Multiple sequence alignment - TraesCS5A01G332200

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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 TraesCS5A01G332200 chr5A 100.000 2468 0 0 1 2468 540625039 540622572 0 4558
1 TraesCS5A01G332200 chr5A 93.012 2490 98 20 1 2468 417905915 417908350 0 3565
2 TraesCS5A01G332200 chr1A 96.961 2468 66 4 1 2468 77263498 77265956 0 4133
3 TraesCS5A01G332200 chr1A 95.502 2468 83 3 1 2468 25270874 25268435 0 3917
4 TraesCS5A01G332200 chr1A 95.167 1800 57 10 1 1795 405515422 405513648 0 2815
5 TraesCS5A01G332200 chr6A 96.718 2468 73 2 1 2468 587986692 587984233 0 4102
6 TraesCS5A01G332200 chr3A 96.235 2470 62 3 1 2468 693613496 693611056 0 4017
7 TraesCS5A01G332200 chr4D 95.615 2486 78 7 1 2468 491381621 491384093 0 3958
8 TraesCS5A01G332200 chr1D 95.615 2486 76 9 1 2468 316243836 316241366 0 3956
9 TraesCS5A01G332200 chr2D 95.535 2486 78 9 1 2468 617340877 617343347 0 3945
10 TraesCS5A01G332200 chr3D 95.334 2486 84 8 1 2468 334265 336736 0 3919
11 TraesCS5A01G332200 chr3D 94.576 1014 31 11 1457 2468 610059701 610058710 0 1546
12 TraesCS5A01G332200 chr5D 94.891 2486 90 9 1 2468 78602802 78600336 0 3853
13 TraesCS5A01G332200 chr5D 94.883 2482 82 18 1 2468 552028914 552026464 0 3838
14 TraesCS5A01G332200 chr5D 94.584 757 30 1 1 757 333080463 333081208 0 1160
15 TraesCS5A01G332200 chr7D 94.644 2483 92 19 1 2468 586698558 586696102 0 3810
16 TraesCS5A01G332200 chr4A 94.478 2481 108 17 1 2468 731637217 731634753 0 3795
17 TraesCS5A01G332200 chr4A 93.349 2481 106 18 1 2468 478227266 478229700 0 3613
18 TraesCS5A01G332200 chr7A 97.392 1802 46 1 668 2468 70256082 70254281 0 3066
19 TraesCS5A01G332200 chr7A 95.549 674 24 1 1 674 70265479 70264812 0 1074
20 TraesCS5A01G332200 chr7B 89.763 1817 122 33 1 1794 43570262 43572037 0 2266
21 TraesCS5A01G332200 chr7B 87.615 977 74 24 1 956 156416647 156415697 0 1090


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 TraesCS5A01G332200 chr5A 540622572 540625039 2467 True 4558 4558 100.000 1 2468 1 chr5A.!!$R1 2467
1 TraesCS5A01G332200 chr5A 417905915 417908350 2435 False 3565 3565 93.012 1 2468 1 chr5A.!!$F1 2467
2 TraesCS5A01G332200 chr1A 77263498 77265956 2458 False 4133 4133 96.961 1 2468 1 chr1A.!!$F1 2467
3 TraesCS5A01G332200 chr1A 25268435 25270874 2439 True 3917 3917 95.502 1 2468 1 chr1A.!!$R1 2467
4 TraesCS5A01G332200 chr1A 405513648 405515422 1774 True 2815 2815 95.167 1 1795 1 chr1A.!!$R2 1794
5 TraesCS5A01G332200 chr6A 587984233 587986692 2459 True 4102 4102 96.718 1 2468 1 chr6A.!!$R1 2467
6 TraesCS5A01G332200 chr3A 693611056 693613496 2440 True 4017 4017 96.235 1 2468 1 chr3A.!!$R1 2467
7 TraesCS5A01G332200 chr4D 491381621 491384093 2472 False 3958 3958 95.615 1 2468 1 chr4D.!!$F1 2467
8 TraesCS5A01G332200 chr1D 316241366 316243836 2470 True 3956 3956 95.615 1 2468 1 chr1D.!!$R1 2467
9 TraesCS5A01G332200 chr2D 617340877 617343347 2470 False 3945 3945 95.535 1 2468 1 chr2D.!!$F1 2467
10 TraesCS5A01G332200 chr3D 334265 336736 2471 False 3919 3919 95.334 1 2468 1 chr3D.!!$F1 2467
11 TraesCS5A01G332200 chr3D 610058710 610059701 991 True 1546 1546 94.576 1457 2468 1 chr3D.!!$R1 1011
12 TraesCS5A01G332200 chr5D 78600336 78602802 2466 True 3853 3853 94.891 1 2468 1 chr5D.!!$R1 2467
13 TraesCS5A01G332200 chr5D 552026464 552028914 2450 True 3838 3838 94.883 1 2468 1 chr5D.!!$R2 2467
14 TraesCS5A01G332200 chr5D 333080463 333081208 745 False 1160 1160 94.584 1 757 1 chr5D.!!$F1 756
15 TraesCS5A01G332200 chr7D 586696102 586698558 2456 True 3810 3810 94.644 1 2468 1 chr7D.!!$R1 2467
16 TraesCS5A01G332200 chr4A 731634753 731637217 2464 True 3795 3795 94.478 1 2468 1 chr4A.!!$R1 2467
17 TraesCS5A01G332200 chr4A 478227266 478229700 2434 False 3613 3613 93.349 1 2468 1 chr4A.!!$F1 2467
18 TraesCS5A01G332200 chr7A 70254281 70256082 1801 True 3066 3066 97.392 668 2468 1 chr7A.!!$R1 1800
19 TraesCS5A01G332200 chr7A 70264812 70265479 667 True 1074 1074 95.549 1 674 1 chr7A.!!$R2 673
20 TraesCS5A01G332200 chr7B 43570262 43572037 1775 False 2266 2266 89.763 1 1794 1 chr7B.!!$F1 1793
21 TraesCS5A01G332200 chr7B 156415697 156416647 950 True 1090 1090 87.615 1 956 1 chr7B.!!$R1 955

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
409 426 1.010046 GGGTTAGGGTTAGGGTAGGGT 59.990 57.143 0.00 0.0 0.0 4.34 F
972 1039 1.518367 CCCCCTGGCCTGTAATTCTA 58.482 55.000 3.32 0.0 0.0 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1462 1542 1.055040 AGAGAGCTGCCACTTCACTT 58.945 50.0 0.0 0.0 0.00 3.16 R
2303 2418 1.097232 CATGCCCATCGACATGTTGT 58.903 50.0 12.9 0.0 39.05 3.32 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
401 418 5.482878 TGTTCTGTTCTAGGGTTAGGGTTAG 59.517 44.000 0.00 0.00 0.00 2.34
402 419 4.617593 TCTGTTCTAGGGTTAGGGTTAGG 58.382 47.826 0.00 0.00 0.00 2.69
403 420 3.710165 CTGTTCTAGGGTTAGGGTTAGGG 59.290 52.174 0.00 0.00 0.00 3.53
404 421 3.079534 TGTTCTAGGGTTAGGGTTAGGGT 59.920 47.826 0.00 0.00 0.00 4.34
405 422 4.297393 TGTTCTAGGGTTAGGGTTAGGGTA 59.703 45.833 0.00 0.00 0.00 3.69
406 423 4.821532 TCTAGGGTTAGGGTTAGGGTAG 57.178 50.000 0.00 0.00 0.00 3.18
407 424 2.883326 AGGGTTAGGGTTAGGGTAGG 57.117 55.000 0.00 0.00 0.00 3.18
408 425 1.296215 AGGGTTAGGGTTAGGGTAGGG 59.704 57.143 0.00 0.00 0.00 3.53
409 426 1.010046 GGGTTAGGGTTAGGGTAGGGT 59.990 57.143 0.00 0.00 0.00 4.34
410 427 2.565222 GGGTTAGGGTTAGGGTAGGGTT 60.565 54.545 0.00 0.00 0.00 4.11
411 428 3.311327 GGGTTAGGGTTAGGGTAGGGTTA 60.311 52.174 0.00 0.00 0.00 2.85
532 558 4.081642 TGTGATAGACCCTAGTTTCTGTGC 60.082 45.833 1.42 0.00 0.00 4.57
613 639 1.547372 GGCATTTGAAGGCACTGACAT 59.453 47.619 2.69 0.00 40.86 3.06
704 730 6.092122 TGAATTTCTGCTATGTAGTGGAAACG 59.908 38.462 0.00 0.00 33.03 3.60
728 755 6.401153 CGGAGTGTTTAGTTGCTGTTATTCTC 60.401 42.308 0.00 0.00 0.00 2.87
972 1039 1.518367 CCCCCTGGCCTGTAATTCTA 58.482 55.000 3.32 0.00 0.00 2.10
1455 1535 5.938125 GCTGGACAAGATAAAGGAAGTTGTA 59.062 40.000 0.00 0.00 31.57 2.41
1462 1542 8.383175 ACAAGATAAAGGAAGTTGTAATGGAGA 58.617 33.333 0.00 0.00 29.63 3.71
1542 1624 4.040217 GCCTAGGAATGATCAGTCTGATGT 59.960 45.833 20.20 5.84 37.20 3.06
1821 1906 7.503566 TCAGACAAATTCAGAGAAGTTTGGAAT 59.496 33.333 13.70 0.00 36.23 3.01
1835 1921 7.621683 AGAAGTTTGGAATACATCTAGTCTCCT 59.378 37.037 0.00 0.00 34.77 3.69
2183 2298 1.153086 GGGCGATGATCTGCAGGTT 60.153 57.895 15.13 1.19 0.00 3.50
2187 2302 1.863267 CGATGATCTGCAGGTTCTCC 58.137 55.000 15.13 6.76 0.00 3.71
2303 2418 0.482446 ACCTCCTTCATTGCCCACAA 59.518 50.000 0.00 0.00 40.87 3.33
2394 2509 1.066858 GTCATCGCCTTCTTCCTCACA 60.067 52.381 0.00 0.00 0.00 3.58
2451 2566 7.281841 TGTTGTATCTCATGGCAATCTTCATA 58.718 34.615 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
260 267 2.815298 CGTTGTTGTTCGGCCACGT 61.815 57.895 2.24 0.00 41.85 4.49
401 418 2.914941 TCTTCAAACCCTAACCCTACCC 59.085 50.000 0.00 0.00 0.00 3.69
402 419 4.857130 ATCTTCAAACCCTAACCCTACC 57.143 45.455 0.00 0.00 0.00 3.18
403 420 8.050930 TCAAATATCTTCAAACCCTAACCCTAC 58.949 37.037 0.00 0.00 0.00 3.18
404 421 8.165267 TCAAATATCTTCAAACCCTAACCCTA 57.835 34.615 0.00 0.00 0.00 3.53
405 422 7.036863 TCTCAAATATCTTCAAACCCTAACCCT 60.037 37.037 0.00 0.00 0.00 4.34
406 423 7.116736 TCTCAAATATCTTCAAACCCTAACCC 58.883 38.462 0.00 0.00 0.00 4.11
407 424 8.753497 ATCTCAAATATCTTCAAACCCTAACC 57.247 34.615 0.00 0.00 0.00 2.85
468 492 8.806177 TGCAAAAGCAAAAGCATATCTATATG 57.194 30.769 5.73 5.73 42.30 1.78
532 558 2.407090 TGTCAGATTCAGTCACAAGCG 58.593 47.619 0.00 0.00 0.00 4.68
582 608 1.850377 TCAAATGCCACAAACTTGCG 58.150 45.000 0.00 0.00 0.00 4.85
613 639 3.718434 ACATCCTATGAATCTCCTGCCAA 59.282 43.478 0.00 0.00 0.00 4.52
704 730 6.426937 TGAGAATAACAGCAACTAAACACTCC 59.573 38.462 0.00 0.00 0.00 3.85
924 991 2.643551 CACTCCAGAACACCACAGTTT 58.356 47.619 0.00 0.00 0.00 2.66
1089 1156 1.151668 GCTGGCTATACTGATTGGCG 58.848 55.000 0.00 0.00 36.37 5.69
1158 1225 2.737359 GCTTGTGCAATCCATGTCATGG 60.737 50.000 23.92 23.92 44.69 3.66
1182 1249 4.654915 TCTCCTTCAGTTCATTGATTGCA 58.345 39.130 0.00 0.00 0.00 4.08
1290 1370 8.462016 GTGTTTTGGATTATATCAGCTTGACTT 58.538 33.333 0.00 0.00 0.00 3.01
1455 1535 2.787994 CTGCCACTTCACTTCTCCATT 58.212 47.619 0.00 0.00 0.00 3.16
1462 1542 1.055040 AGAGAGCTGCCACTTCACTT 58.945 50.000 0.00 0.00 0.00 3.16
1542 1624 9.944376 GTTCATAAGTAGATCAGGGCATATTTA 57.056 33.333 0.00 0.00 0.00 1.40
2303 2418 1.097232 CATGCCCATCGACATGTTGT 58.903 50.000 12.90 0.00 39.05 3.32
2394 2509 2.806019 GCTCGTGGATGCATCAGAAGAT 60.806 50.000 27.25 0.00 33.87 2.40


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

AutoCloner maintained by Alex Coulton.