Multiple sequence alignment - TraesCS7A01G476900

Loading Multiple Alignment...

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 TraesCS7A01G476900 chr7A 100.000 2321 0 0 1 2321 670865878 670863558 0.000000e+00 4287.0
1 TraesCS7A01G476900 chr7A 80.558 967 87 47 437 1379 671200422 671201311 0.000000e+00 651.0
2 TraesCS7A01G476900 chr7A 73.732 552 71 45 1829 2321 20547429 20546893 5.170000e-32 148.0
3 TraesCS7A01G476900 chr7A 90.164 61 3 3 165 224 671195488 671195546 2.470000e-10 76.8
4 TraesCS7A01G476900 chr7D 87.867 1772 110 45 104 1814 578811551 578809824 0.000000e+00 1984.0
5 TraesCS7A01G476900 chr7D 84.926 1214 88 39 367 1524 578913043 578911869 0.000000e+00 1140.0
6 TraesCS7A01G476900 chr7D 80.081 989 86 53 437 1390 579361867 579362779 1.170000e-177 632.0
7 TraesCS7A01G476900 chr7D 81.781 483 58 20 1858 2321 379311037 379310566 6.050000e-101 377.0
8 TraesCS7A01G476900 chr7D 94.262 244 10 4 104 347 578914308 578914069 1.010000e-98 370.0
9 TraesCS7A01G476900 chr7D 81.198 484 60 21 1858 2321 379310098 379309626 6.100000e-96 361.0
10 TraesCS7A01G476900 chr7D 80.903 487 42 24 1855 2320 595397873 595398329 1.030000e-88 337.0
11 TraesCS7A01G476900 chr7D 84.775 289 25 8 2033 2321 365487152 365487421 2.940000e-69 272.0
12 TraesCS7A01G476900 chr7D 88.205 195 17 4 1831 2024 365484528 365484717 6.450000e-56 228.0
13 TraesCS7A01G476900 chr7D 95.455 66 0 1 43 105 578914432 578914367 4.080000e-18 102.0
14 TraesCS7A01G476900 chr7D 92.308 65 0 2 46 105 578811674 578811610 1.140000e-13 87.9
15 TraesCS7A01G476900 chr7B 85.903 1284 100 39 417 1651 642832061 642830810 0.000000e+00 1293.0
16 TraesCS7A01G476900 chr7B 86.447 1033 70 22 605 1628 642974372 642973401 0.000000e+00 1068.0
17 TraesCS7A01G476900 chr7B 86.157 1033 73 23 605 1628 643002741 643001770 0.000000e+00 1051.0
18 TraesCS7A01G476900 chr7B 85.963 1033 75 21 605 1628 642989445 642988474 0.000000e+00 1040.0
19 TraesCS7A01G476900 chr7B 85.479 1033 71 25 605 1628 643015699 643014737 0.000000e+00 1003.0
20 TraesCS7A01G476900 chr7B 84.116 894 53 33 433 1288 645266092 645265250 0.000000e+00 782.0
21 TraesCS7A01G476900 chr7B 85.430 453 26 17 104 532 643017236 643016800 3.540000e-118 435.0
22 TraesCS7A01G476900 chr7B 84.989 453 28 17 104 532 642990982 642990546 7.670000e-115 424.0
23 TraesCS7A01G476900 chr7B 85.235 447 26 17 110 532 643004272 643003842 7.670000e-115 424.0
24 TraesCS7A01G476900 chr7B 84.106 453 31 18 104 532 642975908 642975473 1.290000e-107 399.0
25 TraesCS7A01G476900 chr7B 91.787 207 15 2 104 310 642834486 642834282 1.050000e-73 287.0
26 TraesCS7A01G476900 chr7B 93.043 115 6 2 104 218 645266793 645266681 1.430000e-37 167.0
27 TraesCS7A01G476900 chr7B 95.082 61 0 1 46 103 642991119 642991059 2.460000e-15 93.5
28 TraesCS7A01G476900 chr7B 90.625 64 3 1 43 103 642976048 642975985 5.320000e-12 82.4
29 TraesCS7A01G476900 chr3D 83.817 482 46 21 1849 2321 60008537 60008995 1.650000e-116 429.0
30 TraesCS7A01G476900 chr6B 82.466 519 56 15 1834 2321 676678946 676678432 2.760000e-114 422.0
31 TraesCS7A01G476900 chr3B 80.344 524 63 26 1831 2321 614615154 614615670 6.100000e-96 361.0
32 TraesCS7A01G476900 chr3B 76.998 513 75 32 1838 2321 378214171 378214669 1.060000e-63 254.0
33 TraesCS7A01G476900 chr3B 75.967 491 75 33 1864 2321 460121558 460121078 1.810000e-51 213.0
34 TraesCS7A01G476900 chr4B 80.038 521 66 25 1831 2320 639237902 639237389 3.670000e-93 351.0
35 TraesCS7A01G476900 chr6D 80.116 518 55 30 1848 2321 270186469 270185956 2.210000e-90 342.0
36 TraesCS7A01G476900 chr5D 80.753 478 53 30 1865 2321 520430639 520430180 1.030000e-88 337.0
37 TraesCS7A01G476900 chr2B 77.087 515 83 23 1831 2321 648088989 648088486 4.920000e-67 265.0
38 TraesCS7A01G476900 chr2B 77.936 281 40 15 1831 2092 238975280 238975557 3.090000e-34 156.0
39 TraesCS7A01G476900 chr2B 100.000 29 0 0 1 29 720586547 720586575 1.000000e-03 54.7
40 TraesCS7A01G476900 chr2B 100.000 29 0 0 1 29 732643878 732643906 1.000000e-03 54.7
41 TraesCS7A01G476900 chr2A 88.732 213 18 4 2110 2319 645803715 645803506 2.960000e-64 255.0
42 TraesCS7A01G476900 chr1D 77.087 515 55 33 1857 2321 353645840 353645339 2.980000e-59 239.0
43 TraesCS7A01G476900 chr1D 76.415 530 74 35 1831 2321 400034964 400035481 2.980000e-59 239.0
44 TraesCS7A01G476900 chr1D 88.298 188 14 5 2137 2321 78403402 78403584 3.880000e-53 219.0
45 TraesCS7A01G476900 chr1D 77.041 392 40 26 1854 2222 389212521 389212157 1.830000e-41 180.0
46 TraesCS7A01G476900 chr4D 74.583 539 77 34 1831 2315 222967720 222967188 5.090000e-42 182.0
47 TraesCS7A01G476900 chr5B 100.000 30 0 0 1 30 672235359 672235388 3.220000e-04 56.5
48 TraesCS7A01G476900 chr1A 100.000 28 0 0 1 28 29008497 29008524 4.000000e-03 52.8
49 TraesCS7A01G476900 chr1A 100.000 28 0 0 1 28 549124992 549125019 4.000000e-03 52.8


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 TraesCS7A01G476900 chr7A 670863558 670865878 2320 True 4287.000000 4287 100.000000 1 2321 1 chr7A.!!$R2 2320
1 TraesCS7A01G476900 chr7A 671200422 671201311 889 False 651.000000 651 80.558000 437 1379 1 chr7A.!!$F2 942
2 TraesCS7A01G476900 chr7D 578809824 578811674 1850 True 1035.950000 1984 90.087500 46 1814 2 chr7D.!!$R2 1768
3 TraesCS7A01G476900 chr7D 579361867 579362779 912 False 632.000000 632 80.081000 437 1390 1 chr7D.!!$F1 953
4 TraesCS7A01G476900 chr7D 578911869 578914432 2563 True 537.333333 1140 91.547667 43 1524 3 chr7D.!!$R3 1481
5 TraesCS7A01G476900 chr7D 379309626 379311037 1411 True 369.000000 377 81.489500 1858 2321 2 chr7D.!!$R1 463
6 TraesCS7A01G476900 chr7D 365484528 365487421 2893 False 250.000000 272 86.490000 1831 2321 2 chr7D.!!$F3 490
7 TraesCS7A01G476900 chr7B 642830810 642834486 3676 True 790.000000 1293 88.845000 104 1651 2 chr7B.!!$R1 1547
8 TraesCS7A01G476900 chr7B 643001770 643004272 2502 True 737.500000 1051 85.696000 110 1628 2 chr7B.!!$R4 1518
9 TraesCS7A01G476900 chr7B 643014737 643017236 2499 True 719.000000 1003 85.454500 104 1628 2 chr7B.!!$R5 1524
10 TraesCS7A01G476900 chr7B 642988474 642991119 2645 True 519.166667 1040 88.678000 46 1628 3 chr7B.!!$R3 1582
11 TraesCS7A01G476900 chr7B 642973401 642976048 2647 True 516.466667 1068 87.059333 43 1628 3 chr7B.!!$R2 1585
12 TraesCS7A01G476900 chr7B 645265250 645266793 1543 True 474.500000 782 88.579500 104 1288 2 chr7B.!!$R6 1184
13 TraesCS7A01G476900 chr6B 676678432 676678946 514 True 422.000000 422 82.466000 1834 2321 1 chr6B.!!$R1 487
14 TraesCS7A01G476900 chr3B 614615154 614615670 516 False 361.000000 361 80.344000 1831 2321 1 chr3B.!!$F2 490
15 TraesCS7A01G476900 chr4B 639237389 639237902 513 True 351.000000 351 80.038000 1831 2320 1 chr4B.!!$R1 489
16 TraesCS7A01G476900 chr6D 270185956 270186469 513 True 342.000000 342 80.116000 1848 2321 1 chr6D.!!$R1 473
17 TraesCS7A01G476900 chr2B 648088486 648088989 503 True 265.000000 265 77.087000 1831 2321 1 chr2B.!!$R1 490
18 TraesCS7A01G476900 chr1D 353645339 353645840 501 True 239.000000 239 77.087000 1857 2321 1 chr1D.!!$R1 464
19 TraesCS7A01G476900 chr1D 400034964 400035481 517 False 239.000000 239 76.415000 1831 2321 1 chr1D.!!$F2 490

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
38 39 0.179067 GGACGGGGCGTGATATTGAA 60.179 55.000 0.0 0.0 41.37 2.69 F
41 42 1.140052 ACGGGGCGTGATATTGAATCA 59.860 47.619 0.0 0.0 39.18 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1005 5497 0.176680 ACGAGGCATTTCGCTGATCT 59.823 50.0 4.68 0.0 44.15 2.75 R
1817 6360 0.529119 GGACGTCGTGTGTTGGAGTT 60.529 55.0 9.92 0.0 0.00 3.01 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
34 35 3.239253 GGGGACGGGGCGTGATAT 61.239 66.667 0.00 0.00 41.37 1.63
35 36 2.814835 GGGGACGGGGCGTGATATT 61.815 63.158 0.00 0.00 41.37 1.28
36 37 1.597027 GGGACGGGGCGTGATATTG 60.597 63.158 0.00 0.00 41.37 1.90
37 38 1.444250 GGACGGGGCGTGATATTGA 59.556 57.895 0.00 0.00 41.37 2.57
38 39 0.179067 GGACGGGGCGTGATATTGAA 60.179 55.000 0.00 0.00 41.37 2.69
39 40 1.542547 GGACGGGGCGTGATATTGAAT 60.543 52.381 0.00 0.00 41.37 2.57
40 41 1.798813 GACGGGGCGTGATATTGAATC 59.201 52.381 0.00 0.00 41.37 2.52
41 42 1.140052 ACGGGGCGTGATATTGAATCA 59.860 47.619 0.00 0.00 39.18 2.57
140 222 3.628193 GAGCGCGCATGCAGAGAG 61.628 66.667 35.10 4.39 42.97 3.20
278 373 4.634184 TCTATTTTCTCGGTCTTCGGAG 57.366 45.455 0.00 0.00 40.74 4.63
281 376 1.906990 TTTCTCGGTCTTCGGAGTCT 58.093 50.000 0.00 0.00 40.42 3.24
473 3861 1.673767 TCCCTTGATTCCTGGAGCTT 58.326 50.000 0.00 0.00 0.00 3.74
474 3862 2.845659 TCCCTTGATTCCTGGAGCTTA 58.154 47.619 0.00 0.00 0.00 3.09
475 3863 2.774234 TCCCTTGATTCCTGGAGCTTAG 59.226 50.000 0.00 0.00 0.00 2.18
476 3864 2.570135 CCTTGATTCCTGGAGCTTAGC 58.430 52.381 0.00 0.00 0.00 3.09
477 3865 2.172293 CCTTGATTCCTGGAGCTTAGCT 59.828 50.000 6.37 6.37 43.88 3.32
478 3866 3.371380 CCTTGATTCCTGGAGCTTAGCTT 60.371 47.826 8.58 0.00 39.88 3.74
479 3867 4.141620 CCTTGATTCCTGGAGCTTAGCTTA 60.142 45.833 8.58 0.00 39.88 3.09
480 3868 4.408182 TGATTCCTGGAGCTTAGCTTAC 57.592 45.455 8.58 5.53 39.88 2.34
481 3869 4.033709 TGATTCCTGGAGCTTAGCTTACT 58.966 43.478 8.58 0.00 39.88 2.24
578 4327 2.733858 GCAACCGAAAAAGCAACTCACA 60.734 45.455 0.00 0.00 0.00 3.58
579 4328 2.844122 ACCGAAAAAGCAACTCACAC 57.156 45.000 0.00 0.00 0.00 3.82
764 5225 3.129502 CTCTCGTACGTCCGGGCA 61.130 66.667 16.05 0.00 0.00 5.36
765 5226 3.392595 CTCTCGTACGTCCGGGCAC 62.393 68.421 16.05 0.00 0.00 5.01
766 5227 3.740397 CTCGTACGTCCGGGCACA 61.740 66.667 16.05 0.00 0.00 4.57
767 5228 3.060020 CTCGTACGTCCGGGCACAT 62.060 63.158 16.05 0.00 0.00 3.21
768 5229 2.883730 CGTACGTCCGGGCACATG 60.884 66.667 6.96 0.00 0.00 3.21
789 5250 1.884464 CACATGGGATGCGAGACGG 60.884 63.158 0.00 0.00 0.00 4.79
817 5294 4.380945 ACCACCCCGCCCTACGTA 62.381 66.667 0.00 0.00 41.42 3.57
827 5312 1.861971 GCCCTACGTATTTTCTCCCG 58.138 55.000 0.00 0.00 0.00 5.14
865 5350 2.202987 CACTGCCGGATCAGCTCC 60.203 66.667 5.05 0.00 41.07 4.70
920 5406 4.753662 TCTCCCACCTACGCCGCT 62.754 66.667 0.00 0.00 0.00 5.52
921 5407 4.514577 CTCCCACCTACGCCGCTG 62.515 72.222 0.00 0.00 0.00 5.18
989 5477 2.543067 AATCAACCGGAGCAGGAGCC 62.543 60.000 9.46 0.00 43.56 4.70
1005 5497 2.552819 GCCGTCGATCGAGATGGGA 61.553 63.158 20.09 0.00 45.20 4.37
1012 5504 1.135431 CGATCGAGATGGGAGATCAGC 60.135 57.143 10.26 0.00 40.39 4.26
1201 5705 3.884581 TACGCGCGCAACTTCGACT 62.885 57.895 32.58 8.80 0.00 4.18
1268 5773 0.036952 CACCTCTGCCACCACTACAG 60.037 60.000 0.00 0.00 0.00 2.74
1323 5831 4.277593 CGCCAGCCGCTCTAGGAG 62.278 72.222 0.00 0.00 34.21 3.69
1324 5832 3.151022 GCCAGCCGCTCTAGGAGT 61.151 66.667 0.00 0.00 31.39 3.85
1328 5836 1.234821 CAGCCGCTCTAGGAGTCTAG 58.765 60.000 0.00 0.00 43.27 2.43
1329 5837 0.109723 AGCCGCTCTAGGAGTCTAGG 59.890 60.000 0.00 0.00 42.42 3.02
1330 5838 0.108963 GCCGCTCTAGGAGTCTAGGA 59.891 60.000 0.00 0.00 42.42 2.94
1331 5839 1.886886 CCGCTCTAGGAGTCTAGGAC 58.113 60.000 0.00 0.00 42.42 3.85
1332 5840 1.504359 CGCTCTAGGAGTCTAGGACG 58.496 60.000 0.00 0.00 42.42 4.79
1333 5841 1.874739 CGCTCTAGGAGTCTAGGACGG 60.875 61.905 0.00 0.00 42.42 4.79
1334 5842 1.886886 CTCTAGGAGTCTAGGACGGC 58.113 60.000 0.00 0.00 42.42 5.68
1335 5843 1.141254 CTCTAGGAGTCTAGGACGGCA 59.859 57.143 0.00 0.00 42.42 5.69
1336 5844 1.141254 TCTAGGAGTCTAGGACGGCAG 59.859 57.143 0.00 0.00 42.42 4.85
1450 5983 3.672808 GCGGAGTAGCTAGTAGATGGTA 58.327 50.000 0.00 0.00 0.00 3.25
1530 6069 2.039405 CACTTGGAGAGCTGCAGGC 61.039 63.158 17.12 7.98 42.19 4.85
1561 6100 5.050159 GCCAAGTGGATGAAATGTTTTCAAC 60.050 40.000 0.18 4.57 37.39 3.18
1629 6172 6.262496 CCGTCTCTAATGTTCCTGATAGTACA 59.738 42.308 0.00 0.00 0.00 2.90
1632 6175 9.303537 GTCTCTAATGTTCCTGATAGTACAAAC 57.696 37.037 0.00 0.00 0.00 2.93
1640 6183 6.716934 TCCTGATAGTACAAACCATCTCTC 57.283 41.667 0.00 0.00 0.00 3.20
1654 6197 1.568504 TCTCTCCATACGCCCTTTGT 58.431 50.000 0.00 0.00 0.00 2.83
1656 6199 1.207089 CTCTCCATACGCCCTTTGTCA 59.793 52.381 0.00 0.00 0.00 3.58
1658 6201 1.207089 CTCCATACGCCCTTTGTCAGA 59.793 52.381 0.00 0.00 0.00 3.27
1659 6202 1.626321 TCCATACGCCCTTTGTCAGAA 59.374 47.619 0.00 0.00 0.00 3.02
1660 6203 2.039216 TCCATACGCCCTTTGTCAGAAA 59.961 45.455 0.00 0.00 0.00 2.52
1665 6208 3.020984 ACGCCCTTTGTCAGAAAGAAAA 58.979 40.909 0.00 0.00 0.00 2.29
1666 6209 3.066760 ACGCCCTTTGTCAGAAAGAAAAG 59.933 43.478 0.00 0.00 0.00 2.27
1667 6210 3.315191 CGCCCTTTGTCAGAAAGAAAAGA 59.685 43.478 0.00 0.00 31.63 2.52
1671 6214 6.763135 GCCCTTTGTCAGAAAGAAAAGAAAAT 59.237 34.615 0.00 0.00 31.63 1.82
1674 6217 8.534778 CCTTTGTCAGAAAGAAAAGAAAATTCG 58.465 33.333 0.00 0.00 31.63 3.34
1751 6294 1.001641 GAGTCCAGGCTGGCATTGT 60.002 57.895 29.02 10.46 37.47 2.71
1763 6306 3.004106 GCTGGCATTGTATCAAGTGATCC 59.996 47.826 0.00 0.00 36.05 3.36
1767 6310 4.514441 GGCATTGTATCAAGTGATCCAGAG 59.486 45.833 0.00 0.00 36.05 3.35
1796 6339 4.274459 GGAGGAGTACAATAATTGCTGCTG 59.726 45.833 0.00 0.00 0.00 4.41
1814 6357 2.408271 TGCTGAGGATGCAGTTTAGG 57.592 50.000 0.00 0.00 38.17 2.69
1815 6358 1.020437 GCTGAGGATGCAGTTTAGGC 58.980 55.000 0.00 0.00 38.17 3.93
1816 6359 1.673168 CTGAGGATGCAGTTTAGGCC 58.327 55.000 0.00 0.00 0.00 5.19
1817 6360 0.991146 TGAGGATGCAGTTTAGGCCA 59.009 50.000 5.01 0.00 0.00 5.36
1818 6361 1.354031 TGAGGATGCAGTTTAGGCCAA 59.646 47.619 5.01 0.00 0.00 4.52
1819 6362 1.745653 GAGGATGCAGTTTAGGCCAAC 59.254 52.381 5.01 0.60 0.00 3.77
1820 6363 1.355720 AGGATGCAGTTTAGGCCAACT 59.644 47.619 5.01 3.60 37.49 3.16
1821 6364 1.745653 GGATGCAGTTTAGGCCAACTC 59.254 52.381 5.01 2.33 34.60 3.01
1822 6365 1.745653 GATGCAGTTTAGGCCAACTCC 59.254 52.381 5.01 0.00 34.60 3.85
1823 6366 0.476338 TGCAGTTTAGGCCAACTCCA 59.524 50.000 5.01 0.00 34.60 3.86
1824 6367 1.133637 TGCAGTTTAGGCCAACTCCAA 60.134 47.619 5.01 0.00 34.60 3.53
1825 6368 1.269723 GCAGTTTAGGCCAACTCCAAC 59.730 52.381 5.01 0.00 34.60 3.77
1826 6369 2.582052 CAGTTTAGGCCAACTCCAACA 58.418 47.619 5.01 0.00 34.60 3.33
1827 6370 2.293399 CAGTTTAGGCCAACTCCAACAC 59.707 50.000 5.01 0.00 34.60 3.32
1828 6371 2.092103 AGTTTAGGCCAACTCCAACACA 60.092 45.455 5.01 0.00 30.76 3.72
1829 6372 1.975660 TTAGGCCAACTCCAACACAC 58.024 50.000 5.01 0.00 0.00 3.82
1853 6396 2.031157 CGTCCGTTTTGCTTGGATTCTT 60.031 45.455 0.00 0.00 33.63 2.52
1958 6505 6.891361 TCAAATTATGTCTGGGATGAACATGT 59.109 34.615 0.00 0.00 0.00 3.21
1990 6559 8.712341 AAAAATCGCAAACTCAAATAAAATGC 57.288 26.923 0.00 0.00 0.00 3.56
2067 9086 5.652452 GGCCTCCACAGTTAGAACATAATTT 59.348 40.000 0.00 0.00 0.00 1.82
2101 10065 3.636282 AACAAAATACAAGTGTCGCCC 57.364 42.857 0.00 0.00 0.00 6.13
2102 10066 1.533731 ACAAAATACAAGTGTCGCCCG 59.466 47.619 0.00 0.00 0.00 6.13
2103 10067 1.533731 CAAAATACAAGTGTCGCCCGT 59.466 47.619 0.00 0.00 0.00 5.28
2104 10068 1.435577 AAATACAAGTGTCGCCCGTC 58.564 50.000 0.00 0.00 0.00 4.79
2105 10069 0.734942 AATACAAGTGTCGCCCGTCG 60.735 55.000 0.00 0.00 40.15 5.12
2106 10070 1.870055 ATACAAGTGTCGCCCGTCGT 61.870 55.000 0.00 0.00 39.67 4.34
2107 10071 2.462255 TACAAGTGTCGCCCGTCGTC 62.462 60.000 0.00 0.00 39.67 4.20
2108 10072 4.695231 AAGTGTCGCCCGTCGTCG 62.695 66.667 0.00 0.00 39.67 5.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 2.814835 AATATCACGCCCCGTCCCC 61.815 63.158 0.00 0.00 38.32 4.81
18 19 1.597027 CAATATCACGCCCCGTCCC 60.597 63.158 0.00 0.00 38.32 4.46
19 20 0.179067 TTCAATATCACGCCCCGTCC 60.179 55.000 0.00 0.00 38.32 4.79
20 21 1.798813 GATTCAATATCACGCCCCGTC 59.201 52.381 0.00 0.00 38.32 4.79
21 22 1.140052 TGATTCAATATCACGCCCCGT 59.860 47.619 0.00 0.00 42.36 5.28
22 23 1.800586 CTGATTCAATATCACGCCCCG 59.199 52.381 0.00 0.00 0.00 5.73
23 24 3.126001 TCTGATTCAATATCACGCCCC 57.874 47.619 0.00 0.00 0.00 5.80
24 25 3.369147 CGATCTGATTCAATATCACGCCC 59.631 47.826 8.57 0.00 0.00 6.13
25 26 3.990469 ACGATCTGATTCAATATCACGCC 59.010 43.478 0.00 0.00 0.00 5.68
26 27 4.681483 TCACGATCTGATTCAATATCACGC 59.319 41.667 0.00 0.00 0.00 5.34
27 28 6.805760 AGATCACGATCTGATTCAATATCACG 59.194 38.462 8.75 0.00 45.77 4.35
278 373 2.012673 GATGCATGGGACTTGACAGAC 58.987 52.381 2.46 0.00 0.00 3.51
281 376 0.392863 CCGATGCATGGGACTTGACA 60.393 55.000 22.34 0.00 0.00 3.58
345 2700 4.957296 ACTACCCATGAATAAACTAGGCG 58.043 43.478 0.00 0.00 0.00 5.52
423 3801 3.039988 CAGCACTGCAGCAAGCTT 58.960 55.556 21.85 0.00 45.94 3.74
493 3881 4.527509 ACACTATGATGATTAGGGAGCG 57.472 45.455 0.00 0.00 0.00 5.03
578 4327 2.088423 CCTAGTGAGCAAGTCTCGAGT 58.912 52.381 13.13 0.00 44.86 4.18
579 4328 2.088423 ACCTAGTGAGCAAGTCTCGAG 58.912 52.381 5.93 5.93 44.86 4.04
678 5138 9.614792 GTATGGTTCTGTCTTGGTTTATTATCT 57.385 33.333 0.00 0.00 0.00 1.98
694 5154 5.067936 CCAGTGTAGAGTAGGTATGGTTCTG 59.932 48.000 0.00 0.00 0.00 3.02
726 5186 5.887035 AGAGCGTATAGAAAAGTACACTCCT 59.113 40.000 0.00 0.00 32.90 3.69
764 5225 1.759299 GCATCCCATGTGGCCATGT 60.759 57.895 9.72 0.00 45.83 3.21
765 5226 2.852180 CGCATCCCATGTGGCCATG 61.852 63.158 9.72 3.41 46.65 3.66
766 5227 2.520020 CGCATCCCATGTGGCCAT 60.520 61.111 9.72 0.00 37.14 4.40
767 5228 3.702529 CTCGCATCCCATGTGGCCA 62.703 63.158 0.00 0.00 41.01 5.36
768 5229 2.903855 CTCGCATCCCATGTGGCC 60.904 66.667 0.00 0.00 41.01 5.36
772 5233 2.501128 CCGTCTCGCATCCCATGT 59.499 61.111 0.00 0.00 0.00 3.21
773 5234 2.280389 CCCGTCTCGCATCCCATG 60.280 66.667 0.00 0.00 0.00 3.66
774 5235 1.622607 TTTCCCGTCTCGCATCCCAT 61.623 55.000 0.00 0.00 0.00 4.00
775 5236 2.287274 TTTCCCGTCTCGCATCCCA 61.287 57.895 0.00 0.00 0.00 4.37
789 5250 2.671963 GGGTGGTGAGCGGTTTCC 60.672 66.667 0.00 0.00 0.00 3.13
812 5289 2.620242 GGTTGCGGGAGAAAATACGTA 58.380 47.619 0.00 0.00 0.00 3.57
813 5290 1.445871 GGTTGCGGGAGAAAATACGT 58.554 50.000 0.00 0.00 0.00 3.57
815 5292 1.100510 GGGGTTGCGGGAGAAAATAC 58.899 55.000 0.00 0.00 0.00 1.89
816 5293 0.393267 CGGGGTTGCGGGAGAAAATA 60.393 55.000 0.00 0.00 0.00 1.40
817 5294 1.677633 CGGGGTTGCGGGAGAAAAT 60.678 57.895 0.00 0.00 0.00 1.82
865 5350 2.221055 GCGCCGATTTATAGGAGTTGTG 59.779 50.000 0.00 0.00 0.00 3.33
920 5406 0.254462 TTGGACTGTTGGAGTGTGCA 59.746 50.000 0.00 0.00 33.83 4.57
921 5407 0.663153 GTTGGACTGTTGGAGTGTGC 59.337 55.000 0.00 0.00 33.83 4.57
922 5408 1.308998 GGTTGGACTGTTGGAGTGTG 58.691 55.000 0.00 0.00 33.83 3.82
923 5409 0.916086 TGGTTGGACTGTTGGAGTGT 59.084 50.000 0.00 0.00 33.83 3.55
924 5410 1.676006 GTTGGTTGGACTGTTGGAGTG 59.324 52.381 0.00 0.00 33.83 3.51
925 5411 1.409661 GGTTGGTTGGACTGTTGGAGT 60.410 52.381 0.00 0.00 37.76 3.85
989 5477 1.129624 GATCTCCCATCTCGATCGACG 59.870 57.143 15.15 10.75 44.09 5.12
1005 5497 0.176680 ACGAGGCATTTCGCTGATCT 59.823 50.000 4.68 0.00 44.15 2.75
1012 5504 1.730593 GACGACGACGAGGCATTTCG 61.731 60.000 15.32 0.42 45.70 3.46
1316 5824 1.141254 CTGCCGTCCTAGACTCCTAGA 59.859 57.143 0.00 0.00 44.00 2.43
1445 5978 3.814842 CCACATATGAACACGCATACCAT 59.185 43.478 10.38 0.00 33.88 3.55
1450 5983 1.064758 ACCCCACATATGAACACGCAT 60.065 47.619 10.38 0.00 0.00 4.73
1530 6069 6.400568 ACATTTCATCCACTTGGCTAATTTG 58.599 36.000 0.00 0.00 34.44 2.32
1629 6172 1.141053 GGGCGTATGGAGAGATGGTTT 59.859 52.381 0.00 0.00 0.00 3.27
1632 6175 1.051812 AAGGGCGTATGGAGAGATGG 58.948 55.000 0.00 0.00 0.00 3.51
1640 6183 2.107950 TTCTGACAAAGGGCGTATGG 57.892 50.000 0.00 0.00 0.00 2.74
1654 6197 8.438676 AGAGACGAATTTTCTTTTCTTTCTGA 57.561 30.769 0.00 0.00 0.00 3.27
1656 6199 8.893727 TGAAGAGACGAATTTTCTTTTCTTTCT 58.106 29.630 16.10 0.00 35.95 2.52
1665 6208 7.224362 CAGAGCATATGAAGAGACGAATTTTCT 59.776 37.037 6.97 0.00 0.00 2.52
1666 6209 7.223582 TCAGAGCATATGAAGAGACGAATTTTC 59.776 37.037 6.97 0.00 0.00 2.29
1667 6210 7.044181 TCAGAGCATATGAAGAGACGAATTTT 58.956 34.615 6.97 0.00 0.00 1.82
1671 6214 5.582689 TTCAGAGCATATGAAGAGACGAA 57.417 39.130 6.97 0.00 32.96 3.85
1674 6217 8.229137 GCATAATTTCAGAGCATATGAAGAGAC 58.771 37.037 6.97 0.00 37.91 3.36
1726 6269 2.284995 AGCCTGGACTCACCTCCC 60.285 66.667 0.00 0.00 39.86 4.30
1736 6279 0.918258 TGATACAATGCCAGCCTGGA 59.082 50.000 16.85 0.00 40.96 3.86
1738 6281 2.098607 CACTTGATACAATGCCAGCCTG 59.901 50.000 0.00 0.00 0.00 4.85
1751 6294 4.080919 CCAACCACTCTGGATCACTTGATA 60.081 45.833 0.00 0.00 40.96 2.15
1763 6306 2.248248 TGTACTCCTCCAACCACTCTG 58.752 52.381 0.00 0.00 0.00 3.35
1767 6310 5.163652 GCAATTATTGTACTCCTCCAACCAC 60.164 44.000 6.81 0.00 0.00 4.16
1796 6339 1.020437 GCCTAAACTGCATCCTCAGC 58.980 55.000 0.00 0.00 37.59 4.26
1814 6357 1.647084 GTCGTGTGTTGGAGTTGGC 59.353 57.895 0.00 0.00 0.00 4.52
1815 6358 0.808453 ACGTCGTGTGTTGGAGTTGG 60.808 55.000 0.00 0.00 0.00 3.77
1816 6359 0.575390 GACGTCGTGTGTTGGAGTTG 59.425 55.000 0.63 0.00 0.00 3.16
1817 6360 0.529119 GGACGTCGTGTGTTGGAGTT 60.529 55.000 9.92 0.00 0.00 3.01
1818 6361 1.066918 GGACGTCGTGTGTTGGAGT 59.933 57.895 9.92 0.00 0.00 3.85
1819 6362 2.014554 CGGACGTCGTGTGTTGGAG 61.015 63.158 9.92 0.00 0.00 3.86
1820 6363 2.026445 CGGACGTCGTGTGTTGGA 59.974 61.111 9.92 0.00 0.00 3.53
1829 6372 1.083015 CCAAGCAAAACGGACGTCG 60.083 57.895 9.92 7.64 45.88 5.12
1862 6405 4.506255 GGCTACCCCATTGCCGCT 62.506 66.667 0.00 0.00 39.52 5.52
1927 6473 2.689983 CCCAGACATAATTTGAGGTGCC 59.310 50.000 0.00 0.00 0.00 5.01
1933 6479 6.891361 ACATGTTCATCCCAGACATAATTTGA 59.109 34.615 0.00 0.00 0.00 2.69
2020 6605 7.855904 GGCCGTGAAGACTATAATGTTTAATTG 59.144 37.037 0.00 0.00 0.00 2.32
2110 10074 3.188100 ATGGCATCGACGTGCACG 61.188 61.111 35.99 35.99 46.81 5.34
2111 10075 2.400798 CATGGCATCGACGTGCAC 59.599 61.111 19.15 6.82 46.81 4.57
2114 10078 3.576356 GGGCATGGCATCGACGTG 61.576 66.667 22.06 0.00 0.00 4.49
2252 10261 4.717629 CAGTCACCGGAGCGCGAA 62.718 66.667 12.10 0.00 0.00 4.70


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

AutoCloner maintained by Alex Coulton.