Multiple sequence alignment - TraesCS4A01G360600

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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 TraesCS4A01G360600 chr4A 100.000 2486 0 0 1 2486 633685853 633688338 0.000000e+00 4591
1 TraesCS4A01G360600 chr4A 98.070 2487 47 1 1 2486 633467260 633469746 0.000000e+00 4325
2 TraesCS4A01G360600 chr4A 97.830 2488 49 3 1 2486 633533379 633535863 0.000000e+00 4290
3 TraesCS4A01G360600 chr4A 97.470 2490 58 1 2 2486 633508735 633511224 0.000000e+00 4244
4 TraesCS4A01G360600 chr4A 97.433 2493 56 2 2 2486 633425073 633427565 0.000000e+00 4242
5 TraesCS4A01G360600 chrUn 96.598 2440 77 6 1 2435 282364697 282362259 0.000000e+00 4041
6 TraesCS4A01G360600 chrUn 96.311 2440 84 6 1 2435 86510013 86507575 0.000000e+00 4002
7 TraesCS4A01G360600 chrUn 98.333 60 1 0 2427 2486 150804224 150804283 3.380000e-19 106
8 TraesCS4A01G360600 chr6B 96.436 2441 79 8 1 2435 596620323 596622761 0.000000e+00 4019
9 TraesCS4A01G360600 chr3B 96.066 2440 87 9 1 2435 92317837 92320272 0.000000e+00 3965
10 TraesCS4A01G360600 chr2B 96.023 2439 88 9 1 2435 30670612 30668179 0.000000e+00 3958
11 TraesCS4A01G360600 chr1D 98.333 60 1 0 2427 2486 326358202 326358143 3.380000e-19 106
12 TraesCS4A01G360600 chr1D 98.333 60 1 0 2427 2486 326365013 326364954 3.380000e-19 106
13 TraesCS4A01G360600 chr1D 98.333 60 1 0 2427 2486 431137745 431137686 3.380000e-19 106
14 TraesCS4A01G360600 chr1D 98.333 60 1 0 2427 2486 461246476 461246417 3.380000e-19 106


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 TraesCS4A01G360600 chr4A 633685853 633688338 2485 False 4591 4591 100.000 1 2486 1 chr4A.!!$F5 2485
1 TraesCS4A01G360600 chr4A 633467260 633469746 2486 False 4325 4325 98.070 1 2486 1 chr4A.!!$F2 2485
2 TraesCS4A01G360600 chr4A 633533379 633535863 2484 False 4290 4290 97.830 1 2486 1 chr4A.!!$F4 2485
3 TraesCS4A01G360600 chr4A 633508735 633511224 2489 False 4244 4244 97.470 2 2486 1 chr4A.!!$F3 2484
4 TraesCS4A01G360600 chr4A 633425073 633427565 2492 False 4242 4242 97.433 2 2486 1 chr4A.!!$F1 2484
5 TraesCS4A01G360600 chrUn 282362259 282364697 2438 True 4041 4041 96.598 1 2435 1 chrUn.!!$R2 2434
6 TraesCS4A01G360600 chrUn 86507575 86510013 2438 True 4002 4002 96.311 1 2435 1 chrUn.!!$R1 2434
7 TraesCS4A01G360600 chr6B 596620323 596622761 2438 False 4019 4019 96.436 1 2435 1 chr6B.!!$F1 2434
8 TraesCS4A01G360600 chr3B 92317837 92320272 2435 False 3965 3965 96.066 1 2435 1 chr3B.!!$F1 2434
9 TraesCS4A01G360600 chr2B 30668179 30670612 2433 True 3958 3958 96.023 1 2435 1 chr2B.!!$R1 2434

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
114 116 0.463654 TCGAAGCCCAATTAGCGCAT 60.464 50.0 11.47 0.0 34.64 4.73 F
843 846 0.548926 TGGGTCAACCAGGCCAGATA 60.549 55.0 5.01 0.0 46.80 1.98 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1400 1407 2.335933 GGTTTATGAGCCCTAGCCCTA 58.664 52.381 0.0 0.0 41.25 3.53 R
2151 2162 1.605753 TCTACCTCATCCCGATCACG 58.394 55.000 0.0 0.0 39.43 4.35 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
63 64 4.072131 GTTTAGGACAGAACATGCCTCAA 58.928 43.478 0.00 0.0 36.93 3.02
67 68 2.615912 GGACAGAACATGCCTCAATAGC 59.384 50.000 0.00 0.0 0.00 2.97
72 73 2.133281 ACATGCCTCAATAGCAAGCA 57.867 45.000 0.00 0.0 44.83 3.91
114 116 0.463654 TCGAAGCCCAATTAGCGCAT 60.464 50.000 11.47 0.0 34.64 4.73
160 162 2.466846 ACGAGTACACAAACTTGGTCG 58.533 47.619 0.00 0.0 35.50 4.79
341 343 9.770097 CACCTTACAATAACATATGAGAGACAT 57.230 33.333 10.38 0.0 42.39 3.06
515 518 3.950794 TTCGCCTAAGCACGGCCTG 62.951 63.158 0.00 0.0 44.73 4.85
759 762 3.611057 CGAAGTAACGTAACAGGAGCACT 60.611 47.826 0.00 0.0 0.00 4.40
761 764 4.431661 AGTAACGTAACAGGAGCACTAC 57.568 45.455 0.00 0.0 0.00 2.73
843 846 0.548926 TGGGTCAACCAGGCCAGATA 60.549 55.000 5.01 0.0 46.80 1.98
916 919 9.409949 GAGTGAATAGAAAATCGAAAATGTACG 57.590 33.333 0.00 0.0 0.00 3.67
1028 1031 2.445487 TGTGCAACGTCGAAAGAGTCG 61.445 52.381 0.00 0.0 46.87 4.18
1359 1366 2.114616 TGGTCAAAATGGGTTTGTGCT 58.885 42.857 0.00 0.0 45.83 4.40
1520 1527 5.604758 TCTCTTCACACCTCATATCAAGG 57.395 43.478 0.00 0.0 39.96 3.61
1565 1572 7.733773 TGGTCTCACTATTGGAAATTCTAGA 57.266 36.000 0.00 0.0 0.00 2.43
1844 1853 5.233689 ACAAAGTCACTTAGCTCAACGTTAC 59.766 40.000 0.00 0.0 0.00 2.50
2151 2162 2.158842 CCATCATGGTGAACCTCTCCTC 60.159 54.545 7.78 0.0 36.82 3.71
2251 2271 5.990668 ACAGTTCTCCTTAAACTTCTGTGT 58.009 37.500 0.00 0.0 34.79 3.72
2266 2286 5.422012 ACTTCTGTGTTTGGTGGAAAAGAAT 59.578 36.000 0.00 0.0 0.00 2.40
2333 2353 0.249657 GGATCGCTCACCAGCTAAGG 60.250 60.000 0.00 0.0 44.40 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 2.599659 GCGAAAAAGCTTGCTTGCTAT 58.400 42.857 8.73 0.00 43.24 2.97
67 68 2.031037 TACGCGAAAAAGCTTGCTTG 57.969 45.000 15.93 0.00 34.40 4.01
72 73 3.311596 GGTGGATATACGCGAAAAAGCTT 59.688 43.478 15.93 0.00 34.40 3.74
160 162 1.095807 GCACCGTCTAAATGCTCCCC 61.096 60.000 0.00 0.00 36.40 4.81
332 334 7.602753 TCGACAAAATAGAAAGATGTCTCTCA 58.397 34.615 0.00 0.00 38.54 3.27
341 343 7.981142 ACTTGTTGTTCGACAAAATAGAAAGA 58.019 30.769 6.99 0.00 40.15 2.52
759 762 4.323257 GGATCCGGAGAAGTTTTGAAGGTA 60.323 45.833 11.34 0.00 0.00 3.08
761 764 3.010420 GGATCCGGAGAAGTTTTGAAGG 58.990 50.000 11.34 0.00 0.00 3.46
843 846 7.011109 CGACCCGATCAAACTATTTCACTTATT 59.989 37.037 0.00 0.00 0.00 1.40
916 919 4.251268 AGTATTTCCGCTGGAACAACTAC 58.749 43.478 15.70 12.01 41.87 2.73
920 923 3.886505 ACAAAGTATTTCCGCTGGAACAA 59.113 39.130 9.15 0.00 41.87 2.83
1028 1031 2.460918 CGAACGATCCCACTACATCAC 58.539 52.381 0.00 0.00 0.00 3.06
1359 1366 5.008331 AGAGTAGATCGTTCAACACCTACA 58.992 41.667 11.34 0.00 31.55 2.74
1400 1407 2.335933 GGTTTATGAGCCCTAGCCCTA 58.664 52.381 0.00 0.00 41.25 3.53
1520 1527 3.418684 TCTTGACAAGCTACCTTTCCC 57.581 47.619 10.50 0.00 0.00 3.97
1565 1572 4.099419 AGAGCCGGTGAAAACAAAAGAAAT 59.901 37.500 1.90 0.00 0.00 2.17
1844 1853 7.565768 AGGGTATTCCTCCTTTACTCTCTTAAG 59.434 40.741 0.00 0.00 44.06 1.85
2151 2162 1.605753 TCTACCTCATCCCGATCACG 58.394 55.000 0.00 0.00 39.43 4.35
2251 2271 5.584253 TTGTTCGATTCTTTTCCACCAAA 57.416 34.783 0.00 0.00 0.00 3.28
2394 2414 2.434359 GAGAGGTTGTTCCGCCCG 60.434 66.667 0.00 0.00 41.99 6.13


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

AutoCloner maintained by Alex Coulton.