Multiple sequence alignment - TraesCS3B01G437400

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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 TraesCS3B01G437400 chr3B 100.000 6063 0 0 1 6063 676276774 676270712 0.000000e+00 11197.0
1 TraesCS3B01G437400 chr3D 93.066 5408 201 70 629 5917 513953571 513948219 0.000000e+00 7749.0
2 TraesCS3B01G437400 chr3D 87.821 624 66 7 1 617 513954176 513953556 0.000000e+00 723.0
3 TraesCS3B01G437400 chr3D 97.500 40 1 0 5760 5799 513948337 513948298 1.090000e-07 69.4
4 TraesCS3B01G437400 chr3A 94.782 2319 88 13 2830 5131 648870447 648868145 0.000000e+00 3581.0
5 TraesCS3B01G437400 chr3A 90.771 1972 96 33 638 2561 648872702 648870769 0.000000e+00 2555.0
6 TraesCS3B01G437400 chr3A 85.667 900 48 34 5085 5931 648868150 648867279 0.000000e+00 872.0
7 TraesCS3B01G437400 chr3A 82.835 635 88 13 1 617 648874410 648873779 3.190000e-152 549.0
8 TraesCS3B01G437400 chr3A 96.694 242 5 2 2591 2831 648870768 648870529 3.400000e-107 399.0
9 TraesCS3B01G437400 chr3A 80.897 513 84 8 109 609 648873511 648873001 5.700000e-105 392.0
10 TraesCS3B01G437400 chr3A 95.918 49 2 0 5760 5808 648867407 648867359 5.040000e-11 80.5
11 TraesCS3B01G437400 chr6B 89.157 83 9 0 2446 2528 10313869 10313787 2.990000e-18 104.0
12 TraesCS3B01G437400 chr1D 92.000 75 5 1 4325 4398 356154912 356154838 2.990000e-18 104.0
13 TraesCS3B01G437400 chr1A 92.000 75 5 1 4325 4398 456941372 456941298 2.990000e-18 104.0
14 TraesCS3B01G437400 chr1A 91.837 49 3 1 2445 2492 45840206 45840254 3.920000e-07 67.6
15 TraesCS3B01G437400 chr5A 92.453 53 4 0 2445 2497 505496758 505496810 6.520000e-10 76.8
16 TraesCS3B01G437400 chr2D 86.154 65 5 4 2477 2539 291859396 291859334 3.920000e-07 67.6
17 TraesCS3B01G437400 chr6D 89.130 46 5 0 2495 2540 150786062 150786017 2.360000e-04 58.4
18 TraesCS3B01G437400 chr6D 88.889 45 5 0 2445 2489 157659514 157659470 8.490000e-04 56.5
19 TraesCS3B01G437400 chr7B 100.000 28 0 0 2442 2469 693954271 693954298 1.100000e-02 52.8
20 TraesCS3B01G437400 chr7A 100.000 28 0 0 2445 2472 716231985 716231958 1.100000e-02 52.8
21 TraesCS3B01G437400 chr4A 100.000 28 0 0 2441 2468 546196560 546196587 1.100000e-02 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 TraesCS3B01G437400 chr3B 676270712 676276774 6062 True 11197.000000 11197 100.000 1 6063 1 chr3B.!!$R1 6062
1 TraesCS3B01G437400 chr3D 513948219 513953571 5352 True 7749.000000 7749 93.066 629 5917 1 chr3D.!!$R1 5288
2 TraesCS3B01G437400 chr3D 513953556 513954176 620 True 723.000000 723 87.821 1 617 1 chr3D.!!$R3 616
3 TraesCS3B01G437400 chr3A 648867279 648874410 7131 True 1204.071429 3581 89.652 1 5931 7 chr3A.!!$R1 5930


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
856 1955 1.027357 CTCCATCTTGGCATTTCCGG 58.973 55.0 0.00 0.0 37.47 5.14 F
1224 2337 0.108992 GGAAGTACGTGGTCGATGCA 60.109 55.0 0.00 0.0 40.62 3.96 F
2339 3491 0.396435 CCCGGGTGCTATTGCTATCA 59.604 55.0 14.18 0.0 40.48 2.15 F
2713 3866 1.059098 TGTGATTGTGGTCCTGCTCT 58.941 50.0 0.00 0.0 0.00 4.09 F
4280 5529 0.033504 TCTGACTGTGGTCCTTTCGC 59.966 55.0 0.00 0.0 41.47 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2049 3197 2.009774 CCTGCAGCCATAGTGTGTAAC 58.990 52.381 8.66 0.00 37.35 2.50 R
3146 4380 1.215647 GGTGCGAGTTGAGGTCGAT 59.784 57.895 0.00 0.00 39.92 3.59 R
3611 4851 0.106708 GCACAACAGACCTCACCTGA 59.893 55.000 0.00 0.00 35.69 3.86 R
4537 5788 0.038801 GCTTTGCTTGGTCCTTGAGC 60.039 55.000 5.76 5.76 36.95 4.26 R
5992 7414 0.036105 GGGGTGTATTTCGACCGGTT 60.036 55.000 9.42 0.00 32.48 4.44 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.