Multiple sequence alignment - TraesCS3B01G544100

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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 TraesCS3B01G544100 chr3B 100.000 2339 0 0 1 2339 781488560 781490898 0.000000e+00 4320.0
1 TraesCS3B01G544100 chr3B 84.411 263 33 6 3 263 781346594 781346338 3.860000e-63 252.0
2 TraesCS3B01G544100 chr3B 83.858 254 27 8 21 264 781217251 781217002 1.810000e-56 230.0
3 TraesCS3B01G544100 chr2B 96.498 971 34 0 397 1367 325637201 325638171 0.000000e+00 1605.0
4 TraesCS3B01G544100 chr2A 96.366 963 35 0 401 1363 382856246 382855284 0.000000e+00 1585.0
5 TraesCS3B01G544100 chr2A 96.078 969 38 0 397 1365 77802217 77803185 0.000000e+00 1580.0
6 TraesCS3B01G544100 chr4B 96.074 968 32 1 400 1361 364053469 364052502 0.000000e+00 1572.0
7 TraesCS3B01G544100 chr3D 96.058 964 38 0 399 1362 90829462 90830425 0.000000e+00 1570.0
8 TraesCS3B01G544100 chr3D 88.301 983 91 16 1364 2339 584451636 584452601 0.000000e+00 1157.0
9 TraesCS3B01G544100 chr3D 92.176 409 21 8 1 403 584451217 584451620 3.370000e-158 568.0
10 TraesCS3B01G544100 chr3D 78.947 399 63 16 1732 2122 308760804 308761189 3.860000e-63 252.0
11 TraesCS3B01G544100 chr3D 82.721 272 33 9 3 263 584050760 584050492 1.810000e-56 230.0
12 TraesCS3B01G544100 chr3D 77.394 376 46 25 1739 2103 6422753 6422406 1.100000e-43 187.0
13 TraesCS3B01G544100 chr3D 92.308 52 4 0 3 54 584050836 584050785 8.960000e-10 75.0
14 TraesCS3B01G544100 chr6D 95.692 975 39 3 397 1369 462399352 462398379 0.000000e+00 1565.0
15 TraesCS3B01G544100 chr6D 95.670 970 38 4 399 1366 452071651 452070684 0.000000e+00 1555.0
16 TraesCS3B01G544100 chr1D 95.954 964 36 3 401 1362 176360548 176361510 0.000000e+00 1561.0
17 TraesCS3B01G544100 chr5A 95.248 968 45 1 397 1364 472509593 472510559 0.000000e+00 1531.0
18 TraesCS3B01G544100 chr5A 77.534 365 64 12 1762 2122 684692973 684693323 1.100000e-48 204.0
19 TraesCS3B01G544100 chrUn 88.650 837 70 14 1506 2339 45497423 45498237 0.000000e+00 996.0
20 TraesCS3B01G544100 chrUn 89.125 423 38 8 1506 1927 469375649 469376064 9.580000e-144 520.0
21 TraesCS3B01G544100 chrUn 93.485 307 19 1 1 307 45500750 45500445 2.740000e-124 455.0
22 TraesCS3B01G544100 chrUn 90.667 150 11 3 1364 1511 45500384 45500236 1.830000e-46 196.0
23 TraesCS3B01G544100 chr6B 78.920 389 67 11 1736 2122 64742912 64743287 1.390000e-62 250.0
24 TraesCS3B01G544100 chr5B 78.635 337 54 14 1760 2092 417005675 417005353 8.470000e-50 207.0
25 TraesCS3B01G544100 chr1A 77.337 353 62 11 1760 2110 544998729 544998393 2.370000e-45 193.0
26 TraesCS3B01G544100 chr1A 87.143 70 6 3 2247 2315 495716153 495716086 2.490000e-10 76.8
27 TraesCS3B01G544100 chr7D 78.019 323 56 10 1739 2058 487773345 487773035 3.070000e-44 189.0


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 TraesCS3B01G544100 chr3B 781488560 781490898 2338 False 4320.0 4320 100.0000 1 2339 1 chr3B.!!$F1 2338
1 TraesCS3B01G544100 chr2B 325637201 325638171 970 False 1605.0 1605 96.4980 397 1367 1 chr2B.!!$F1 970
2 TraesCS3B01G544100 chr2A 382855284 382856246 962 True 1585.0 1585 96.3660 401 1363 1 chr2A.!!$R1 962
3 TraesCS3B01G544100 chr2A 77802217 77803185 968 False 1580.0 1580 96.0780 397 1365 1 chr2A.!!$F1 968
4 TraesCS3B01G544100 chr4B 364052502 364053469 967 True 1572.0 1572 96.0740 400 1361 1 chr4B.!!$R1 961
5 TraesCS3B01G544100 chr3D 90829462 90830425 963 False 1570.0 1570 96.0580 399 1362 1 chr3D.!!$F1 963
6 TraesCS3B01G544100 chr3D 584451217 584452601 1384 False 862.5 1157 90.2385 1 2339 2 chr3D.!!$F3 2338
7 TraesCS3B01G544100 chr6D 462398379 462399352 973 True 1565.0 1565 95.6920 397 1369 1 chr6D.!!$R2 972
8 TraesCS3B01G544100 chr6D 452070684 452071651 967 True 1555.0 1555 95.6700 399 1366 1 chr6D.!!$R1 967
9 TraesCS3B01G544100 chr1D 176360548 176361510 962 False 1561.0 1561 95.9540 401 1362 1 chr1D.!!$F1 961
10 TraesCS3B01G544100 chr5A 472509593 472510559 966 False 1531.0 1531 95.2480 397 1364 1 chr5A.!!$F1 967
11 TraesCS3B01G544100 chrUn 45497423 45498237 814 False 996.0 996 88.6500 1506 2339 1 chrUn.!!$F1 833
12 TraesCS3B01G544100 chrUn 45500236 45500750 514 True 325.5 455 92.0760 1 1511 2 chrUn.!!$R1 1510


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
81 83 0.030773 TGATGTACGATGAGAGGCGC 59.969 55.0 0.0 0.0 0.0 6.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1730 1868 0.407918 GGGATCCAAAACACCTCCCA 59.592 55.0 15.23 0.0 44.23 4.37 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.