Multiple sequence alignment - TraesCS5D01G350900

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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 TraesCS5D01G350900 chr5D 100.000 2444 0 0 1 2444 434687697 434690140 0.000000e+00 4514.0
1 TraesCS5D01G350900 chr5D 87.892 1817 156 28 668 2442 434567322 434565528 0.000000e+00 2078.0
2 TraesCS5D01G350900 chr5D 85.437 927 106 9 671 1579 434600546 434599631 0.000000e+00 937.0
3 TraesCS5D01G350900 chr5D 81.316 760 76 32 751 1469 434548909 434548175 7.630000e-155 556.0
4 TraesCS5D01G350900 chr5D 84.926 544 58 17 761 1292 434666569 434667100 1.660000e-146 529.0
5 TraesCS5D01G350900 chr5D 87.316 339 42 1 1013 1351 434675699 434676036 1.060000e-103 387.0
6 TraesCS5D01G350900 chr5D 78.305 295 33 18 1824 2108 434599633 434599360 6.990000e-36 161.0
7 TraesCS5D01G350900 chr5D 80.795 151 17 3 528 669 181951970 181952117 9.240000e-20 108.0
8 TraesCS5D01G350900 chr5D 87.500 48 6 0 1643 1690 439474464 439474511 3.390000e-04 56.5
9 TraesCS5D01G350900 chr5B 87.129 1818 138 41 668 2443 527601650 527599887 0.000000e+00 1973.0
10 TraesCS5D01G350900 chr5B 88.432 1435 120 24 756 2162 527769556 527768140 0.000000e+00 1688.0
11 TraesCS5D01G350900 chr5B 85.011 874 84 22 763 1604 527492232 527491374 0.000000e+00 845.0
12 TraesCS5D01G350900 chr5B 86.786 280 32 3 2168 2443 527764842 527764564 8.490000e-80 307.0
13 TraesCS5D01G350900 chr5A 88.536 881 78 10 751 1615 548658103 548657230 0.000000e+00 1046.0
14 TraesCS5D01G350900 chr5A 81.149 870 106 25 761 1605 548503680 548504516 0.000000e+00 645.0
15 TraesCS5D01G350900 chr5A 79.825 114 20 1 528 641 217397134 217397244 2.010000e-11 80.5
16 TraesCS5D01G350900 chr1B 84.231 260 35 5 2188 2444 639168686 639168942 5.220000e-62 248.0
17 TraesCS5D01G350900 chr4A 78.448 348 56 12 2106 2444 623360999 623361336 2.460000e-50 209.0
18 TraesCS5D01G350900 chr4A 94.737 38 2 0 1788 1825 712126415 712126452 2.620000e-05 60.2
19 TraesCS5D01G350900 chr3D 76.923 338 61 11 2108 2441 501303417 501303093 2.500000e-40 176.0
20 TraesCS5D01G350900 chr3D 82.759 145 16 6 532 671 63775659 63775519 1.190000e-23 121.0
21 TraesCS5D01G350900 chr3D 90.789 76 7 0 1746 1821 571358666 571358741 4.300000e-18 102.0
22 TraesCS5D01G350900 chr1A 90.110 91 9 0 583 673 5608362 5608272 4.270000e-23 119.0
23 TraesCS5D01G350900 chr1A 83.951 81 8 4 1747 1824 516739031 516739109 3.370000e-09 73.1
24 TraesCS5D01G350900 chr7B 80.625 160 22 3 1675 1833 59823763 59823612 5.520000e-22 115.0
25 TraesCS5D01G350900 chr7B 78.919 185 20 9 1642 1823 60064685 60064517 9.240000e-20 108.0
26 TraesCS5D01G350900 chr6D 82.069 145 13 5 535 670 433443100 433443240 7.140000e-21 111.0
27 TraesCS5D01G350900 chr6D 89.744 78 5 2 543 620 388557920 388557846 2.000000e-16 97.1
28 TraesCS5D01G350900 chr3B 87.129 101 10 2 540 640 99469066 99468969 7.140000e-21 111.0
29 TraesCS5D01G350900 chr1D 81.290 155 14 6 528 671 48513487 48513337 7.140000e-21 111.0
30 TraesCS5D01G350900 chr1D 88.679 53 3 3 1633 1685 90378264 90378313 7.300000e-06 62.1
31 TraesCS5D01G350900 chr1D 92.683 41 2 1 1645 1684 462155551 462155591 9.440000e-05 58.4
32 TraesCS5D01G350900 chr3A 77.436 195 29 11 1644 1837 59465779 59465599 4.300000e-18 102.0
33 TraesCS5D01G350900 chr3A 94.595 37 0 2 1749 1785 127962774 127962740 3.390000e-04 56.5
34 TraesCS5D01G350900 chr7D 94.030 67 3 1 1760 1826 403152367 403152432 1.550000e-17 100.0
35 TraesCS5D01G350900 chr6A 87.356 87 11 0 1738 1824 22807379 22807293 1.550000e-17 100.0
36 TraesCS5D01G350900 chr6A 88.312 77 9 0 1749 1825 609828549 609828625 2.590000e-15 93.5
37 TraesCS5D01G350900 chrUn 90.411 73 7 0 1749 1821 302454775 302454847 2.000000e-16 97.1
38 TraesCS5D01G350900 chrUn 90.411 73 7 0 1749 1821 330584479 330584551 2.000000e-16 97.1
39 TraesCS5D01G350900 chrUn 88.158 76 9 0 1749 1824 17495973 17495898 9.310000e-15 91.6
40 TraesCS5D01G350900 chr2D 80.769 130 19 5 532 659 80033450 80033325 2.000000e-16 97.1
41 TraesCS5D01G350900 chr6B 88.158 76 9 0 1746 1821 706534437 706534512 9.310000e-15 91.6
42 TraesCS5D01G350900 chr6B 89.362 47 5 0 1644 1690 34193180 34193134 2.620000e-05 60.2
43 TraesCS5D01G350900 chr7A 90.909 66 4 2 1711 1774 729569711 729569646 1.200000e-13 87.9
44 TraesCS5D01G350900 chr7A 90.476 42 1 3 1628 1669 106747731 106747693 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 TraesCS5D01G350900 chr5D 434687697 434690140 2443 False 4514.0 4514 100.000 1 2444 1 chr5D.!!$F4 2443
1 TraesCS5D01G350900 chr5D 434565528 434567322 1794 True 2078.0 2078 87.892 668 2442 1 chr5D.!!$R2 1774
2 TraesCS5D01G350900 chr5D 434548175 434548909 734 True 556.0 556 81.316 751 1469 1 chr5D.!!$R1 718
3 TraesCS5D01G350900 chr5D 434599360 434600546 1186 True 549.0 937 81.871 671 2108 2 chr5D.!!$R3 1437
4 TraesCS5D01G350900 chr5D 434666569 434667100 531 False 529.0 529 84.926 761 1292 1 chr5D.!!$F2 531
5 TraesCS5D01G350900 chr5B 527599887 527601650 1763 True 1973.0 1973 87.129 668 2443 1 chr5B.!!$R2 1775
6 TraesCS5D01G350900 chr5B 527764564 527769556 4992 True 997.5 1688 87.609 756 2443 2 chr5B.!!$R3 1687
7 TraesCS5D01G350900 chr5B 527491374 527492232 858 True 845.0 845 85.011 763 1604 1 chr5B.!!$R1 841
8 TraesCS5D01G350900 chr5A 548657230 548658103 873 True 1046.0 1046 88.536 751 1615 1 chr5A.!!$R1 864
9 TraesCS5D01G350900 chr5A 548503680 548504516 836 False 645.0 645 81.149 761 1605 1 chr5A.!!$F2 844


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
223 224 0.03467 GCATCAGCCAGGTCTTCCTT 60.035 55.0 0.0 0.0 43.07 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2270 0.376152 GGCGATCGTTGACTCGACTA 59.624 55.0 17.81 0.0 42.56 2.59 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.