Multiple sequence alignment - TraesCS3A01G236100

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 TraesCS3A01G236100 chr3A 100.000 6554 0 0 1 6554 440641401 440634848 0.000000e+00 12104.0
1 TraesCS3A01G236100 chr3A 91.650 491 39 2 4306 4795 440636922 440636433 0.000000e+00 678.0
2 TraesCS3A01G236100 chr3A 91.650 491 39 2 4480 4969 440637096 440636607 0.000000e+00 678.0
3 TraesCS3A01G236100 chr3A 88.328 317 35 2 4306 4621 440636748 440636433 4.800000e-101 379.0
4 TraesCS3A01G236100 chr3A 88.328 317 35 2 4654 4969 440637096 440636781 4.800000e-101 379.0
5 TraesCS3A01G236100 chr3A 80.882 136 20 6 1475 1606 15428697 15428830 1.160000e-17 102.0
6 TraesCS3A01G236100 chr3A 81.343 134 18 6 1480 1607 53727028 53726896 1.160000e-17 102.0
7 TraesCS3A01G236100 chr3A 97.500 40 1 0 6114 6153 709465100 709465061 1.180000e-07 69.4
8 TraesCS3A01G236100 chr3B 96.665 5037 105 12 1145 6148 422467170 422472176 0.000000e+00 8312.0
9 TraesCS3A01G236100 chr3B 97.387 1148 29 1 1 1147 422465992 422467139 0.000000e+00 1953.0
10 TraesCS3A01G236100 chr3B 91.498 494 40 2 4477 4969 422470332 422470824 0.000000e+00 678.0
11 TraesCS3A01G236100 chr3B 91.224 490 41 2 4307 4795 422470510 422470998 0.000000e+00 665.0
12 TraesCS3A01G236100 chr3B 91.479 399 22 5 6157 6554 422472333 422472720 7.480000e-149 538.0
13 TraesCS3A01G236100 chr3B 88.715 319 36 0 4651 4969 422470332 422470650 2.220000e-104 390.0
14 TraesCS3A01G236100 chr3B 87.500 320 38 2 4303 4621 422470680 422470998 1.040000e-97 368.0
15 TraesCS3A01G236100 chr3B 81.022 137 17 8 1478 1608 189413296 189413429 4.180000e-17 100.0
16 TraesCS3A01G236100 chr3B 86.301 73 10 0 5254 5326 794334190 794334118 5.450000e-11 80.5
17 TraesCS3A01G236100 chr3D 95.581 5205 160 41 1145 6316 326960199 326955032 0.000000e+00 8274.0
18 TraesCS3A01G236100 chr3D 95.906 1148 43 3 1 1147 326961374 326960230 0.000000e+00 1857.0
19 TraesCS3A01G236100 chr3D 91.837 490 40 0 4480 4969 326957041 326956552 0.000000e+00 684.0
20 TraesCS3A01G236100 chr3D 91.650 491 39 2 4306 4795 326956867 326956378 0.000000e+00 678.0
21 TraesCS3A01G236100 chr3D 89.274 317 32 2 4654 4969 326957041 326956726 4.760000e-106 396.0
22 TraesCS3A01G236100 chr3D 88.013 317 36 2 4306 4621 326956693 326956378 2.230000e-99 374.0
23 TraesCS3A01G236100 chr3D 93.496 123 2 2 6432 6554 326954993 326954877 1.880000e-40 178.0
24 TraesCS3A01G236100 chr3D 100.000 28 0 0 1362 1389 961609 961636 1.200000e-02 52.8
25 TraesCS3A01G236100 chr7A 92.857 84 5 1 6361 6444 68881099 68881181 3.210000e-23 121.0
26 TraesCS3A01G236100 chr2D 75.817 306 36 21 1320 1607 407968041 407967756 3.210000e-23 121.0
27 TraesCS3A01G236100 chr2D 97.561 41 1 0 6114 6154 6663505 6663465 3.280000e-08 71.3
28 TraesCS3A01G236100 chr2D 93.478 46 2 1 6139 6184 119022978 119022934 4.240000e-07 67.6
29 TraesCS3A01G236100 chr4D 92.857 84 3 2 6364 6445 15786198 15786280 1.150000e-22 119.0
30 TraesCS3A01G236100 chr4D 92.157 51 3 1 6105 6155 211328690 211328641 3.280000e-08 71.3
31 TraesCS3A01G236100 chr4D 90.476 42 4 0 1332 1373 479313193 479313234 1.000000e-03 56.5
32 TraesCS3A01G236100 chr6A 95.890 73 2 1 6364 6435 501479290 501479362 4.150000e-22 117.0
33 TraesCS3A01G236100 chr7D 95.833 72 2 1 6363 6434 46702662 46702732 1.490000e-21 115.0
34 TraesCS3A01G236100 chr7D 87.912 91 6 3 6357 6445 236822687 236822600 1.160000e-17 102.0
35 TraesCS3A01G236100 chr7D 83.544 79 7 5 5248 5326 364125863 364125791 1.180000e-07 69.4
36 TraesCS3A01G236100 chr7D 88.462 52 6 0 6139 6190 215222242 215222293 5.490000e-06 63.9
37 TraesCS3A01G236100 chr2B 94.737 76 1 1 6364 6436 417500837 417500762 1.490000e-21 115.0
38 TraesCS3A01G236100 chr2B 94.521 73 4 0 6364 6436 5666242 5666170 5.370000e-21 113.0
39 TraesCS3A01G236100 chr2B 88.462 52 6 0 6139 6190 679426314 679426365 5.490000e-06 63.9
40 TraesCS3A01G236100 chr2B 87.273 55 6 1 6139 6193 685280556 685280609 1.970000e-05 62.1
41 TraesCS3A01G236100 chr7B 89.130 92 5 3 6357 6444 419032273 419032183 6.950000e-20 110.0
42 TraesCS3A01G236100 chr7B 85.965 57 3 3 6335 6391 718350987 718351038 1.000000e-03 56.5
43 TraesCS3A01G236100 chr5B 86.275 102 12 2 1362 1461 441667297 441667398 6.950000e-20 110.0
44 TraesCS3A01G236100 chr5B 89.552 67 2 1 5255 5316 623210865 623210799 5.450000e-11 80.5
45 TraesCS3A01G236100 chr5B 89.552 67 2 1 5255 5316 626872261 626872195 5.450000e-11 80.5
46 TraesCS3A01G236100 chr5D 75.188 266 40 24 1363 1612 495954929 495954674 1.160000e-17 102.0
47 TraesCS3A01G236100 chr5D 97.619 42 1 0 6114 6155 179264199 179264240 9.120000e-09 73.1
48 TraesCS3A01G236100 chr2A 80.916 131 17 7 1484 1609 733424608 733424481 5.410000e-16 97.1
49 TraesCS3A01G236100 chr2A 97.500 40 0 1 5250 5288 446565867 446565906 4.240000e-07 67.6
50 TraesCS3A01G236100 chrUn 81.102 127 16 7 1485 1606 71016248 71016371 1.950000e-15 95.3
51 TraesCS3A01G236100 chr1A 76.142 197 29 14 1394 1579 80310122 80309933 3.260000e-13 87.9
52 TraesCS3A01G236100 chr1A 90.196 51 4 1 6139 6189 560307918 560307967 1.530000e-06 65.8
53 TraesCS3A01G236100 chr4B 93.878 49 3 0 1321 1369 432819155 432819203 2.530000e-09 75.0
54 TraesCS3A01G236100 chr4B 97.619 42 1 0 6114 6155 126324500 126324541 9.120000e-09 73.1
55 TraesCS3A01G236100 chr4B 89.362 47 5 0 5288 5334 660686929 660686975 7.100000e-05 60.2
56 TraesCS3A01G236100 chr6D 97.619 42 1 0 6114 6155 389141621 389141662 9.120000e-09 73.1
57 TraesCS3A01G236100 chr6D 88.679 53 5 1 6139 6191 27329320 27329269 5.490000e-06 63.9
58 TraesCS3A01G236100 chr5A 97.619 42 1 0 6114 6155 568267745 568267704 9.120000e-09 73.1
59 TraesCS3A01G236100 chr5A 95.238 42 2 0 5247 5288 32882727 32882686 4.240000e-07 67.6
60 TraesCS3A01G236100 chr4A 73.361 244 46 16 1375 1605 501712678 501712915 9.120000e-09 73.1
61 TraesCS3A01G236100 chr4A 93.478 46 3 0 6142 6187 615884848 615884803 1.180000e-07 69.4
62 TraesCS3A01G236100 chr4A 88.679 53 5 1 6139 6191 684637546 684637495 5.490000e-06 63.9
63 TraesCS3A01G236100 chr1D 75.882 170 21 7 1332 1498 86065149 86064997 1.180000e-07 69.4
64 TraesCS3A01G236100 chr1D 95.122 41 2 0 5288 5328 407673049 407673009 1.530000e-06 65.8
65 TraesCS3A01G236100 chr1D 100.000 28 0 0 1342 1369 49923821 49923848 1.200000e-02 52.8
66 TraesCS3A01G236100 chr1B 83.562 73 10 2 5256 5327 583691408 583691479 4.240000e-07 67.6
67 TraesCS3A01G236100 chr1B 86.441 59 6 2 6134 6191 309931228 309931171 5.490000e-06 63.9
68 TraesCS3A01G236100 chr1B 100.000 29 0 0 1340 1368 303679205 303679233 3.000000e-03 54.7


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 TraesCS3A01G236100 chr3A 440634848 440641401 6553 True 12104.000000 12104 100.000000 1 6554 1 chr3A.!!$R2 6553
1 TraesCS3A01G236100 chr3A 440636433 440637096 663 True 528.500000 678 89.989000 4306 4969 4 chr3A.!!$R4 663
2 TraesCS3A01G236100 chr3B 422465992 422472720 6728 False 1843.428571 8312 92.066857 1 6554 7 chr3B.!!$F2 6553
3 TraesCS3A01G236100 chr3D 326954877 326961374 6497 True 1777.285714 8274 92.251000 1 6554 7 chr3D.!!$R1 6553

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
857 859 0.183492 TTCCTTCAACTGGCAGCACT 59.817 50.000 15.89 0.0 0.00 4.40 F
1411 1479 2.445427 CCACCTCAACATGCAACCATA 58.555 47.619 0.00 0.0 0.00 2.74 F
2239 2312 0.900647 ACCTCAGCTAGTCGGTTGCT 60.901 55.000 0.00 0.0 37.56 3.91 F
2349 2422 0.905357 TCCTAGGCAACCTGAGCTTC 59.095 55.000 2.96 0.0 34.61 3.86 F
2572 2645 3.009143 AGACACAAAAGGTATGGAGGTCC 59.991 47.826 0.00 0.0 0.00 4.46 F
3371 3444 4.454678 TGATAAATACAGAGCAGCCCTTG 58.545 43.478 0.00 0.0 0.00 3.61 F
4111 4184 3.397482 CACCTGGAGTTCTTGAAGTGAG 58.603 50.000 0.00 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2148 0.116342 TCTGAGTGCTACTTCCCCCA 59.884 55.000 0.00 0.0 0.00 4.96 R
3165 3238 0.743097 GAAGCAGACCATTCATGCCC 59.257 55.000 0.00 0.0 40.89 5.36 R
3857 3930 0.468226 TGGAACACTCTGACCCACAC 59.532 55.000 0.00 0.0 0.00 3.82 R
3977 4050 1.405933 CGGATGTCTCTGCAATCACCA 60.406 52.381 0.00 0.0 0.00 4.17 R
4111 4184 4.260948 GGCAGGAAATCTGTCGATTTGATC 60.261 45.833 5.15 0.0 46.87 2.92 R
5299 5399 4.905456 TCCCTCCGATCCATATTACTTGTT 59.095 41.667 0.00 0.0 0.00 2.83 R
5929 6037 0.106149 CTCATTACCGGCCTACACCC 59.894 60.000 0.00 0.0 0.00 4.61 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
66 68 1.293924 CAGCATAGAACTGAAGGCCG 58.706 55.000 0.00 0.00 37.32 6.13
267 269 1.895798 TCGAGATGCTGTCCTTTGTCT 59.104 47.619 0.00 0.00 0.00 3.41
316 318 2.035312 AGGAGCACCCGTAGTCGT 59.965 61.111 0.00 0.00 40.87 4.34
367 369 4.274459 GCAATCTACTTTCGGCAATGATCT 59.726 41.667 0.00 0.00 0.00 2.75
376 378 2.019249 CGGCAATGATCTGGTCACAAT 58.981 47.619 0.00 0.00 40.28 2.71
391 393 8.902806 TCTGGTCACAATAATTCCAACAATATC 58.097 33.333 0.00 0.00 0.00 1.63
653 655 1.704641 TATGGTCTAGCAGGCGATGT 58.295 50.000 0.00 0.00 0.00 3.06
844 846 9.449719 TCTTATGGTTAATTCAGACTTTCCTTC 57.550 33.333 0.00 0.00 0.00 3.46
857 859 0.183492 TTCCTTCAACTGGCAGCACT 59.817 50.000 15.89 0.00 0.00 4.40
905 907 4.985538 TTGTTTTCCGGAAGCTTTACAA 57.014 36.364 17.97 18.34 0.00 2.41
967 969 2.981784 TGATATAGGGGTGAGCATTGCT 59.018 45.455 11.79 11.79 43.88 3.91
1160 1228 5.357596 GGTACCCTGTGTGTTAACTTTTTCA 59.642 40.000 7.22 0.00 0.00 2.69
1255 1323 8.714906 AGGTAGAATATTTGGTAACTGCTACAT 58.285 33.333 0.00 0.00 37.61 2.29
1303 1371 7.648039 TTGTACCATTTAGACCTTTGTTGTT 57.352 32.000 0.00 0.00 0.00 2.83
1388 1456 5.806818 ACATTCAATCATGCATGGGAAAAA 58.193 33.333 25.97 14.19 34.90 1.94
1411 1479 2.445427 CCACCTCAACATGCAACCATA 58.555 47.619 0.00 0.00 0.00 2.74
1672 1743 3.575687 CCTTTGGATCTTATGATTGGGGC 59.424 47.826 0.00 0.00 32.19 5.80
1729 1801 5.447279 CCTCGATTCCATAAGAAAACCAACG 60.447 44.000 0.00 0.00 38.21 4.10
1775 1847 5.356882 TTTAGAAGTTCAATTGGCTGTCG 57.643 39.130 5.42 0.00 0.00 4.35
1821 1893 6.015180 CACTCCCTTTTCATTCCTCAAAATGA 60.015 38.462 0.00 0.00 42.42 2.57
1863 1935 5.192927 ACGAATCATTGGAAGGCATCTTTA 58.807 37.500 0.00 0.00 32.52 1.85
2007 2080 4.693566 GTCCATCCTTTGATCGTGTTTGTA 59.306 41.667 0.00 0.00 0.00 2.41
2168 2241 6.259608 ACCATTTTTCTGAGATAGATGAAGCG 59.740 38.462 5.26 0.00 34.80 4.68
2239 2312 0.900647 ACCTCAGCTAGTCGGTTGCT 60.901 55.000 0.00 0.00 37.56 3.91
2349 2422 0.905357 TCCTAGGCAACCTGAGCTTC 59.095 55.000 2.96 0.00 34.61 3.86
2572 2645 3.009143 AGACACAAAAGGTATGGAGGTCC 59.991 47.826 0.00 0.00 0.00 4.46
2843 2916 8.686334 ACAAAGTCTAATGAAAACTCACATGTT 58.314 29.630 0.00 0.00 0.00 2.71
3371 3444 4.454678 TGATAAATACAGAGCAGCCCTTG 58.545 43.478 0.00 0.00 0.00 3.61
3857 3930 4.577693 CCTGATGATGGTAATGTGAAGGTG 59.422 45.833 0.00 0.00 0.00 4.00
3976 4049 8.352201 CAGAGTCATAAAAATTTGTTCCAGTGA 58.648 33.333 0.00 0.00 0.00 3.41
3977 4050 9.082313 AGAGTCATAAAAATTTGTTCCAGTGAT 57.918 29.630 0.00 0.00 0.00 3.06
4111 4184 3.397482 CACCTGGAGTTCTTGAAGTGAG 58.603 50.000 0.00 0.00 0.00 3.51
4163 4236 6.862209 TGATGTTGGCATAAAAATACCTGAC 58.138 36.000 0.00 0.00 35.07 3.51
4970 5043 3.812053 GGATCTGTGATTCACATAGTGGC 59.188 47.826 19.29 6.77 43.71 5.01
5286 5360 4.546570 CGATCCATATTACTTGTCGCTCA 58.453 43.478 0.00 0.00 0.00 4.26
5288 5362 5.635280 CGATCCATATTACTTGTCGCTCAAT 59.365 40.000 0.00 0.00 35.35 2.57
5289 5363 6.183360 CGATCCATATTACTTGTCGCTCAATC 60.183 42.308 0.00 0.00 35.35 2.67
5290 5364 5.297547 TCCATATTACTTGTCGCTCAATCC 58.702 41.667 0.00 0.00 35.35 3.01
5291 5365 5.056480 CCATATTACTTGTCGCTCAATCCA 58.944 41.667 0.00 0.00 35.35 3.41
5292 5366 5.702670 CCATATTACTTGTCGCTCAATCCAT 59.297 40.000 0.00 0.00 35.35 3.41
5293 5367 6.128445 CCATATTACTTGTCGCTCAATCCATC 60.128 42.308 0.00 0.00 35.35 3.51
5340 5440 5.646793 GGAGGGATTAGTTTTGTTGTACTCC 59.353 44.000 0.00 0.00 33.68 3.85
5341 5441 6.449830 AGGGATTAGTTTTGTTGTACTCCT 57.550 37.500 0.00 0.00 0.00 3.69
5476 5576 8.933653 CCCATGTAAAAATTATATTTGACCCCT 58.066 33.333 0.00 0.00 0.00 4.79
5552 5652 3.355378 TGATTTCCACAGGCAGGTTATG 58.645 45.455 0.00 0.00 0.00 1.90
5593 5693 6.509418 TTGCGCTAAAAGGAAGATATGTTT 57.491 33.333 9.73 0.00 0.00 2.83
5647 5748 3.699038 AGCCACTTTTACTTGTGAAGCAA 59.301 39.130 0.00 0.00 36.38 3.91
5691 5792 9.561069 GGTCTGATCTAATATAACACAAATGGT 57.439 33.333 0.00 0.00 0.00 3.55
5737 5838 4.569761 TTTGGTTTGTAGCGTGCATTTA 57.430 36.364 0.00 0.00 0.00 1.40
5829 5932 0.874390 CCTGTGCTTTCGCTTTGCTA 59.126 50.000 0.00 0.00 36.97 3.49
5847 5950 8.032451 GCTTTGCTAAGAATTACCCATTGTTTA 58.968 33.333 12.29 0.00 31.01 2.01
5931 6039 2.188469 CGGTAATGACACCCGGGG 59.812 66.667 27.92 16.65 38.09 5.73
5932 6040 2.662070 CGGTAATGACACCCGGGGT 61.662 63.158 27.92 20.14 38.09 4.95
5944 6052 3.076278 CGGGGTGTAGGCCGGTAA 61.076 66.667 1.90 0.00 0.00 2.85
5945 6053 2.437396 CGGGGTGTAGGCCGGTAAT 61.437 63.158 1.90 0.00 0.00 1.89
5946 6054 1.147600 GGGGTGTAGGCCGGTAATG 59.852 63.158 1.90 0.00 0.00 1.90
5947 6055 1.339644 GGGGTGTAGGCCGGTAATGA 61.340 60.000 1.90 0.00 0.00 2.57
5948 6056 0.106149 GGGTGTAGGCCGGTAATGAG 59.894 60.000 1.90 0.00 0.00 2.90
5949 6057 1.117150 GGTGTAGGCCGGTAATGAGA 58.883 55.000 1.90 0.00 0.00 3.27
5950 6058 1.202498 GGTGTAGGCCGGTAATGAGAC 60.202 57.143 1.90 0.00 0.00 3.36
5951 6059 1.117150 TGTAGGCCGGTAATGAGACC 58.883 55.000 1.90 0.00 36.00 3.85
5952 6060 0.391966 GTAGGCCGGTAATGAGACCC 59.608 60.000 1.90 0.00 35.95 4.46
5953 6061 1.111116 TAGGCCGGTAATGAGACCCG 61.111 60.000 1.90 0.00 41.37 5.28
5994 6102 0.740737 CCCTCCGCTAAAATTGGCAG 59.259 55.000 2.43 0.00 33.91 4.85
6066 6176 3.584406 TCTGTGGTGTCTGAATCCAAGAT 59.416 43.478 4.10 0.00 32.82 2.40
6086 6198 6.882768 AGATCCATATTCTTCACCTATCCC 57.117 41.667 0.00 0.00 0.00 3.85
6111 6223 3.078837 GCCTGGTTCCTTCGAAATTACA 58.921 45.455 0.00 0.00 0.00 2.41
6121 6233 1.822990 TCGAAATTACAGCCTCCGTCT 59.177 47.619 0.00 0.00 0.00 4.18
6137 6249 4.482386 TCCGTCTCAAAATAAGTGACTCG 58.518 43.478 0.00 0.00 0.00 4.18
6149 6261 9.754382 AAAATAAGTGACTCGAGTTTGTACTAA 57.246 29.630 21.08 1.57 33.84 2.24
6153 6265 6.803642 AGTGACTCGAGTTTGTACTAACTTT 58.196 36.000 21.08 8.61 38.43 2.66
6155 6267 5.981315 TGACTCGAGTTTGTACTAACTTTGG 59.019 40.000 21.08 15.73 38.43 3.28
6170 6400 7.064229 ACTAACTTTGGGTCACTTATTTTGGA 58.936 34.615 0.00 0.00 0.00 3.53
6235 6492 1.143183 GTCGGAGCTGGGCGATTAA 59.857 57.895 0.00 0.00 0.00 1.40
6253 6510 1.673808 AACGATAGGTGGAGGCGTCC 61.674 60.000 18.69 18.69 42.13 4.79
6284 6541 2.032549 GGTATTCACAGCGATGACATGC 60.033 50.000 8.12 0.00 0.00 4.06
6321 6578 9.987272 CTATCCATAACAAGATGTCTATCAACA 57.013 33.333 0.00 0.00 35.70 3.33
6325 6582 5.505181 AACAAGATGTCTATCAACAGGGT 57.495 39.130 0.00 0.00 35.70 4.34
6343 6600 2.945668 GGGTCTTCTTGCGATATGCTTT 59.054 45.455 0.00 0.00 46.63 3.51
6408 6665 3.433615 AGAGCGTAGTGTCAAAAATGCTC 59.566 43.478 13.10 13.10 46.58 4.26
6420 6677 9.683069 GTGTCAAAAATGCTCTTATATTATGGG 57.317 33.333 0.00 0.00 0.00 4.00
6475 6733 2.203070 GGACCGGCTGCCAGTATG 60.203 66.667 20.29 1.09 0.00 2.39
6476 6734 2.897350 GACCGGCTGCCAGTATGC 60.897 66.667 20.29 0.00 31.97 3.14
6537 6795 3.506810 CTGCTAGCAGTTGACTACTCAC 58.493 50.000 32.46 0.00 39.10 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
104 106 4.839121 TGACTGGTTGGTGTATATTGGTC 58.161 43.478 0.00 0.00 0.00 4.02
206 208 2.445845 TCATCCCTACCCCAGGCG 60.446 66.667 0.00 0.00 43.98 5.52
267 269 8.558700 CATATGAAATCAACATGATACACCGAA 58.441 33.333 0.00 0.00 35.76 4.30
316 318 4.319190 CGATTTTGTTAACGAGGTTCAGCA 60.319 41.667 0.26 0.00 0.00 4.41
367 369 8.821686 AGATATTGTTGGAATTATTGTGACCA 57.178 30.769 0.00 0.00 0.00 4.02
376 378 7.554211 TGCATTGCAAGATATTGTTGGAATTA 58.446 30.769 9.33 6.02 41.54 1.40
513 515 5.523552 GGGTGCAATTAAATAATGGAAGTGC 59.476 40.000 0.00 0.00 42.74 4.40
653 655 4.661222 TCATTAGATGGTTTCCTGCAACA 58.339 39.130 0.00 0.00 0.00 3.33
827 829 5.473504 GCCAGTTGAAGGAAAGTCTGAATTA 59.526 40.000 0.00 0.00 0.00 1.40
844 846 1.866880 GCTCAAAAGTGCTGCCAGTTG 60.867 52.381 0.00 0.00 34.89 3.16
857 859 9.550406 AAAAATGAGAATGAATTCAGCTCAAAA 57.450 25.926 31.07 18.09 41.36 2.44
887 889 3.316868 CCTGTTGTAAAGCTTCCGGAAAA 59.683 43.478 19.39 4.64 0.00 2.29
905 907 8.211629 AGAAGTTGTTGTATTCTTACTTCCTGT 58.788 33.333 0.00 0.00 41.30 4.00
967 969 6.231258 AGCTGATGAAATGAGATGACACTA 57.769 37.500 0.00 0.00 23.63 2.74
1255 1323 8.454894 CAAAATGCATCCATCATTGAAAATTCA 58.545 29.630 0.00 0.00 34.67 2.57
1324 1392 6.053650 GTGGGGATCACCTACTTAATTGTAC 58.946 44.000 16.81 0.00 46.50 2.90
1388 1456 1.039856 GTTGCATGTTGAGGTGGGTT 58.960 50.000 0.00 0.00 0.00 4.11
1411 1479 2.745281 GCATTTGAGCCATTTTGCATGT 59.255 40.909 0.00 0.00 0.00 3.21
1548 1616 9.837525 GATTGCTTCCAATATATTCAATGAGAC 57.162 33.333 11.86 0.00 41.60 3.36
1581 1649 1.906574 AGATGATACCCCACACGTTGT 59.093 47.619 0.00 0.00 0.00 3.32
1775 1847 4.393371 GTGGAAAGTGGAAACAGATAGAGC 59.607 45.833 0.00 0.00 44.46 4.09
1928 2001 5.393068 AATCATTAAAGGCCTCCTGATCA 57.607 39.130 5.23 0.00 32.13 2.92
1998 2071 5.347364 CCCCTTTTGCATAATTACAAACACG 59.653 40.000 0.00 0.00 35.60 4.49
2007 2080 3.135167 CCATCAGCCCCTTTTGCATAATT 59.865 43.478 0.00 0.00 0.00 1.40
2075 2148 0.116342 TCTGAGTGCTACTTCCCCCA 59.884 55.000 0.00 0.00 0.00 4.96
2168 2241 2.591715 ATGTAAGCCCGATGCCGC 60.592 61.111 0.00 0.00 42.71 6.53
2572 2645 2.510238 CTTTCTCTCCGGCCAGCG 60.510 66.667 2.24 0.00 0.00 5.18
2620 2693 5.574055 TCACGACGTGAACATATTCCTTTAC 59.426 40.000 27.44 0.00 39.78 2.01
2628 2701 2.647529 TGCTCACGACGTGAACATAT 57.352 45.000 28.86 0.00 42.26 1.78
2843 2916 3.244735 TGCTGCTGTACTTGGGACATAAA 60.245 43.478 0.00 0.00 39.30 1.40
3033 3106 5.840243 TTATCAGCTTGCTTTGTATGCAT 57.160 34.783 3.79 3.79 40.34 3.96
3165 3238 0.743097 GAAGCAGACCATTCATGCCC 59.257 55.000 0.00 0.00 40.89 5.36
3371 3444 3.003480 GTTTGTACCACTGAGGCATCTC 58.997 50.000 0.00 0.00 43.14 2.75
3750 3823 3.713764 TGTTCAAACCATTTGGGACCATT 59.286 39.130 0.96 0.00 40.98 3.16
3756 3829 3.252944 GGCATTTGTTCAAACCATTTGGG 59.747 43.478 0.96 0.00 40.98 4.12
3831 3904 4.694760 TCACATTACCATCATCAGGAGG 57.305 45.455 0.00 0.00 0.00 4.30
3857 3930 0.468226 TGGAACACTCTGACCCACAC 59.532 55.000 0.00 0.00 0.00 3.82
3976 4049 2.744166 CGGATGTCTCTGCAATCACCAT 60.744 50.000 0.00 0.00 0.00 3.55
3977 4050 1.405933 CGGATGTCTCTGCAATCACCA 60.406 52.381 0.00 0.00 0.00 4.17
4111 4184 4.260948 GGCAGGAAATCTGTCGATTTGATC 60.261 45.833 5.15 0.00 46.87 2.92
4970 5043 5.556915 TCATCAGTACTTAGTTTTGGTGGG 58.443 41.667 0.00 0.00 0.00 4.61
5286 5360 7.230108 CCATATTACTTGTTGCTCAGATGGATT 59.770 37.037 0.00 0.00 0.00 3.01
5288 5362 6.057533 CCATATTACTTGTTGCTCAGATGGA 58.942 40.000 0.00 0.00 0.00 3.41
5289 5363 6.057533 TCCATATTACTTGTTGCTCAGATGG 58.942 40.000 0.00 0.00 0.00 3.51
5290 5364 7.359849 CGATCCATATTACTTGTTGCTCAGATG 60.360 40.741 0.00 0.00 0.00 2.90
5291 5365 6.648310 CGATCCATATTACTTGTTGCTCAGAT 59.352 38.462 0.00 0.00 0.00 2.90
5292 5366 5.985530 CGATCCATATTACTTGTTGCTCAGA 59.014 40.000 0.00 0.00 0.00 3.27
5293 5367 5.178252 CCGATCCATATTACTTGTTGCTCAG 59.822 44.000 0.00 0.00 0.00 3.35
5299 5399 4.905456 TCCCTCCGATCCATATTACTTGTT 59.095 41.667 0.00 0.00 0.00 2.83
5462 5562 6.147437 ACCAACAGAAGGGGTCAAATATAA 57.853 37.500 0.00 0.00 0.00 0.98
5552 5652 3.663493 CGCAAAGTTTACGCCTACTTGTC 60.663 47.826 0.00 0.00 34.95 3.18
5593 5693 3.056536 CAGAAGGAAGATCCGTTGACTCA 60.057 47.826 0.00 0.00 42.75 3.41
5647 5748 9.220767 GATCAGACCTGTTTTAACTTAGACAAT 57.779 33.333 0.00 0.00 0.00 2.71
5691 5792 2.240921 TGGCTGCATCACCCTGTATAAA 59.759 45.455 0.50 0.00 0.00 1.40
5737 5838 7.962995 TTGTGAGAAGAGACCTAGATAATGT 57.037 36.000 0.00 0.00 0.00 2.71
5814 5917 5.619086 GGTAATTCTTAGCAAAGCGAAAGCA 60.619 40.000 0.00 0.00 45.73 3.91
5929 6037 0.106149 CTCATTACCGGCCTACACCC 59.894 60.000 0.00 0.00 0.00 4.61
5930 6038 1.117150 TCTCATTACCGGCCTACACC 58.883 55.000 0.00 0.00 0.00 4.16
5931 6039 1.202498 GGTCTCATTACCGGCCTACAC 60.202 57.143 0.00 0.00 0.00 2.90
5932 6040 1.117150 GGTCTCATTACCGGCCTACA 58.883 55.000 0.00 0.00 0.00 2.74
5933 6041 0.391966 GGGTCTCATTACCGGCCTAC 59.608 60.000 0.00 0.00 40.73 3.18
5934 6042 1.111116 CGGGTCTCATTACCGGCCTA 61.111 60.000 0.00 0.00 43.69 3.93
5935 6043 2.432300 CGGGTCTCATTACCGGCCT 61.432 63.158 0.00 0.00 43.69 5.19
5936 6044 2.108362 CGGGTCTCATTACCGGCC 59.892 66.667 0.00 0.00 43.69 6.13
5939 6047 3.738830 TTTATCCGGGTCTCATTACCG 57.261 47.619 0.00 0.00 46.79 4.02
5940 6048 4.773013 TGTTTTATCCGGGTCTCATTACC 58.227 43.478 0.00 0.00 38.94 2.85
5941 6049 4.272748 GCTGTTTTATCCGGGTCTCATTAC 59.727 45.833 0.00 0.00 0.00 1.89
5942 6050 4.080807 TGCTGTTTTATCCGGGTCTCATTA 60.081 41.667 0.00 0.00 0.00 1.90
5943 6051 3.279434 GCTGTTTTATCCGGGTCTCATT 58.721 45.455 0.00 0.00 0.00 2.57
5944 6052 2.238646 TGCTGTTTTATCCGGGTCTCAT 59.761 45.455 0.00 0.00 0.00 2.90
5945 6053 1.626321 TGCTGTTTTATCCGGGTCTCA 59.374 47.619 0.00 0.00 0.00 3.27
5946 6054 2.396590 TGCTGTTTTATCCGGGTCTC 57.603 50.000 0.00 0.00 0.00 3.36
5947 6055 2.871096 TTGCTGTTTTATCCGGGTCT 57.129 45.000 0.00 0.00 0.00 3.85
5948 6056 3.571571 GTTTTGCTGTTTTATCCGGGTC 58.428 45.455 0.00 0.00 0.00 4.46
5949 6057 2.030628 CGTTTTGCTGTTTTATCCGGGT 60.031 45.455 0.00 0.00 0.00 5.28
5950 6058 2.591133 CGTTTTGCTGTTTTATCCGGG 58.409 47.619 0.00 0.00 0.00 5.73
5951 6059 1.982913 GCGTTTTGCTGTTTTATCCGG 59.017 47.619 0.00 0.00 41.73 5.14
5952 6060 2.656085 TGCGTTTTGCTGTTTTATCCG 58.344 42.857 0.00 0.00 46.63 4.18
5953 6061 3.183574 GGTTGCGTTTTGCTGTTTTATCC 59.816 43.478 0.00 0.00 46.63 2.59
5994 6102 5.106396 ACTCATAACAGCAAGCTCATTTGTC 60.106 40.000 0.00 0.00 0.00 3.18
6066 6176 3.260884 GCGGGATAGGTGAAGAATATGGA 59.739 47.826 0.00 0.00 0.00 3.41
6086 6198 3.121030 CGAAGGAACCAGGCTGCG 61.121 66.667 9.56 5.16 0.00 5.18
6111 6223 3.260884 TCACTTATTTTGAGACGGAGGCT 59.739 43.478 0.00 0.00 0.00 4.58
6121 6233 7.924412 AGTACAAACTCGAGTCACTTATTTTGA 59.076 33.333 20.33 4.80 0.00 2.69
6137 6249 6.053650 AGTGACCCAAAGTTAGTACAAACTC 58.946 40.000 0.00 0.00 38.76 3.01
6149 6261 5.221165 CGTTCCAAAATAAGTGACCCAAAGT 60.221 40.000 0.00 0.00 0.00 2.66
6153 6265 3.150767 CCGTTCCAAAATAAGTGACCCA 58.849 45.455 0.00 0.00 0.00 4.51
6155 6267 3.439129 CCTCCGTTCCAAAATAAGTGACC 59.561 47.826 0.00 0.00 0.00 4.02
6170 6400 4.468510 TCACAAACATATACTCCCTCCGTT 59.531 41.667 0.00 0.00 0.00 4.44
6235 6492 2.125961 GGACGCCTCCACCTATCGT 61.126 63.158 0.00 0.00 36.42 3.73
6253 6510 3.611530 CGCTGTGAATACCAACCAAAAGG 60.612 47.826 0.00 0.00 0.00 3.11
6343 6600 9.974980 GGGAGTAAAATTTAAACACAAGATCAA 57.025 29.630 0.00 0.00 0.00 2.57
6408 6665 7.147811 GCTACTCCCTCTGTCCCATAATATAAG 60.148 44.444 0.00 0.00 0.00 1.73
6475 6733 3.567478 ACATCCTAAAGACCATCCAGC 57.433 47.619 0.00 0.00 0.00 4.85
6476 6734 5.358160 GGAAAACATCCTAAAGACCATCCAG 59.642 44.000 0.00 0.00 45.56 3.86


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

AutoCloner maintained by Alex Coulton.