Multiple sequence alignment - TraesCS6A01G092000

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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 TraesCS6A01G092000 chr6A 100.000 3709 0 0 1 3709 60404961 60408669 0 6850
1 TraesCS6A01G092000 chr7A 97.978 3710 71 4 1 3709 419035434 419031728 0 6433
2 TraesCS6A01G092000 chr2A 97.790 3711 76 5 1 3709 705954437 705958143 0 6394
3 TraesCS6A01G092000 chr2A 97.709 3710 62 8 1 3709 36902203 36905890 0 6359
4 TraesCS6A01G092000 chr6B 84.246 1498 175 36 1 1453 664384046 664382565 0 1402
5 TraesCS6A01G092000 chr6B 82.368 1191 171 24 1676 2838 664382538 664381359 0 1000
6 TraesCS6A01G092000 chr6B 89.157 747 78 3 2964 3709 664381318 664380574 0 928


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 TraesCS6A01G092000 chr6A 60404961 60408669 3708 False 6850 6850 100.000 1 3709 1 chr6A.!!$F1 3708
1 TraesCS6A01G092000 chr7A 419031728 419035434 3706 True 6433 6433 97.978 1 3709 1 chr7A.!!$R1 3708
2 TraesCS6A01G092000 chr2A 705954437 705958143 3706 False 6394 6394 97.790 1 3709 1 chr2A.!!$F2 3708
3 TraesCS6A01G092000 chr2A 36902203 36905890 3687 False 6359 6359 97.709 1 3709 1 chr2A.!!$F1 3708
4 TraesCS6A01G092000 chr6B 664380574 664384046 3472 True 1110 1402 85.257 1 3709 3 chr6B.!!$R1 3708

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
649 665 1.079336 GGCGTTGTACCACTCCTCC 60.079 63.158 0.0 0.0 0.00 4.30 F
2350 2402 1.960040 TAGGTCCTCGTGCCATGCAG 61.960 60.000 0.0 0.0 40.08 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2412 2464 1.164411 CGCTGTGTTAGGGCAAATGA 58.836 50.00 0.0 0.0 32.19 2.57 R
3568 3634 4.963373 TCAAACCAGAATAAGAACGGACA 58.037 39.13 0.0 0.0 0.00 4.02 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
41 42 3.999663 CTCGTTCAGCTTGGATTCTCTTT 59.000 43.478 0.00 0.0 0.00 2.52
144 145 6.890979 ACAAGAGCAAAAGAATCTTTAGCT 57.109 33.333 8.83 0.0 30.99 3.32
180 181 7.661437 ACTGAACTGAATCTGCTACATTTTGTA 59.339 33.333 0.00 0.0 0.00 2.41
489 491 2.263540 GTCGTGCCCATACGGTGT 59.736 61.111 0.00 0.0 43.85 4.16
649 665 1.079336 GGCGTTGTACCACTCCTCC 60.079 63.158 0.00 0.0 0.00 4.30
670 686 6.211587 TCCCTAATTGATGCATGTTTTCTG 57.788 37.500 2.46 0.0 0.00 3.02
684 700 9.900710 TGCATGTTTTCTGTTATTTTAATACGT 57.099 25.926 0.00 0.0 0.00 3.57
825 863 4.441913 GCCCCATTTTCATATCAACACTGG 60.442 45.833 0.00 0.0 0.00 4.00
874 915 3.924114 TCCCACTGAGAAACAAGTCAA 57.076 42.857 0.00 0.0 0.00 3.18
1800 1842 4.346730 TGCCATGAATGACAGATTCCTTT 58.653 39.130 0.00 0.0 0.00 3.11
2350 2402 1.960040 TAGGTCCTCGTGCCATGCAG 61.960 60.000 0.00 0.0 40.08 4.41
2679 2736 3.184628 AGTCCTCCATCTGAATTGGTCA 58.815 45.455 0.00 0.0 35.64 4.02
2977 3043 1.203518 ACCCTTACACCCCATACCACT 60.204 52.381 0.00 0.0 0.00 4.00
3307 3373 0.035630 CTGCTCTGCTTGCTAGGGTT 60.036 55.000 0.00 0.0 0.00 4.11
3568 3634 2.875804 GCAAGCAGCAGGCCCTTTT 61.876 57.895 0.00 0.0 46.50 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.835284 TGTACTGGAGGAATACATGCAA 57.165 40.909 0.00 0.00 0.00 4.08
144 145 4.772624 AGATTCAGTTCAGTACCTGCACTA 59.227 41.667 0.00 0.00 35.95 2.74
489 491 3.749088 ACAACTTTATTGTTCGATCGGCA 59.251 39.130 16.41 11.99 0.00 5.69
494 496 5.995282 TGACCTCACAACTTTATTGTTCGAT 59.005 36.000 0.00 0.00 0.00 3.59
536 552 2.807967 CTCCTCTCAAACAACGATGCAA 59.192 45.455 0.00 0.00 0.00 4.08
649 665 9.590451 AATAACAGAAAACATGCATCAATTAGG 57.410 29.630 0.00 0.00 0.00 2.69
670 686 8.272545 AGGGAAAGTGGACGTATTAAAATAAC 57.727 34.615 0.00 0.00 0.00 1.89
684 700 2.649742 AGATGAGGAGGGAAAGTGGA 57.350 50.000 0.00 0.00 0.00 4.02
833 872 6.070078 TGGGATACACGGTTAAGGAAAATAGT 60.070 38.462 0.00 0.00 39.74 2.12
890 932 0.177373 AAGGGAGGCGTTATCCGAAC 59.823 55.000 0.00 0.00 39.56 3.95
894 936 0.765510 ATCCAAGGGAGGCGTTATCC 59.234 55.000 0.00 0.00 34.05 2.59
1219 1261 2.091111 TGAGAGTGGATGGATGAGCCTA 60.091 50.000 0.00 0.00 37.63 3.93
1362 1404 4.729868 AGAACAGCTAGTGGATGGTTTTT 58.270 39.130 0.00 0.00 35.35 1.94
2338 2390 3.189376 TTGGTCCTGCATGGCACGA 62.189 57.895 0.00 0.00 33.79 4.35
2350 2402 7.650504 GGAACTTTATGTTTTAACTGTTGGTCC 59.349 37.037 2.69 0.00 39.30 4.46
2412 2464 1.164411 CGCTGTGTTAGGGCAAATGA 58.836 50.000 0.00 0.00 32.19 2.57
2749 2806 7.861629 TGATAGGTCTAACTGAAAATCCACAT 58.138 34.615 0.00 0.00 0.00 3.21
2977 3043 5.073144 ACAGATGTTAGTTTGGGGAAGAAGA 59.927 40.000 0.00 0.00 0.00 2.87
3568 3634 4.963373 TCAAACCAGAATAAGAACGGACA 58.037 39.130 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.