Multiple sequence alignment - TraesCS3D01G209900

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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 TraesCS3D01G209900 chr3D 100.000 4806 0 0 1 4806 277542086 277537281 0.000000e+00 8876.0
1 TraesCS3D01G209900 chr3D 92.727 55 4 0 4622 4676 567708588 567708642 3.990000e-11 80.5
2 TraesCS3D01G209900 chr3A 96.765 3524 64 17 1 3487 361991567 361995077 0.000000e+00 5830.0
3 TraesCS3D01G209900 chr3A 96.095 1050 34 3 3578 4622 361995074 361996121 0.000000e+00 1705.0
4 TraesCS3D01G209900 chr3A 92.857 154 9 1 4655 4806 361996115 361996268 6.260000e-54 222.0
5 TraesCS3D01G209900 chr3B 95.871 3439 80 29 1 3408 372838900 372842307 0.000000e+00 5507.0
6 TraesCS3D01G209900 chr3B 92.724 1072 28 13 3580 4622 372842306 372843356 0.000000e+00 1502.0
7 TraesCS3D01G209900 chr3B 87.662 154 15 3 4656 4806 372843351 372843503 4.940000e-40 176.0
8 TraesCS3D01G209900 chr3B 96.000 50 2 0 4618 4667 628478802 628478851 1.110000e-11 82.4
9 TraesCS3D01G209900 chr3B 92.593 54 4 0 4617 4670 26648172 26648225 1.430000e-10 78.7
10 TraesCS3D01G209900 chr4D 93.636 110 6 1 3472 3580 26253940 26254049 3.850000e-36 163.0
11 TraesCS3D01G209900 chr7B 94.286 105 4 2 3483 3586 589348318 589348421 4.980000e-35 159.0
12 TraesCS3D01G209900 chr1A 93.519 108 6 1 3484 3590 351606858 351606751 4.980000e-35 159.0
13 TraesCS3D01G209900 chr7A 94.175 103 5 1 3481 3582 511927312 511927414 6.440000e-34 156.0
14 TraesCS3D01G209900 chr7A 93.333 105 5 2 3483 3586 628008575 628008472 2.320000e-33 154.0
15 TraesCS3D01G209900 chr7A 94.231 52 3 0 4620 4671 639594990 639594939 3.990000e-11 80.5
16 TraesCS3D01G209900 chr7D 93.333 105 5 2 3483 3586 545397537 545397640 2.320000e-33 154.0
17 TraesCS3D01G209900 chr7D 91.379 58 3 2 4608 4665 199127653 199127708 1.430000e-10 78.7
18 TraesCS3D01G209900 chr1B 91.892 111 7 2 3484 3592 56752488 56752378 2.320000e-33 154.0
19 TraesCS3D01G209900 chr1B 91.228 57 3 2 4618 4673 423585133 423585078 5.160000e-10 76.8
20 TraesCS3D01G209900 chr6D 90.351 114 8 3 3477 3589 368755201 368755090 3.880000e-31 147.0
21 TraesCS3D01G209900 chr4B 89.655 116 11 1 3480 3594 595278781 595278896 3.880000e-31 147.0
22 TraesCS3D01G209900 chr6B 94.545 55 1 2 4618 4672 277158983 277159035 3.080000e-12 84.2
23 TraesCS3D01G209900 chrUn 96.000 50 2 0 4618 4667 100223781 100223830 1.110000e-11 82.4
24 TraesCS3D01G209900 chr6A 92.727 55 2 2 4617 4670 613997767 613997714 1.430000e-10 78.7


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 TraesCS3D01G209900 chr3D 277537281 277542086 4805 True 8876.000000 8876 100.000000 1 4806 1 chr3D.!!$R1 4805
1 TraesCS3D01G209900 chr3A 361991567 361996268 4701 False 2585.666667 5830 95.239000 1 4806 3 chr3A.!!$F1 4805
2 TraesCS3D01G209900 chr3B 372838900 372843503 4603 False 2395.000000 5507 92.085667 1 4806 3 chr3B.!!$F3 4805


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
391 397 0.321034 ACATGATCCCATCGCCGATG 60.321 55.000 19.87 19.87 39.52 3.84 F
868 883 1.235281 ACAGCACGCGTGTAGAGAGA 61.235 55.000 36.80 0.00 0.00 3.10 F
969 1014 2.126734 CGTAAACCGACCGCTCGT 60.127 61.111 0.00 0.00 38.32 4.18 F
2057 2105 2.279517 CAGACGAGTATGCGGGCC 60.280 66.667 0.00 0.00 35.12 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1386 1431 0.654160 AGCGATCGTCGTCGTTGATA 59.346 50.000 17.81 0.0 42.81 2.15 R
2333 2384 2.489329 CAAAAAGTGCATCGGGTCTGAT 59.511 45.455 0.00 0.0 0.00 2.90 R
2341 2392 3.607422 TGAGTGACAAAAAGTGCATCG 57.393 42.857 0.00 0.0 0.00 3.84 R
3836 3888 1.004918 GTGAACTGCACGGCTAGGT 60.005 57.895 0.00 0.0 37.83 3.08 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.