Multiple sequence alignment - TraesCS5A01G386100

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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 TraesCS5A01G386100 chr5A 100.000 2585 0 0 1 2585 583688052 583685468 0.000000e+00 4774
1 TraesCS5A01G386100 chr5A 99.417 857 4 1 1 857 379237321 379238176 0.000000e+00 1554
2 TraesCS5A01G386100 chr5A 98.953 860 8 1 1 860 53464392 53463534 0.000000e+00 1537
3 TraesCS5A01G386100 chr5A 94.915 118 6 0 1679 1796 594645791 594645674 4.390000e-43 185
4 TraesCS5A01G386100 chr5A 95.652 46 2 0 1 46 671984228 671984273 9.920000e-10 75
5 TraesCS5A01G386100 chr3B 99.183 857 7 0 1 857 583084832 583083976 0.000000e+00 1544
6 TraesCS5A01G386100 chr1B 99.068 858 7 1 1 858 223147531 223146675 0.000000e+00 1539
7 TraesCS5A01G386100 chr2B 99.067 857 7 1 1 857 408299309 408300164 0.000000e+00 1537
8 TraesCS5A01G386100 chr2B 95.352 753 30 4 106 856 691269764 691270513 0.000000e+00 1192
9 TraesCS5A01G386100 chr2B 87.128 839 79 14 857 1669 597225515 597224680 0.000000e+00 924
10 TraesCS5A01G386100 chr6D 93.510 755 43 5 108 860 51335691 51334941 0.000000e+00 1118
11 TraesCS5A01G386100 chrUn 93.501 754 42 6 106 857 61007576 61008324 0.000000e+00 1114
12 TraesCS5A01G386100 chrUn 91.667 120 10 0 1677 1796 82538064 82538183 1.590000e-37 167
13 TraesCS5A01G386100 chr5D 92.432 740 41 4 886 1610 463635545 463634806 0.000000e+00 1042
14 TraesCS5A01G386100 chr5D 93.023 559 30 9 1813 2364 463634790 463634234 0.000000e+00 808
15 TraesCS5A01G386100 chr1D 93.211 707 39 8 106 810 18608154 18607455 0.000000e+00 1031
16 TraesCS5A01G386100 chr5B 89.676 833 45 14 875 1681 570380594 570379777 0.000000e+00 1024
17 TraesCS5A01G386100 chr5B 91.930 632 45 5 1809 2438 570379758 570379131 0.000000e+00 880
18 TraesCS5A01G386100 chr2D 87.366 839 77 11 857 1669 508093309 508092474 0.000000e+00 935
19 TraesCS5A01G386100 chr2A 87.089 790 68 18 908 1669 652594915 652594132 0.000000e+00 863
20 TraesCS5A01G386100 chr2A 91.057 123 10 1 1674 1796 634615430 634615551 5.720000e-37 165
21 TraesCS5A01G386100 chr2A 89.147 129 13 1 1677 1805 78848938 78848811 2.660000e-35 159
22 TraesCS5A01G386100 chr2A 89.831 59 5 1 800 858 520611489 520611432 9.920000e-10 75
23 TraesCS5A01G386100 chr6A 93.388 121 7 1 1675 1795 407693481 407693362 7.350000e-41 178
24 TraesCS5A01G386100 chr6A 91.736 121 9 1 1679 1799 117376355 117376236 1.590000e-37 167
25 TraesCS5A01G386100 chr4B 90.984 122 9 2 1675 1796 667341303 667341422 2.060000e-36 163
26 TraesCS5A01G386100 chr7B 88.148 135 13 3 1672 1805 352434576 352434708 9.580000e-35 158
27 TraesCS5A01G386100 chr7B 88.636 132 12 3 1675 1805 604493975 604493846 9.580000e-35 158
28 TraesCS5A01G386100 chr4D 92.523 107 8 0 1 107 490407377 490407483 1.240000e-33 154


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 TraesCS5A01G386100 chr5A 583685468 583688052 2584 True 4774 4774 100.0000 1 2585 1 chr5A.!!$R2 2584
1 TraesCS5A01G386100 chr5A 379237321 379238176 855 False 1554 1554 99.4170 1 857 1 chr5A.!!$F1 856
2 TraesCS5A01G386100 chr5A 53463534 53464392 858 True 1537 1537 98.9530 1 860 1 chr5A.!!$R1 859
3 TraesCS5A01G386100 chr3B 583083976 583084832 856 True 1544 1544 99.1830 1 857 1 chr3B.!!$R1 856
4 TraesCS5A01G386100 chr1B 223146675 223147531 856 True 1539 1539 99.0680 1 858 1 chr1B.!!$R1 857
5 TraesCS5A01G386100 chr2B 408299309 408300164 855 False 1537 1537 99.0670 1 857 1 chr2B.!!$F1 856
6 TraesCS5A01G386100 chr2B 691269764 691270513 749 False 1192 1192 95.3520 106 856 1 chr2B.!!$F2 750
7 TraesCS5A01G386100 chr2B 597224680 597225515 835 True 924 924 87.1280 857 1669 1 chr2B.!!$R1 812
8 TraesCS5A01G386100 chr6D 51334941 51335691 750 True 1118 1118 93.5100 108 860 1 chr6D.!!$R1 752
9 TraesCS5A01G386100 chrUn 61007576 61008324 748 False 1114 1114 93.5010 106 857 1 chrUn.!!$F1 751
10 TraesCS5A01G386100 chr5D 463634234 463635545 1311 True 925 1042 92.7275 886 2364 2 chr5D.!!$R1 1478
11 TraesCS5A01G386100 chr1D 18607455 18608154 699 True 1031 1031 93.2110 106 810 1 chr1D.!!$R1 704
12 TraesCS5A01G386100 chr5B 570379131 570380594 1463 True 952 1024 90.8030 875 2438 2 chr5B.!!$R1 1563
13 TraesCS5A01G386100 chr2D 508092474 508093309 835 True 935 935 87.3660 857 1669 1 chr2D.!!$R1 812
14 TraesCS5A01G386100 chr2A 652594132 652594915 783 True 863 863 87.0890 908 1669 1 chr2A.!!$R3 761


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
932 953 0.808755 TCAGCTACGCACTCATCGAA 59.191 50.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2452 2513 0.039035 AGTCTCTTGGAGCCGAGTCT 59.961 55.0 3.76 0.0 0.0 3.24 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.