 58.653 39.130 0.00 0.00 0.00 2.57
215 1349 7.440523 AAAAAGAATAGTGCTAGGTCTGTTG 57.559 36.000 0.00 0.00 0.00 3.33
445 1590 0.455633 CAGGCATCAGCTCGCAAAAC 60.456 55.000 2.05 0.00 41.70 2.43
539 1785 1.002888 ACCAGAAGCACACCATCAGAG 59.997 52.381 0.00 0.00 0.00 3.35
818 2068 8.084985 TGGATGTAAATATTGTACCTCTGTCA 57.915 34.615 0.00 0.00 0.00 3.58
1049 2303 2.270527 GAGGGTCCTTCTGCAGGC 59.729 66.667 15.13 0.00 43.55 4.85
1082 2340 0.676782 ACGGGGCAGAGGAAAAATCG 60.677 55.000 0.00 0.00 0.00 3.34
1109 2367 1.860641 TTCGGGGCAAGATCTAGACA 58.139 50.000 0.00 0.00 0.00 3.41
1432 3521 1.884075 TAGTGCTACAGGGTGGTGCG 61.884 60.000 0.00 0.00 0.00 5.34
1683 3930 7.088905 CGGTATGCGTTAATAGACTAAGGAAT 58.911 38.462 0.00 0.00 0.00 3.01
1894 4143 6.868339 ACATTTACAATGCTAAAGTTGCTTCC 59.132 34.615 0.00 0.00 0.00 3.46
1895 4144 7.873739 ACATTTACAATGCTAAAGTTGCTTC 57.126 32.000 0.00 0.00 0.00 3.86
1896 4145 7.307337 GCAACATTTACAATGCTAAAGTTGCTT 60.307 33.333 22.12 0.00 41.06 3.91
1897 4146 6.146021 GCAACATTTACAATGCTAAAGTTGCT 59.854 34.615 22.12 0.01 41.06 3.91
1898 4147 6.298853 GCAACATTTACAATGCTAAAGTTGC 58.701 36.000 18.10 18.10 39.74 4.17
1899 4148 6.143758 ACGCAACATTTACAATGCTAAAGTTG 59.856 34.615 9.92 9.92 36.67 3.16
1900 4149 6.212955 ACGCAACATTTACAATGCTAAAGTT 58.787 32.000 0.00 0.00 36.67 2.66
1901 4150 5.768317 ACGCAACATTTACAATGCTAAAGT 58.232 33.333 0.00 0.00 36.67 2.66
1902 4151 7.789341 TTACGCAACATTTACAATGCTAAAG 57.211 32.000 0.00 0.00 36.67 1.85
1903 4152 8.749841 ATTTACGCAACATTTACAATGCTAAA 57.250 26.923 0.00 0.00 36.67 1.85
1904 4153 8.240682 AGATTTACGCAACATTTACAATGCTAA 58.759 29.630 0.00 0.00 36.67 3.09
1905 4154 7.696035 CAGATTTACGCAACATTTACAATGCTA 59.304 33.333 0.00 0.00 36.67 3.49
1906 4155 6.527722 CAGATTTACGCAACATTTACAATGCT 59.472 34.615 0.00 0.00 36.67 3.79
1907 4156 6.526325 TCAGATTTACGCAACATTTACAATGC 59.474 34.615 0.00 0.00 35.49 3.56
1908 4157 8.619146 ATCAGATTTACGCAACATTTACAATG 57.381 30.769 0.00 0.00 0.00 2.82
1909 4158 9.638239 AAATCAGATTTACGCAACATTTACAAT 57.362 25.926 6.60 0.00 0.00 2.71
1910 4159 8.910666 CAAATCAGATTTACGCAACATTTACAA 58.089 29.630 8.12 0.00 0.00 2.41
1911 4160 8.293157 TCAAATCAGATTTACGCAACATTTACA 58.707 29.630 8.12 0.00 0.00 2.41
1912 4161 8.667987 TCAAATCAGATTTACGCAACATTTAC 57.332 30.769 8.12 0.00 0.00 2.01
1913 4162 8.726068 TCTCAAATCAGATTTACGCAACATTTA 58.274 29.630 8.12 0.00 0.00 1.40
1914 4163 7.592938 TCTCAAATCAGATTTACGCAACATTT 58.407 30.769 8.12 0.00 0.00 2.32
1915 4164 7.144722 TCTCAAATCAGATTTACGCAACATT 57.855 32.000 8.12 0.00 0.00 2.71
1916 4165 6.741992 TCTCAAATCAGATTTACGCAACAT 57.258 33.333 8.12 0.00 0.00 2.71
1917 4166 6.552859 TTCTCAAATCAGATTTACGCAACA 57.447 33.333 8.12 0.00 0.00 3.33
1918 4167 6.855914 TGTTTCTCAAATCAGATTTACGCAAC 59.144 34.615 8.12 9.26 0.00 4.17
1919 4168 6.964908 TGTTTCTCAAATCAGATTTACGCAA 58.035 32.000 8.12 0.00 0.00 4.85
1920 4169 6.552859 TGTTTCTCAAATCAGATTTACGCA 57.447 33.333 8.12 0.64 0.00 5.24
1921 4170 7.298122 TCTTGTTTCTCAAATCAGATTTACGC 58.702 34.615 8.12 0.00 35.48 4.42
1922 4171 9.107367 GTTCTTGTTTCTCAAATCAGATTTACG 57.893 33.333 8.12 3.14 35.48 3.18
1923 4172 9.950680 TGTTCTTGTTTCTCAAATCAGATTTAC 57.049 29.630 8.12 3.76 35.48 2.01
1925 4174 8.689972 ACTGTTCTTGTTTCTCAAATCAGATTT 58.310 29.630 2.20 2.20 35.48 2.17
1926 4175 8.230472 ACTGTTCTTGTTTCTCAAATCAGATT 57.770 30.769 0.00 0.00 35.48 2.40
1927 4176 7.814264 ACTGTTCTTGTTTCTCAAATCAGAT 57.186 32.000 0.00 0.00 35.48 2.90
1928 4177 7.226720 GGTACTGTTCTTGTTTCTCAAATCAGA 59.773 37.037 0.00 0.00 35.48 3.27
1929 4178 7.012327 TGGTACTGTTCTTGTTTCTCAAATCAG 59.988 37.037 0.00 0.00 35.48 2.90
1930 4179 6.826231 TGGTACTGTTCTTGTTTCTCAAATCA 59.174 34.615 0.00 0.00 35.48 2.57
1931 4180 7.259290 TGGTACTGTTCTTGTTTCTCAAATC 57.741 36.000 0.00 0.00 35.48 2.17
1932 4181 7.040409 GGATGGTACTGTTCTTGTTTCTCAAAT 60.040 37.037 0.00 0.00 35.48 2.32
1933 4182 6.262273 GGATGGTACTGTTCTTGTTTCTCAAA 59.738 38.462 0.00 0.00 35.48 2.69
1934 4183 5.763204 GGATGGTACTGTTCTTGTTTCTCAA 59.237 40.000 0.00 0.00 34.61 3.02
1935 4184 5.071788 AGGATGGTACTGTTCTTGTTTCTCA 59.928 40.000 0.00 0.00 0.00 3.27
1936 4185 5.552178 AGGATGGTACTGTTCTTGTTTCTC 58.448 41.667 0.00 0.00 0.00 2.87
1937 4186 5.568620 AGGATGGTACTGTTCTTGTTTCT 57.431 39.130 0.00 0.00 0.00 2.52
1938 4187 6.148976 GGTTAGGATGGTACTGTTCTTGTTTC 59.851 42.308 0.00 0.00 0.00 2.78
1939 4188 6.002082 GGTTAGGATGGTACTGTTCTTGTTT 58.998 40.000 0.00 0.00 0.00 2.83
1940 4189 5.072600 TGGTTAGGATGGTACTGTTCTTGTT 59.927 40.000 0.00 0.00 0.00 2.83
1941 4190 4.595781 TGGTTAGGATGGTACTGTTCTTGT 59.404 41.667 0.00 0.00 0.00 3.16
1942 4191 5.160607 TGGTTAGGATGGTACTGTTCTTG 57.839 43.478 0.00 0.00 0.00 3.02
1943 4192 5.836024 TTGGTTAGGATGGTACTGTTCTT 57.164 39.130 0.00 0.00 0.00 2.52
1944 4193 6.901300 TCTATTGGTTAGGATGGTACTGTTCT 59.099 38.462 0.00 0.00 0.00 3.01
1945 4194 7.120923 TCTATTGGTTAGGATGGTACTGTTC 57.879 40.000 0.00 0.00 0.00 3.18
1946 4195 6.099845 CCTCTATTGGTTAGGATGGTACTGTT 59.900 42.308 0.00 0.00 31.64 3.16
1947 4196 5.602978 CCTCTATTGGTTAGGATGGTACTGT 59.397 44.000 0.00 0.00 31.64 3.55
1956 4205 6.150332 TGATGATTCCCTCTATTGGTTAGGA 58.850 40.000 0.00 0.00 31.64 2.94
1959 4208 7.348274 ACTCTTGATGATTCCCTCTATTGGTTA 59.652 37.037 0.00 0.00 0.00 2.85
1962 4211 6.185114 ACTCTTGATGATTCCCTCTATTGG 57.815 41.667 0.00 0.00 0.00 3.16
1969 4218 6.328672 ACATAAGCTACTCTTGATGATTCCCT 59.671 38.462 0.00 0.00 36.25 4.20
1971 4220 8.443953 AAACATAAGCTACTCTTGATGATTCC 57.556 34.615 0.00 0.00 36.25 3.01
1986 4409 6.622427 ACCTCACCTACTAAAACATAAGCT 57.378 37.500 0.00 0.00 0.00 3.74
2124 4752 3.003480 GACATCCACTGAAGCCACTTAC 58.997 50.000 0.00 0.00 0.00 2.34
2146 4774 1.774217 AAGTCACCCAGGAGCCCAA 60.774 57.895 0.00 0.00 0.00 4.12
2150 4778 0.326264 ACATCAAGTCACCCAGGAGC 59.674 55.000 0.00 0.00 0.00 4.70
2246 4874 2.831685 TCCATCATATACACGCCCAC 57.168 50.000 0.00 0.00 0.00 4.61
2648 5316 1.075536 AGGACCCCCAAGACATTTGTC 59.924 52.381 2.41 2.41 39.04 3.18
2917 5616 4.973168 TGTGAGATTAAGTTGCTGAAGGT 58.027 39.130 0.00 0.00 0.00 3.50
3095 5796 4.314440 GTGTCCAGGAGCGTGCCA 62.314 66.667 0.00 0.00 0.00 4.92
3189 5891 0.179103 GGGGGAAATGCATTTCAGCG 60.179 55.000 39.11 0.00 46.03 5.18
3242 5958 5.934935 AAGTACACAAATGGAAGTAACCG 57.065 39.130 0.00 0.00 0.00 4.44
3302 6020 1.333619 CACCTGGTTTGTCGTCTTTGG 59.666 52.381 0.00 0.00 0.00 3.28
3411 6130 6.771267 AGGAATCAAGGATTCGGTATAAAACC 59.229 38.462 11.57 0.00 46.47 3.27
3731 6552 6.426646 AGAGGTAAGCCATTCATACCTAAG 57.573 41.667 3.83 0.00 46.25 2.18
3831 6653 0.105964 CGGAGGAGAGGGAATCAGGA 60.106 60.000 0.00 0.00 0.00 3.86
3849 6684 1.659098 GGGACGAGCAACATAAAGTCG 59.341 52.381 0.00 0.00 36.71 4.18
3901 6737 4.611355 CGAGCAAAATGACAAATCAGACGT 60.611 41.667 0.00 0.00 38.57 4.34
3984 6820 4.357142 GCGATTTTCTATCTACACGGACA 58.643 43.478 0.00 0.00 0.00 4.02
4059 6896 3.642705 GAAAGCGAGGACAAGCAAAATT 58.357 40.909 0.00 0.00 35.48 1.82


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

AutoCloner maintained by Alex Coulton.