Multiple sequence alignment - TraesCS2A01G240800

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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 TraesCS2A01G240800 chr2A 100.000 2120 0 0 1 2120 335826301 335824182 0.000000e+00 3916
1 TraesCS2A01G240800 chr2A 96.157 2134 64 7 1 2117 276441052 276443184 0.000000e+00 3470
2 TraesCS2A01G240800 chr2D 97.788 2125 38 6 1 2120 628285689 628283569 0.000000e+00 3655
3 TraesCS2A01G240800 chr6D 97.184 2131 41 8 1 2120 431400048 431397926 0.000000e+00 3585
4 TraesCS2A01G240800 chr1D 97.135 2129 52 4 1 2120 254489723 254487595 0.000000e+00 3585
5 TraesCS2A01G240800 chr1D 95.000 1880 84 7 245 2120 244408395 244406522 0.000000e+00 2942
6 TraesCS2A01G240800 chr1D 94.840 1880 86 7 245 2120 244401944 244400072 0.000000e+00 2924
7 TraesCS2A01G240800 chr1D 93.993 1881 102 6 245 2120 244423932 244422058 0.000000e+00 2837
8 TraesCS2A01G240800 chr3D 96.944 2127 52 5 1 2120 21897576 21895456 0.000000e+00 3555
9 TraesCS2A01G240800 chr5A 96.186 2124 63 7 1 2120 684325610 684323501 0.000000e+00 3458
10 TraesCS2A01G240800 chr1A 97.456 1887 42 6 1 1884 256026145 256028028 0.000000e+00 3214
11 TraesCS2A01G240800 chr7B 95.833 264 7 1 56 319 57836827 57837086 6.990000e-115 424
12 TraesCS2A01G240800 chr3A 99.275 138 1 0 100 237 371665498 371665361 1.260000e-62 250


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 TraesCS2A01G240800 chr2A 335824182 335826301 2119 True 3916 3916 100.000 1 2120 1 chr2A.!!$R1 2119
1 TraesCS2A01G240800 chr2A 276441052 276443184 2132 False 3470 3470 96.157 1 2117 1 chr2A.!!$F1 2116
2 TraesCS2A01G240800 chr2D 628283569 628285689 2120 True 3655 3655 97.788 1 2120 1 chr2D.!!$R1 2119
3 TraesCS2A01G240800 chr6D 431397926 431400048 2122 True 3585 3585 97.184 1 2120 1 chr6D.!!$R1 2119
4 TraesCS2A01G240800 chr1D 254487595 254489723 2128 True 3585 3585 97.135 1 2120 1 chr1D.!!$R4 2119
5 TraesCS2A01G240800 chr1D 244406522 244408395 1873 True 2942 2942 95.000 245 2120 1 chr1D.!!$R2 1875
6 TraesCS2A01G240800 chr1D 244400072 244401944 1872 True 2924 2924 94.840 245 2120 1 chr1D.!!$R1 1875
7 TraesCS2A01G240800 chr1D 244422058 244423932 1874 True 2837 2837 93.993 245 2120 1 chr1D.!!$R3 1875
8 TraesCS2A01G240800 chr3D 21895456 21897576 2120 True 3555 3555 96.944 1 2120 1 chr3D.!!$R1 2119
9 TraesCS2A01G240800 chr5A 684323501 684325610 2109 True 3458 3458 96.186 1 2120 1 chr5A.!!$R1 2119
10 TraesCS2A01G240800 chr1A 256026145 256028028 1883 False 3214 3214 97.456 1 1884 1 chr1A.!!$F1 1883

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
839 853 1.564348 ACCTTCCCTATTCATTGCGGT 59.436 47.619 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1918 1943 1.276622 AGCCGAGGTAGTGGACAAAT 58.723 50.0 0.0 0.0 0.0 2.32 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
59 60 4.670765 AGAGGAGAACAAAAGCATTCCAT 58.329 39.130 0.00 0.0 0.00 3.41
227 228 7.419711 TCCCTATTTCATCTCGTAAAGTTCT 57.580 36.000 0.00 0.0 0.00 3.01
229 230 7.042335 CCCTATTTCATCTCGTAAAGTTCTGT 58.958 38.462 0.00 0.0 0.00 3.41
437 439 8.812329 GCTGCTATTCCGAATTACTCTATTATG 58.188 37.037 0.00 0.0 0.00 1.90
445 447 6.870965 CCGAATTACTCTATTATGCTGAAGCT 59.129 38.462 3.61 0.0 42.66 3.74
447 449 8.855279 CGAATTACTCTATTATGCTGAAGCTAC 58.145 37.037 3.61 0.0 42.66 3.58
684 698 4.579454 TTCTATTTACTGGTCGATCCCG 57.421 45.455 0.00 0.0 34.77 5.14
839 853 1.564348 ACCTTCCCTATTCATTGCGGT 59.436 47.619 0.00 0.0 0.00 5.68
849 864 6.816140 CCCTATTCATTGCGGTTTGTTATTTT 59.184 34.615 0.00 0.0 0.00 1.82
857 872 6.132791 TGCGGTTTGTTATTTTTCAGTACA 57.867 33.333 0.00 0.0 0.00 2.90
858 873 6.740110 TGCGGTTTGTTATTTTTCAGTACAT 58.260 32.000 0.00 0.0 0.00 2.29
1128 1145 8.427012 CAGTTCATCCAACGATAAAACAAATTG 58.573 33.333 0.00 0.0 40.32 2.32
1398 1417 2.901839 GGGGAAATGGCCGATACTACTA 59.098 50.000 0.00 0.0 0.00 1.82
1468 1487 7.227910 TGTGATTGGTTTAGTAGGTGTTTTCTC 59.772 37.037 0.00 0.0 0.00 2.87
1480 1499 6.824305 AGGTGTTTTCTCTTATGGTTCATG 57.176 37.500 0.00 0.0 0.00 3.07
1615 1634 6.769341 ACCCGCGGAATTTTTACTCTTATAAT 59.231 34.615 30.73 0.0 0.00 1.28
1862 1887 9.476202 GAAGTTGAACTTAATTAAACAAGCCAT 57.524 29.630 11.01 0.0 38.80 4.40
1918 1943 3.072476 CCGCCATATTTTCTTCCCCTCTA 59.928 47.826 0.00 0.0 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 228 0.746204 TTGACCAAACTGCGAGCACA 60.746 50.000 0.00 0.00 0.00 4.57
229 230 0.179059 TCTTGACCAAACTGCGAGCA 60.179 50.000 0.00 0.00 0.00 4.26
437 439 7.091443 TCTACTTACTTTTCAGTAGCTTCAGC 58.909 38.462 0.00 0.00 41.59 4.26
614 628 6.223120 AGATTGTCAATTTTGTACCAAAGGC 58.777 36.000 0.00 0.00 0.00 4.35
708 722 9.625747 AACTCCCAAAATTTTTGTACATTCAAT 57.374 25.926 18.05 0.00 0.00 2.57
849 864 7.062956 CACGTCATAAGCTAAACATGTACTGAA 59.937 37.037 0.00 0.00 0.00 3.02
857 872 5.703592 TCCAAACACGTCATAAGCTAAACAT 59.296 36.000 0.00 0.00 0.00 2.71
858 873 5.057819 TCCAAACACGTCATAAGCTAAACA 58.942 37.500 0.00 0.00 0.00 2.83
1128 1145 8.648557 TGATTGTGTCATAGTTCTATAGTTGC 57.351 34.615 0.00 0.00 0.00 4.17
1198 1215 9.541884 AAGTACAAAATGAGTAATAAACCCCAT 57.458 29.630 0.00 0.00 0.00 4.00
1364 1382 3.205282 CCATTTCCCCTACTTTCCTCCAT 59.795 47.826 0.00 0.00 0.00 3.41
1398 1417 4.647564 TCAGCCAAAGAGGAATTCTTCT 57.352 40.909 13.98 13.98 45.41 2.85
1433 1452 3.848272 AAACCAATCACAGCAATACCG 57.152 42.857 0.00 0.00 0.00 4.02
1468 1487 5.068198 CCCAATCCAGAACATGAACCATAAG 59.932 44.000 0.00 0.00 0.00 1.73
1480 1499 4.227864 AGAGATGAACCCAATCCAGAAC 57.772 45.455 0.00 0.00 0.00 3.01
1749 1768 9.959721 AGGCTAGTTGAATAGTTTTGATTAAGA 57.040 29.630 0.00 0.00 0.00 2.10
1918 1943 1.276622 AGCCGAGGTAGTGGACAAAT 58.723 50.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.