Multiple sequence alignment - TraesCS5D01G017400

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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 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 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
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 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)



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AutoCloner maintained by Alex Coulton.