Multiple sequence alignment - TraesCS5D01G017400
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 | TraesCS5D01G017400 | chr5D | 100.000 | 8848 | 0 | 0 | 1 | 8848 | 9957585 | 9948738 | 0.000000e+00 | 16340.0 |
1 | TraesCS5D01G017400 | chr5D | 92.659 | 1730 | 106 | 11 | 2014 | 3723 | 202904499 | 202902771 | 0.000000e+00 | 2471.0 |
2 | TraesCS5D01G017400 | chr5D | 100.000 | 656 | 0 | 0 | 9193 | 9848 | 9948393 | 9947738 | 0.000000e+00 | 1212.0 |
3 | TraesCS5D01G017400 | chr5D | 78.440 | 1526 | 230 | 52 | 3927 | 5414 | 4310975 | 4309511 | 0.000000e+00 | 904.0 |
4 | TraesCS5D01G017400 | chr5D | 95.745 | 47 | 1 | 1 | 9803 | 9848 | 296942198 | 296942152 | 3.810000e-09 | 75.0 |
5 | TraesCS5D01G017400 | chr6A | 93.118 | 1860 | 103 | 12 | 2011 | 3851 | 560577013 | 560578866 | 0.000000e+00 | 2702.0 |
6 | TraesCS5D01G017400 | chr6A | 100.000 | 42 | 0 | 0 | 9807 | 9848 | 135239041 | 135239082 | 2.950000e-10 | 78.7 |
7 | TraesCS5D01G017400 | chr6A | 97.727 | 44 | 1 | 0 | 9805 | 9848 | 39136771 | 39136728 | 1.060000e-09 | 76.8 |
8 | TraesCS5D01G017400 | chr6A | 97.727 | 44 | 1 | 0 | 9805 | 9848 | 384087602 | 384087645 | 1.060000e-09 | 76.8 |
9 | TraesCS5D01G017400 | chr2D | 92.976 | 1865 | 99 | 14 | 2016 | 3853 | 618395628 | 618397487 | 0.000000e+00 | 2689.0 |
10 | TraesCS5D01G017400 | chr2D | 91.765 | 1858 | 100 | 16 | 2016 | 3851 | 60777669 | 60779495 | 0.000000e+00 | 2534.0 |
11 | TraesCS5D01G017400 | chr2D | 90.741 | 54 | 4 | 1 | 9795 | 9848 | 617636719 | 617636771 | 4.930000e-08 | 71.3 |
12 | TraesCS5D01G017400 | chr7D | 92.806 | 1807 | 94 | 19 | 2069 | 3851 | 76472901 | 76471107 | 0.000000e+00 | 2584.0 |
13 | TraesCS5D01G017400 | chr1A | 91.927 | 1858 | 127 | 14 | 2012 | 3851 | 140197762 | 140199614 | 0.000000e+00 | 2579.0 |
14 | TraesCS5D01G017400 | chr1A | 100.000 | 41 | 0 | 0 | 9808 | 9848 | 504725644 | 504725604 | 1.060000e-09 | 76.8 |
15 | TraesCS5D01G017400 | chr3D | 91.946 | 1850 | 119 | 19 | 2016 | 3851 | 68837726 | 68839559 | 0.000000e+00 | 2564.0 |
16 | TraesCS5D01G017400 | chr3D | 100.000 | 42 | 0 | 0 | 9807 | 9848 | 614674939 | 614674898 | 2.950000e-10 | 78.7 |
17 | TraesCS5D01G017400 | chr4A | 91.806 | 1855 | 117 | 15 | 2016 | 3851 | 743531886 | 743530048 | 0.000000e+00 | 2551.0 |
18 | TraesCS5D01G017400 | chr4A | 88.693 | 283 | 19 | 11 | 662 | 931 | 366167065 | 366166783 | 5.700000e-87 | 333.0 |
19 | TraesCS5D01G017400 | chr7B | 91.389 | 1858 | 123 | 13 | 2016 | 3851 | 567543813 | 567545655 | 0.000000e+00 | 2510.0 |
20 | TraesCS5D01G017400 | chr7B | 85.595 | 479 | 60 | 9 | 117 | 590 | 104079763 | 104079289 | 2.470000e-135 | 494.0 |
21 | TraesCS5D01G017400 | chr7B | 90.323 | 279 | 16 | 9 | 664 | 931 | 647941790 | 647941512 | 1.220000e-93 | 355.0 |
22 | TraesCS5D01G017400 | chr7B | 97.778 | 45 | 1 | 0 | 9804 | 9848 | 550980283 | 550980239 | 2.950000e-10 | 78.7 |
23 | TraesCS5D01G017400 | chr4B | 91.007 | 1857 | 129 | 11 | 2014 | 3851 | 478655420 | 478657257 | 0.000000e+00 | 2470.0 |
24 | TraesCS5D01G017400 | chr4B | 91.011 | 356 | 26 | 4 | 2012 | 2362 | 75594332 | 75593978 | 8.950000e-130 | 475.0 |
25 | TraesCS5D01G017400 | chr4B | 89.892 | 277 | 17 | 9 | 666 | 931 | 383226144 | 383226420 | 7.320000e-91 | 346.0 |
26 | TraesCS5D01G017400 | chr4B | 86.525 | 141 | 10 | 4 | 9679 | 9811 | 520401902 | 520402041 | 7.970000e-31 | 147.0 |
27 | TraesCS5D01G017400 | chr4B | 100.000 | 43 | 0 | 0 | 9806 | 9848 | 575778325 | 575778283 | 8.200000e-11 | 80.5 |
28 | TraesCS5D01G017400 | chr4B | 97.778 | 45 | 1 | 0 | 9804 | 9848 | 380656756 | 380656712 | 2.950000e-10 | 78.7 |
29 | TraesCS5D01G017400 | chr4B | 95.652 | 46 | 2 | 0 | 9803 | 9848 | 365625109 | 365625064 | 3.810000e-09 | 75.0 |
30 | TraesCS5D01G017400 | chr5A | 90.474 | 1858 | 140 | 17 | 2014 | 3851 | 219653503 | 219651663 | 0.000000e+00 | 2416.0 |
31 | TraesCS5D01G017400 | chr5A | 78.850 | 922 | 158 | 24 | 3930 | 4825 | 4206184 | 4205274 | 1.100000e-163 | 588.0 |
32 | TraesCS5D01G017400 | chr5A | 85.780 | 218 | 29 | 2 | 4892 | 5108 | 4205165 | 4204949 | 7.690000e-56 | 230.0 |
33 | TraesCS5D01G017400 | chr5A | 100.000 | 42 | 0 | 0 | 9807 | 9848 | 357568715 | 357568756 | 2.950000e-10 | 78.7 |
34 | TraesCS5D01G017400 | chr5A | 90.741 | 54 | 5 | 0 | 9795 | 9848 | 546818528 | 546818581 | 1.370000e-08 | 73.1 |
35 | TraesCS5D01G017400 | chr5B | 92.345 | 1228 | 82 | 6 | 2634 | 3852 | 393999026 | 393997802 | 0.000000e+00 | 1736.0 |
36 | TraesCS5D01G017400 | chr5B | 91.576 | 641 | 40 | 3 | 2012 | 2638 | 394001390 | 394000750 | 0.000000e+00 | 872.0 |
37 | TraesCS5D01G017400 | chr5B | 81.416 | 678 | 94 | 17 | 4214 | 4877 | 7035222 | 7034563 | 8.760000e-145 | 525.0 |
38 | TraesCS5D01G017400 | chr5B | 85.146 | 478 | 65 | 6 | 117 | 590 | 294562597 | 294562122 | 1.490000e-132 | 484.0 |
39 | TraesCS5D01G017400 | chr5B | 81.365 | 542 | 72 | 18 | 4892 | 5413 | 7034517 | 7033985 | 1.980000e-111 | 414.0 |
40 | TraesCS5D01G017400 | chr5B | 89.399 | 283 | 18 | 11 | 664 | 934 | 212389410 | 212389128 | 7.320000e-91 | 346.0 |
41 | TraesCS5D01G017400 | chr5B | 89.855 | 276 | 19 | 7 | 664 | 931 | 675707592 | 675707318 | 7.320000e-91 | 346.0 |
42 | TraesCS5D01G017400 | chr5B | 89.925 | 268 | 16 | 10 | 664 | 920 | 119527437 | 119527704 | 1.580000e-87 | 335.0 |
43 | TraesCS5D01G017400 | chr5B | 78.652 | 445 | 62 | 15 | 4445 | 4874 | 6986933 | 6987359 | 2.110000e-66 | 265.0 |
44 | TraesCS5D01G017400 | chr5B | 84.959 | 246 | 31 | 4 | 4211 | 4452 | 6986220 | 6986463 | 2.750000e-60 | 244.0 |
45 | TraesCS5D01G017400 | chr5B | 97.778 | 45 | 1 | 0 | 9804 | 9848 | 33378731 | 33378687 | 2.950000e-10 | 78.7 |
46 | TraesCS5D01G017400 | chr5B | 95.745 | 47 | 2 | 0 | 9802 | 9848 | 610876476 | 610876522 | 1.060000e-09 | 76.8 |
47 | TraesCS5D01G017400 | chr5B | 92.500 | 40 | 3 | 0 | 4069 | 4108 | 610374530 | 610374491 | 3.840000e-04 | 58.4 |
48 | TraesCS5D01G017400 | chr4D | 94.318 | 1056 | 50 | 6 | 2804 | 3851 | 497199580 | 497198527 | 0.000000e+00 | 1609.0 |
49 | TraesCS5D01G017400 | chr4D | 91.667 | 768 | 47 | 4 | 2006 | 2760 | 497200618 | 497199855 | 0.000000e+00 | 1048.0 |
50 | TraesCS5D01G017400 | chr4D | 85.507 | 138 | 11 | 5 | 9682 | 9811 | 424471479 | 424471615 | 1.730000e-27 | 135.0 |
51 | TraesCS5D01G017400 | chr4D | 100.000 | 41 | 0 | 0 | 9808 | 9848 | 216792654 | 216792694 | 1.060000e-09 | 76.8 |
52 | TraesCS5D01G017400 | chr4D | 100.000 | 40 | 0 | 0 | 9809 | 9848 | 170331538 | 170331577 | 3.810000e-09 | 75.0 |
53 | TraesCS5D01G017400 | chr4D | 100.000 | 40 | 0 | 0 | 9809 | 9848 | 196810820 | 196810781 | 3.810000e-09 | 75.0 |
54 | TraesCS5D01G017400 | chr4D | 97.674 | 43 | 1 | 0 | 9806 | 9848 | 365708184 | 365708142 | 3.810000e-09 | 75.0 |
55 | TraesCS5D01G017400 | chr4D | 97.674 | 43 | 0 | 1 | 9807 | 9848 | 391158577 | 391158535 | 1.370000e-08 | 73.1 |
56 | TraesCS5D01G017400 | chr4D | 100.000 | 39 | 0 | 0 | 9810 | 9848 | 455756675 | 455756713 | 1.370000e-08 | 73.1 |
57 | TraesCS5D01G017400 | chr4D | 97.619 | 42 | 1 | 0 | 9807 | 9848 | 508682615 | 508682574 | 1.370000e-08 | 73.1 |
58 | TraesCS5D01G017400 | chr4D | 97.500 | 40 | 1 | 0 | 9809 | 9848 | 504042096 | 504042057 | 1.770000e-07 | 69.4 |
59 | TraesCS5D01G017400 | chr2A | 92.494 | 906 | 50 | 5 | 2016 | 2904 | 62111876 | 62110972 | 0.000000e+00 | 1280.0 |
60 | TraesCS5D01G017400 | chr2A | 83.333 | 474 | 73 | 6 | 117 | 589 | 323458220 | 323457752 | 5.460000e-117 | 433.0 |
61 | TraesCS5D01G017400 | chr1B | 90.254 | 708 | 42 | 16 | 2041 | 2724 | 53109811 | 53110515 | 0.000000e+00 | 900.0 |
62 | TraesCS5D01G017400 | chr1B | 85.356 | 478 | 60 | 10 | 117 | 588 | 679530886 | 679530413 | 4.130000e-133 | 486.0 |
63 | TraesCS5D01G017400 | chr1B | 84.454 | 476 | 67 | 7 | 117 | 587 | 365591649 | 365592122 | 6.970000e-126 | 462.0 |
64 | TraesCS5D01G017400 | chr1B | 91.265 | 332 | 26 | 3 | 2010 | 2339 | 646193545 | 646193875 | 5.420000e-122 | 449.0 |
65 | TraesCS5D01G017400 | chr1B | 90.580 | 276 | 18 | 6 | 664 | 931 | 503201815 | 503201540 | 9.400000e-95 | 359.0 |
66 | TraesCS5D01G017400 | chr6D | 90.237 | 379 | 29 | 7 | 2006 | 2378 | 46459363 | 46459739 | 1.150000e-133 | 488.0 |
67 | TraesCS5D01G017400 | chr6D | 92.617 | 298 | 20 | 2 | 2077 | 2372 | 424921426 | 424921723 | 2.540000e-115 | 427.0 |
68 | TraesCS5D01G017400 | chr6D | 80.380 | 158 | 30 | 1 | 7552 | 7709 | 23525938 | 23526094 | 1.740000e-22 | 119.0 |
69 | TraesCS5D01G017400 | chr6D | 95.522 | 67 | 3 | 0 | 2016 | 2082 | 424900432 | 424900498 | 3.760000e-19 | 108.0 |
70 | TraesCS5D01G017400 | chr6D | 100.000 | 41 | 0 | 0 | 9808 | 9848 | 105056646 | 105056606 | 1.060000e-09 | 76.8 |
71 | TraesCS5D01G017400 | chr6D | 94.231 | 52 | 0 | 2 | 9800 | 9848 | 392278754 | 392278703 | 1.060000e-09 | 76.8 |
72 | TraesCS5D01G017400 | chr2B | 85.225 | 467 | 62 | 7 | 120 | 581 | 717771924 | 717771460 | 3.220000e-129 | 473.0 |
73 | TraesCS5D01G017400 | chr2B | 90.000 | 280 | 17 | 10 | 662 | 930 | 675210942 | 675210663 | 1.570000e-92 | 351.0 |
74 | TraesCS5D01G017400 | chr2B | 97.778 | 45 | 1 | 0 | 9804 | 9848 | 366523174 | 366523130 | 2.950000e-10 | 78.7 |
75 | TraesCS5D01G017400 | chr2B | 97.826 | 46 | 0 | 1 | 9804 | 9848 | 531994521 | 531994476 | 2.950000e-10 | 78.7 |
76 | TraesCS5D01G017400 | chr6B | 90.625 | 352 | 24 | 5 | 2016 | 2362 | 704508914 | 704508567 | 9.010000e-125 | 459.0 |
77 | TraesCS5D01G017400 | chr3B | 89.964 | 279 | 17 | 10 | 664 | 931 | 105119928 | 105119650 | 5.660000e-92 | 350.0 |
78 | TraesCS5D01G017400 | chr3B | 97.778 | 45 | 1 | 0 | 9804 | 9848 | 96236076 | 96236032 | 2.950000e-10 | 78.7 |
79 | TraesCS5D01G017400 | chrUn | 95.556 | 45 | 2 | 0 | 9804 | 9848 | 84290545 | 84290589 | 1.370000e-08 | 73.1 |
80 | TraesCS5D01G017400 | chrUn | 95.556 | 45 | 2 | 0 | 9804 | 9848 | 226943870 | 226943914 | 1.370000e-08 | 73.1 |
81 | TraesCS5D01G017400 | chrUn | 100.000 | 39 | 0 | 0 | 9810 | 9848 | 264600169 | 264600131 | 1.370000e-08 | 73.1 |
82 | TraesCS5D01G017400 | chrUn | 97.500 | 40 | 1 | 0 | 9809 | 9848 | 294907387 | 294907426 | 1.770000e-07 | 69.4 |
83 | TraesCS5D01G017400 | chrUn | 97.436 | 39 | 1 | 0 | 9810 | 9848 | 26916979 | 26916941 | 6.380000e-07 | 67.6 |
84 | TraesCS5D01G017400 | chrUn | 97.436 | 39 | 1 | 0 | 9810 | 9848 | 97899522 | 97899560 | 6.380000e-07 | 67.6 |
85 | TraesCS5D01G017400 | chrUn | 97.436 | 39 | 1 | 0 | 9810 | 9848 | 97899685 | 97899647 | 6.380000e-07 | 67.6 |
86 | TraesCS5D01G017400 | chrUn | 95.238 | 42 | 2 | 0 | 9807 | 9848 | 101510678 | 101510719 | 6.380000e-07 | 67.6 |
87 | TraesCS5D01G017400 | chrUn | 97.436 | 39 | 1 | 0 | 9810 | 9848 | 101510844 | 101510806 | 6.380000e-07 | 67.6 |
88 | TraesCS5D01G017400 | chrUn | 97.436 | 39 | 1 | 0 | 9810 | 9848 | 137131003 | 137131041 | 6.380000e-07 | 67.6 |
89 | TraesCS5D01G017400 | chrUn | 97.436 | 39 | 1 | 0 | 9810 | 9848 | 340388321 | 340388283 | 6.380000e-07 | 67.6 |
90 | TraesCS5D01G017400 | chr1D | 93.750 | 48 | 3 | 0 | 9801 | 9848 | 143346141 | 143346188 | 1.370000e-08 | 73.1 |
91 | TraesCS5D01G017400 | chr1D | 95.652 | 46 | 1 | 1 | 9803 | 9848 | 283552470 | 283552426 | 1.370000e-08 | 73.1 |
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 | TraesCS5D01G017400 | chr5D | 9947738 | 9957585 | 9847 | True | 8776.0 | 16340 | 100.0000 | 1 | 9848 | 2 | chr5D.!!$R4 | 9847 |
1 | TraesCS5D01G017400 | chr5D | 202902771 | 202904499 | 1728 | True | 2471.0 | 2471 | 92.6590 | 2014 | 3723 | 1 | chr5D.!!$R2 | 1709 |
2 | TraesCS5D01G017400 | chr5D | 4309511 | 4310975 | 1464 | True | 904.0 | 904 | 78.4400 | 3927 | 5414 | 1 | chr5D.!!$R1 | 1487 |
3 | TraesCS5D01G017400 | chr6A | 560577013 | 560578866 | 1853 | False | 2702.0 | 2702 | 93.1180 | 2011 | 3851 | 1 | chr6A.!!$F3 | 1840 |
4 | TraesCS5D01G017400 | chr2D | 618395628 | 618397487 | 1859 | False | 2689.0 | 2689 | 92.9760 | 2016 | 3853 | 1 | chr2D.!!$F3 | 1837 |
5 | TraesCS5D01G017400 | chr2D | 60777669 | 60779495 | 1826 | False | 2534.0 | 2534 | 91.7650 | 2016 | 3851 | 1 | chr2D.!!$F1 | 1835 |
6 | TraesCS5D01G017400 | chr7D | 76471107 | 76472901 | 1794 | True | 2584.0 | 2584 | 92.8060 | 2069 | 3851 | 1 | chr7D.!!$R1 | 1782 |
7 | TraesCS5D01G017400 | chr1A | 140197762 | 140199614 | 1852 | False | 2579.0 | 2579 | 91.9270 | 2012 | 3851 | 1 | chr1A.!!$F1 | 1839 |
8 | TraesCS5D01G017400 | chr3D | 68837726 | 68839559 | 1833 | False | 2564.0 | 2564 | 91.9460 | 2016 | 3851 | 1 | chr3D.!!$F1 | 1835 |
9 | TraesCS5D01G017400 | chr4A | 743530048 | 743531886 | 1838 | True | 2551.0 | 2551 | 91.8060 | 2016 | 3851 | 1 | chr4A.!!$R2 | 1835 |
10 | TraesCS5D01G017400 | chr7B | 567543813 | 567545655 | 1842 | False | 2510.0 | 2510 | 91.3890 | 2016 | 3851 | 1 | chr7B.!!$F1 | 1835 |
11 | TraesCS5D01G017400 | chr4B | 478655420 | 478657257 | 1837 | False | 2470.0 | 2470 | 91.0070 | 2014 | 3851 | 1 | chr4B.!!$F2 | 1837 |
12 | TraesCS5D01G017400 | chr5A | 219651663 | 219653503 | 1840 | True | 2416.0 | 2416 | 90.4740 | 2014 | 3851 | 1 | chr5A.!!$R1 | 1837 |
13 | TraesCS5D01G017400 | chr5A | 4204949 | 4206184 | 1235 | True | 409.0 | 588 | 82.3150 | 3930 | 5108 | 2 | chr5A.!!$R2 | 1178 |
14 | TraesCS5D01G017400 | chr5B | 393997802 | 394001390 | 3588 | True | 1304.0 | 1736 | 91.9605 | 2012 | 3852 | 2 | chr5B.!!$R7 | 1840 |
15 | TraesCS5D01G017400 | chr5B | 7033985 | 7035222 | 1237 | True | 469.5 | 525 | 81.3905 | 4214 | 5413 | 2 | chr5B.!!$R6 | 1199 |
16 | TraesCS5D01G017400 | chr5B | 6986220 | 6987359 | 1139 | False | 254.5 | 265 | 81.8055 | 4211 | 4874 | 2 | chr5B.!!$F3 | 663 |
17 | TraesCS5D01G017400 | chr4D | 497198527 | 497200618 | 2091 | True | 1328.5 | 1609 | 92.9925 | 2006 | 3851 | 2 | chr4D.!!$R6 | 1845 |
18 | TraesCS5D01G017400 | chr2A | 62110972 | 62111876 | 904 | True | 1280.0 | 1280 | 92.4940 | 2016 | 2904 | 1 | chr2A.!!$R1 | 888 |
19 | TraesCS5D01G017400 | chr1B | 53109811 | 53110515 | 704 | False | 900.0 | 900 | 90.2540 | 2041 | 2724 | 1 | chr1B.!!$F1 | 683 |
AutoCloner calculated primer pairsThese primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible. |
---|
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
614 | 615 | 0.025513 | GTCAAGCTAGCAATGACGCG | 59.974 | 55.0 | 27.32 | 3.53 | 34.72 | 6.01 | F |
1353 | 1354 | 0.034767 | TTCTCCAGCTGCAATCCCAG | 60.035 | 55.0 | 8.66 | 0.00 | 35.93 | 4.45 | F |
1414 | 1415 | 0.035630 | AGTGATGTGCAGCTTCTCCC | 60.036 | 55.0 | 0.00 | 0.00 | 0.00 | 4.30 | F |
1881 | 1882 | 0.097674 | CTCGCTTATGTGGTGCTTGC | 59.902 | 55.0 | 0.00 | 0.00 | 0.00 | 4.01 | F |
3266 | 5276 | 0.240945 | GCGCATGTGCCTTGTAACTT | 59.759 | 50.0 | 20.70 | 0.00 | 37.91 | 2.66 | F |
4011 | 6041 | 0.460284 | AATGTCCTCGTCGGATGCAC | 60.460 | 55.0 | 0.00 | 0.00 | 45.44 | 4.57 | F |
5629 | 8257 | 0.033011 | TGCTCTCACCTAGACCTCCC | 60.033 | 60.0 | 0.00 | 0.00 | 0.00 | 4.30 | F |
6434 | 9062 | 0.033796 | CAGGGTTGCCTGACCATCAT | 60.034 | 55.0 | 0.00 | 0.00 | 41.65 | 2.45 | F |
7561 | 10189 | 0.034337 | GTTGGGAGGCACGTTACAGA | 59.966 | 55.0 | 0.00 | 0.00 | 0.00 | 3.41 | F |
Position | MSA Position | Penalty | Sequence | TM | GC | Self any TH | Self end TH | Hairpin | End Stability | Orientation |
---|---|---|---|---|---|---|---|---|---|---|
1862 | 1863 | 0.097674 | GCAAGCACCACATAAGCGAG | 59.902 | 55.000 | 0.00 | 0.00 | 0.00 | 5.03 | R |
3266 | 5276 | 1.600107 | GGGATGGGCAACTACGTCA | 59.400 | 57.895 | 0.00 | 0.00 | 0.00 | 4.35 | R |
3465 | 5475 | 9.439500 | TCTAGCCGTTTATGTTGTAATTAAGTT | 57.561 | 29.630 | 0.00 | 0.00 | 0.00 | 2.66 | R |
3881 | 5905 | 0.102844 | CCAACAACAGTTGTGGCTGG | 59.897 | 55.000 | 19.84 | 18.49 | 44.59 | 4.85 | R |
4896 | 7504 | 0.171903 | GCATGAACCCACTGCATGAC | 59.828 | 55.000 | 0.00 | 0.00 | 41.35 | 3.06 | R |
5803 | 8431 | 0.036294 | CGTCTCCACTTCCTTTCCCC | 60.036 | 60.000 | 0.00 | 0.00 | 0.00 | 4.81 | R |
7542 | 10170 | 0.034337 | TCTGTAACGTGCCTCCCAAC | 59.966 | 55.000 | 0.00 | 0.00 | 0.00 | 3.77 | R |
8198 | 10826 | 0.035739 | GCTGGACCAGTTTCCGGTAA | 59.964 | 55.000 | 22.58 | 0.00 | 43.30 | 2.85 | R |
9595 | 12223 | 0.031449 | AAAAACACCCACGGCGAATG | 59.969 | 50.000 | 16.62 | 8.41 | 0.00 | 2.67 | R |
All possible primersListed 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. |
---|
Based at the University of Bristol with support from BBSRC.
AutoCloner maintained by Alex Coulton.