Multiple sequence alignment - TraesCS2A01G015000

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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 TraesCS2A01G015000 chr2A 100.000 2759 0 0 1 2759 6057378 6054620 0.000000e+00 5096.0
1 TraesCS2A01G015000 chr2A 98.551 2760 39 1 1 2759 6113284 6110525 0.000000e+00 4874.0
2 TraesCS2A01G015000 chr2A 98.152 2760 47 4 1 2759 6021958 6019202 0.000000e+00 4811.0
3 TraesCS2A01G015000 chr2A 98.007 2760 42 3 1 2759 6164985 6162238 0.000000e+00 4780.0
4 TraesCS2A01G015000 chr2A 95.975 1292 42 4 725 2006 6242996 6244287 0.000000e+00 2089.0
5 TraesCS2A01G015000 chr2A 96.523 719 21 2 2002 2720 6249493 6250207 0.000000e+00 1186.0
6 TraesCS2A01G015000 chr2A 89.452 730 62 10 1 725 760334267 760333548 0.000000e+00 907.0
7 TraesCS2A01G015000 chr2A 100.000 28 0 0 2732 2759 6250205 6250232 5.000000e-03 52.8
8 TraesCS2A01G015000 chr3D 93.601 1594 84 13 1180 2759 126614866 126613277 0.000000e+00 2362.0
9 TraesCS2A01G015000 chr3D 95.522 268 12 0 846 1113 126615129 126614862 1.960000e-116 429.0
10 TraesCS2A01G015000 chr3D 88.298 188 18 2 1066 1249 575923893 575923706 3.580000e-54 222.0
11 TraesCS2A01G015000 chr3D 97.638 127 3 0 725 851 126620312 126620186 4.630000e-53 219.0
12 TraesCS2A01G015000 chr3D 86.335 161 7 5 2599 2759 575923651 575923506 7.910000e-36 161.0
13 TraesCS2A01G015000 chr5A 92.938 1586 89 6 725 2288 415198156 415196572 0.000000e+00 2287.0
14 TraesCS2A01G015000 chr5A 91.628 430 11 6 2333 2759 415196575 415196168 3.080000e-159 571.0
15 TraesCS2A01G015000 chr6A 97.796 726 15 1 1 725 601220436 601221161 0.000000e+00 1251.0
16 TraesCS2A01G015000 chr6A 90.539 909 68 11 1700 2599 177814552 177815451 0.000000e+00 1186.0
17 TraesCS2A01G015000 chr6A 90.800 250 23 0 1277 1526 499402189 499402438 4.400000e-88 335.0
18 TraesCS2A01G015000 chr6D 91.570 866 65 6 1738 2599 136473344 136474205 0.000000e+00 1188.0
19 TraesCS2A01G015000 chr6D 84.507 426 49 11 1277 1696 357007891 357008305 3.310000e-109 405.0
20 TraesCS2A01G015000 chr3B 95.041 726 31 4 1 725 765389704 765390425 0.000000e+00 1136.0
21 TraesCS2A01G015000 chr3B 88.630 730 50 16 2 725 27911103 27911805 0.000000e+00 857.0
22 TraesCS2A01G015000 chr6B 90.149 873 70 10 1740 2599 234689312 234690181 0.000000e+00 1122.0
23 TraesCS2A01G015000 chr6B 81.758 455 65 11 1248 1696 538368533 538368975 5.620000e-97 364.0
24 TraesCS2A01G015000 chr6B 83.436 163 10 7 2599 2759 148827646 148827793 4.790000e-28 135.0
25 TraesCS2A01G015000 chr6B 95.000 40 2 0 1700 1739 234689169 234689208 2.290000e-06 63.9
26 TraesCS2A01G015000 chr4B 88.690 725 65 13 1 722 467985104 467985814 0.000000e+00 869.0
27 TraesCS2A01G015000 chr3A 87.671 730 72 11 1 725 501726989 501726273 0.000000e+00 833.0
28 TraesCS2A01G015000 chr7B 87.563 595 58 11 136 726 565654524 565653942 0.000000e+00 675.0
29 TraesCS2A01G015000 chr7D 79.259 270 53 2 2130 2399 168585815 168586081 4.690000e-43 185.0


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 TraesCS2A01G015000 chr2A 6054620 6057378 2758 True 5096.00 5096 100.0000 1 2759 1 chr2A.!!$R2 2758
1 TraesCS2A01G015000 chr2A 6110525 6113284 2759 True 4874.00 4874 98.5510 1 2759 1 chr2A.!!$R3 2758
2 TraesCS2A01G015000 chr2A 6019202 6021958 2756 True 4811.00 4811 98.1520 1 2759 1 chr2A.!!$R1 2758
3 TraesCS2A01G015000 chr2A 6162238 6164985 2747 True 4780.00 4780 98.0070 1 2759 1 chr2A.!!$R4 2758
4 TraesCS2A01G015000 chr2A 6242996 6244287 1291 False 2089.00 2089 95.9750 725 2006 1 chr2A.!!$F1 1281
5 TraesCS2A01G015000 chr2A 760333548 760334267 719 True 907.00 907 89.4520 1 725 1 chr2A.!!$R5 724
6 TraesCS2A01G015000 chr2A 6249493 6250232 739 False 619.40 1186 98.2615 2002 2759 2 chr2A.!!$F2 757
7 TraesCS2A01G015000 chr3D 126613277 126615129 1852 True 1395.50 2362 94.5615 846 2759 2 chr3D.!!$R2 1913
8 TraesCS2A01G015000 chr5A 415196168 415198156 1988 True 1429.00 2287 92.2830 725 2759 2 chr5A.!!$R1 2034
9 TraesCS2A01G015000 chr6A 601220436 601221161 725 False 1251.00 1251 97.7960 1 725 1 chr6A.!!$F3 724
10 TraesCS2A01G015000 chr6A 177814552 177815451 899 False 1186.00 1186 90.5390 1700 2599 1 chr6A.!!$F1 899
11 TraesCS2A01G015000 chr6D 136473344 136474205 861 False 1188.00 1188 91.5700 1738 2599 1 chr6D.!!$F1 861
12 TraesCS2A01G015000 chr3B 765389704 765390425 721 False 1136.00 1136 95.0410 1 725 1 chr3B.!!$F2 724
13 TraesCS2A01G015000 chr3B 27911103 27911805 702 False 857.00 857 88.6300 2 725 1 chr3B.!!$F1 723
14 TraesCS2A01G015000 chr6B 234689169 234690181 1012 False 592.95 1122 92.5745 1700 2599 2 chr6B.!!$F3 899
15 TraesCS2A01G015000 chr4B 467985104 467985814 710 False 869.00 869 88.6900 1 722 1 chr4B.!!$F1 721
16 TraesCS2A01G015000 chr3A 501726273 501726989 716 True 833.00 833 87.6710 1 725 1 chr3A.!!$R1 724
17 TraesCS2A01G015000 chr7B 565653942 565654524 582 True 675.00 675 87.5630 136 726 1 chr7B.!!$R1 590

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
951 962 1.064166 CCTTGCTCATGGGGTTCTGAT 60.064 52.381 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2166 2321 1.597742 TTGGTGCAAGAGAAGACTGC 58.402 50.0 0.0 0.0 0.0 4.4 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
496 502 6.677920 GCATTAGACACATTTAAATGGCTCGT 60.678 38.462 27.43 19.16 40.70 4.18
951 962 1.064166 CCTTGCTCATGGGGTTCTGAT 60.064 52.381 0.00 0.00 0.00 2.90
1419 1450 1.688627 GGTAGGGACCTCCTCATCGTT 60.689 57.143 0.00 0.00 44.06 3.85
1828 1967 3.187637 GGTTGCTTCATGCGTGTAGTTAA 59.812 43.478 13.34 7.19 46.63 2.01
1915 2058 1.083806 TTAGCGCGATGACTGGCTTG 61.084 55.000 12.10 0.00 36.97 4.01
2440 2614 9.101655 CCTCTTGATTTTTGTTTTTCATTCACT 57.898 29.630 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 6.258287 TGAGTGCATGAAATTGAAAACCAAAG 59.742 34.615 0.00 0.00 38.43 2.77
790 801 8.345724 ACTGAAAGATGTAAAATTGAGCATCT 57.654 30.769 11.02 11.02 46.77 2.90
1419 1450 0.106918 AGTTTGGGCCGAAGTCAACA 60.107 50.000 6.41 0.00 0.00 3.33
1796 1934 4.439153 CGCATGAAGCAACCTCAATAATGT 60.439 41.667 0.00 0.00 46.13 2.71
1799 1937 3.081061 ACGCATGAAGCAACCTCAATAA 58.919 40.909 0.00 0.00 46.13 1.40
2166 2321 1.597742 TTGGTGCAAGAGAAGACTGC 58.402 50.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.