Multiple sequence alignment - TraesCS3D01G409000

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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 TraesCS3D01G409000 chr3D 100.000 5168 0 0 1 5168 523176760 523181927 0.000000e+00 9544
1 TraesCS3D01G409000 chr3D 97.317 4249 105 4 920 5168 500119261 500115022 0.000000e+00 7206
2 TraesCS3D01G409000 chr3D 98.630 219 3 0 1 219 121308940 121309158 6.280000e-104 388
3 TraesCS3D01G409000 chr3D 98.630 219 3 0 1 219 523895817 523895599 6.280000e-104 388
4 TraesCS3D01G409000 chr2D 98.536 4646 64 3 523 5168 545779690 545775049 0.000000e+00 8200
5 TraesCS3D01G409000 chr2D 95.238 672 16 8 218 889 78403882 78403227 0.000000e+00 1050
6 TraesCS3D01G409000 chr2D 97.982 446 7 1 218 663 643708171 643708614 0.000000e+00 773
7 TraesCS3D01G409000 chr2D 97.095 241 4 1 218 458 507475008 507475245 2.240000e-108 403
8 TraesCS3D01G409000 chr2D 99.543 219 1 0 1 219 643707896 643708114 2.900000e-107 399
9 TraesCS3D01G409000 chr2D 96.266 241 4 2 218 458 96767897 96768132 1.740000e-104 390
10 TraesCS3D01G409000 chr2D 98.174 219 4 0 1 219 507474733 507474951 2.920000e-102 383
11 TraesCS3D01G409000 chr7D 99.208 4419 31 3 752 5168 21974131 21978547 0.000000e+00 7963
12 TraesCS3D01G409000 chr7D 99.185 4419 34 2 752 5168 116418782 116423200 0.000000e+00 7960
13 TraesCS3D01G409000 chr7D 97.554 4252 97 5 920 5168 555024413 555020166 0.000000e+00 7269
14 TraesCS3D01G409000 chr7D 97.810 3561 47 5 523 4083 10518671 10522200 0.000000e+00 6115
15 TraesCS3D01G409000 chr7D 97.290 3616 61 4 520 4134 51844313 51847892 0.000000e+00 6100
16 TraesCS3D01G409000 chr7D 97.695 2082 19 3 523 2604 72068851 72070903 0.000000e+00 3552
17 TraesCS3D01G409000 chr7D 95.279 466 8 6 218 670 21973681 21974145 0.000000e+00 726
18 TraesCS3D01G409000 chr7D 94.647 467 8 6 218 670 116418333 116418796 0.000000e+00 708
19 TraesCS3D01G409000 chr7D 96.766 402 10 3 523 922 555024879 555024479 0.000000e+00 667
20 TraesCS3D01G409000 chr7D 93.931 346 12 4 218 560 175881143 175880804 9.920000e-142 514
21 TraesCS3D01G409000 chr7D 93.931 346 12 4 218 560 178479900 178480239 9.920000e-142 514
22 TraesCS3D01G409000 chr7D 98.630 219 3 0 1 219 21973406 21973624 6.280000e-104 388
23 TraesCS3D01G409000 chr7D 98.630 219 3 0 1 219 178479625 178479843 6.280000e-104 388
24 TraesCS3D01G409000 chr7D 98.174 219 4 0 1 219 175881418 175881200 2.920000e-102 383
25 TraesCS3D01G409000 chr1D 99.163 4420 33 4 752 5168 211560572 211564990 0.000000e+00 7954
26 TraesCS3D01G409000 chr1D 97.792 453 8 1 218 670 211560136 211560586 0.000000e+00 780
27 TraesCS3D01G409000 chr1D 99.543 219 1 0 1 219 212704523 212704305 2.900000e-107 399
28 TraesCS3D01G409000 chr5D 99.073 4421 37 3 752 5168 538553405 538548985 0.000000e+00 7934
29 TraesCS3D01G409000 chr5D 97.411 4249 104 3 920 5168 559862542 559866784 0.000000e+00 7232
30 TraesCS3D01G409000 chr6D 97.411 4249 103 4 920 5168 436562260 436558019 0.000000e+00 7230
31 TraesCS3D01G409000 chr4D 98.630 219 3 0 1 219 249077914 249078132 6.280000e-104 388


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 TraesCS3D01G409000 chr3D 523176760 523181927 5167 False 9544.000000 9544 100.000000 1 5168 1 chr3D.!!$F2 5167
1 TraesCS3D01G409000 chr3D 500115022 500119261 4239 True 7206.000000 7206 97.317000 920 5168 1 chr3D.!!$R1 4248
2 TraesCS3D01G409000 chr2D 545775049 545779690 4641 True 8200.000000 8200 98.536000 523 5168 1 chr2D.!!$R2 4645
3 TraesCS3D01G409000 chr2D 78403227 78403882 655 True 1050.000000 1050 95.238000 218 889 1 chr2D.!!$R1 671
4 TraesCS3D01G409000 chr2D 643707896 643708614 718 False 586.000000 773 98.762500 1 663 2 chr2D.!!$F3 662
5 TraesCS3D01G409000 chr2D 507474733 507475245 512 False 393.000000 403 97.634500 1 458 2 chr2D.!!$F2 457
6 TraesCS3D01G409000 chr7D 10518671 10522200 3529 False 6115.000000 6115 97.810000 523 4083 1 chr7D.!!$F1 3560
7 TraesCS3D01G409000 chr7D 51844313 51847892 3579 False 6100.000000 6100 97.290000 520 4134 1 chr7D.!!$F2 3614
8 TraesCS3D01G409000 chr7D 116418333 116423200 4867 False 4334.000000 7960 96.916000 218 5168 2 chr7D.!!$F5 4950
9 TraesCS3D01G409000 chr7D 555020166 555024879 4713 True 3968.000000 7269 97.160000 523 5168 2 chr7D.!!$R2 4645
10 TraesCS3D01G409000 chr7D 72068851 72070903 2052 False 3552.000000 3552 97.695000 523 2604 1 chr7D.!!$F3 2081
11 TraesCS3D01G409000 chr7D 21973406 21978547 5141 False 3025.666667 7963 97.705667 1 5168 3 chr7D.!!$F4 5167
12 TraesCS3D01G409000 chr7D 178479625 178480239 614 False 451.000000 514 96.280500 1 560 2 chr7D.!!$F6 559
13 TraesCS3D01G409000 chr7D 175880804 175881418 614 True 448.500000 514 96.052500 1 560 2 chr7D.!!$R1 559
14 TraesCS3D01G409000 chr1D 211560136 211564990 4854 False 4367.000000 7954 98.477500 218 5168 2 chr1D.!!$F1 4950
15 TraesCS3D01G409000 chr5D 538548985 538553405 4420 True 7934.000000 7934 99.073000 752 5168 1 chr5D.!!$R1 4416
16 TraesCS3D01G409000 chr5D 559862542 559866784 4242 False 7232.000000 7232 97.411000 920 5168 1 chr5D.!!$F1 4248
17 TraesCS3D01G409000 chr6D 436558019 436562260 4241 True 7230.000000 7230 97.411000 920 5168 1 chr6D.!!$R1 4248

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
441 505 1.071299 TAGGCGGCATGTGCATAGG 59.929 57.895 13.08 0.0 44.36 2.57 F
673 754 2.028294 CCCATAACAAGCAATGCCACAA 60.028 45.455 0.00 0.0 0.00 3.33 F
1333 1487 0.947180 TTTAGTGCTTCCCGTCGTGC 60.947 55.000 0.00 0.0 0.00 5.34 F
2778 2933 0.110678 AGAGACACGTGAGGGACAGA 59.889 55.000 25.01 0.0 38.45 3.41 F
3803 3960 1.478916 GGCGAGAGGAAGAAGCTAAGT 59.521 52.381 0.00 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1333 1487 0.322648 TCATGTGCAGTGACCTCCTG 59.677 55.000 0.0 0.0 0.0 3.86 R
2537 2691 1.134367 TCGCACTGAGTATACCTGCAC 59.866 52.381 0.0 0.0 0.0 4.57 R
2854 3009 1.277580 CCAACAGCCTCCTCCTCCAT 61.278 60.000 0.0 0.0 0.0 3.41 R
4138 4329 1.064463 ACAATCCCGACATTCCTGCAT 60.064 47.619 0.0 0.0 0.0 3.96 R
5148 5339 1.981254 CAACATCAAACATGGCGTCC 58.019 50.000 0.0 0.0 0.0 4.79 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
195 196 6.699204 TGATGTGAAAATAAATTTGTGTGCGT 59.301 30.769 0.00 0.00 0.00 5.24
424 485 5.382664 AAAGAGTTTGAAGAGTTGGGGTA 57.617 39.130 0.00 0.00 0.00 3.69
441 505 1.071299 TAGGCGGCATGTGCATAGG 59.929 57.895 13.08 0.00 44.36 2.57
673 754 2.028294 CCCATAACAAGCAATGCCACAA 60.028 45.455 0.00 0.00 0.00 3.33
1333 1487 0.947180 TTTAGTGCTTCCCGTCGTGC 60.947 55.000 0.00 0.00 0.00 5.34
1564 1718 1.456296 GCACATGCAGAACCAGATGA 58.544 50.000 0.00 0.00 41.59 2.92
2454 2608 4.997395 GCTTTTGTGGAGAGTGAGAACATA 59.003 41.667 0.00 0.00 0.00 2.29
2537 2691 0.745486 TGCATCCTTCATGACAGGCG 60.745 55.000 15.30 11.29 33.80 5.52
2778 2933 0.110678 AGAGACACGTGAGGGACAGA 59.889 55.000 25.01 0.00 38.45 3.41
2854 3009 2.594303 CAACAGGAACAGCGGCCA 60.594 61.111 2.24 0.00 0.00 5.36
3725 3882 4.695455 CACTAATTGTCCCACTTTCGTCAT 59.305 41.667 0.00 0.00 0.00 3.06
3803 3960 1.478916 GGCGAGAGGAAGAAGCTAAGT 59.521 52.381 0.00 0.00 0.00 2.24
4138 4329 7.064016 GTGGCACTTTGTTCTGAATTTTGTAAA 59.936 33.333 11.13 0.00 0.00 2.01
4408 4599 1.827315 CTTTCGCGCGTCTGGTTGAA 61.827 55.000 30.98 11.22 0.00 2.69
4772 4963 5.484173 TGTAGAGAAAATAATTGCGGCTG 57.516 39.130 0.00 0.00 0.00 4.85
4965 5156 4.468615 GCGAGCGCTCAGACGACT 62.469 66.667 34.69 0.00 38.26 4.18
5148 5339 2.102420 TGTACGGGTTCATGAGCCTATG 59.898 50.000 25.62 18.12 43.98 2.23
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
297 358 1.146930 CTATGCACATGCCGACCCT 59.853 57.895 0.49 0.00 41.18 4.34
424 485 2.203252 CCTATGCACATGCCGCCT 60.203 61.111 0.49 0.00 41.18 5.52
1333 1487 0.322648 TCATGTGCAGTGACCTCCTG 59.677 55.000 0.00 0.00 0.00 3.86
1564 1718 4.703897 TCAACATCGGTGTCTTCTTCTTT 58.296 39.130 0.00 0.00 37.67 2.52
1679 1833 2.478370 CCATCATTCACGGTCATTGCAC 60.478 50.000 0.00 0.00 0.00 4.57
2454 2608 4.792068 TGAAGAACCATGTCCAACTTTCT 58.208 39.130 0.00 0.00 0.00 2.52
2537 2691 1.134367 TCGCACTGAGTATACCTGCAC 59.866 52.381 0.00 0.00 0.00 4.57
2854 3009 1.277580 CCAACAGCCTCCTCCTCCAT 61.278 60.000 0.00 0.00 0.00 3.41
3841 3998 6.594788 ACAAATTTCAGAACATAGTGCCAT 57.405 33.333 0.00 0.00 0.00 4.40
4138 4329 1.064463 ACAATCCCGACATTCCTGCAT 60.064 47.619 0.00 0.00 0.00 3.96
4181 4372 3.578456 GCACCACGATGACCCTTG 58.422 61.111 0.00 0.00 0.00 3.61
4408 4599 1.687123 CGTTTCTCACCCGGGATAGAT 59.313 52.381 32.02 0.00 0.00 1.98
4772 4963 7.478978 GCATTAAGCGAAGAGAAAGTTTTAGTC 59.521 37.037 0.00 0.00 0.00 2.59
4965 5156 4.248174 ACTCCTCTGTCTGATCTGATCA 57.752 45.455 18.61 18.61 37.76 2.92
5148 5339 1.981254 CAACATCAAACATGGCGTCC 58.019 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.