Multiple sequence alignment - TraesCS4A01G155700

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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 TraesCS4A01G155700 chr4A 100.000 2543 0 0 1 2543 310769165 310766623 0.000000e+00 4697.0
1 TraesCS4A01G155700 chr4A 94.201 2552 122 20 2 2541 219303505 219306042 0.000000e+00 3869.0
2 TraesCS4A01G155700 chr4A 98.438 128 1 1 2077 2204 319776736 319776610 9.160000e-55 224.0
3 TraesCS4A01G155700 chr4A 96.907 97 2 1 2011 2106 319776829 319776733 7.280000e-36 161.0
4 TraesCS4A01G155700 chr4A 95.506 89 3 1 2077 2165 159317553 159317466 9.490000e-30 141.0
5 TraesCS4A01G155700 chr4A 85.870 92 10 3 2253 2342 734071675 734071585 7.490000e-16 95.3
6 TraesCS4A01G155700 chr5A 96.038 2549 81 15 2 2541 482022868 482025405 0.000000e+00 4130.0
7 TraesCS4A01G155700 chr3B 95.961 2550 78 19 2 2541 201554277 201556811 0.000000e+00 4115.0
8 TraesCS4A01G155700 chr7B 93.922 2550 130 17 2 2541 105211998 105209464 0.000000e+00 3827.0
9 TraesCS4A01G155700 chr3D 95.728 2341 87 12 2 2334 158932017 158929682 0.000000e+00 3757.0
10 TraesCS4A01G155700 chr3D 95.519 2343 88 15 2 2334 158938132 158935797 0.000000e+00 3729.0
11 TraesCS4A01G155700 chr3D 96.056 2079 72 10 2 2075 589249360 589247287 0.000000e+00 3376.0
12 TraesCS4A01G155700 chr5D 95.436 1928 80 8 2 1925 432405904 432407827 0.000000e+00 3066.0
13 TraesCS4A01G155700 chrUn 95.647 1562 55 10 2 1555 371791564 371790008 0.000000e+00 2495.0
14 TraesCS4A01G155700 chr5B 95.082 1525 59 9 1020 2541 429042125 429040614 0.000000e+00 2386.0


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 TraesCS4A01G155700 chr4A 310766623 310769165 2542 True 4697 4697 100.0000 1 2543 1 chr4A.!!$R2 2542
1 TraesCS4A01G155700 chr4A 219303505 219306042 2537 False 3869 3869 94.2010 2 2541 1 chr4A.!!$F1 2539
2 TraesCS4A01G155700 chr5A 482022868 482025405 2537 False 4130 4130 96.0380 2 2541 1 chr5A.!!$F1 2539
3 TraesCS4A01G155700 chr3B 201554277 201556811 2534 False 4115 4115 95.9610 2 2541 1 chr3B.!!$F1 2539
4 TraesCS4A01G155700 chr7B 105209464 105211998 2534 True 3827 3827 93.9220 2 2541 1 chr7B.!!$R1 2539
5 TraesCS4A01G155700 chr3D 158929682 158938132 8450 True 3743 3757 95.6235 2 2334 2 chr3D.!!$R2 2332
6 TraesCS4A01G155700 chr3D 589247287 589249360 2073 True 3376 3376 96.0560 2 2075 1 chr3D.!!$R1 2073
7 TraesCS4A01G155700 chr5D 432405904 432407827 1923 False 3066 3066 95.4360 2 1925 1 chr5D.!!$F1 1923
8 TraesCS4A01G155700 chrUn 371790008 371791564 1556 True 2495 2495 95.6470 2 1555 1 chrUn.!!$R1 1553
9 TraesCS4A01G155700 chr5B 429040614 429042125 1511 True 2386 2386 95.0820 1020 2541 1 chr5B.!!$R1 1521

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
940 7073 1.792367 GTGGCGGCATTCTTGAAAAAC 59.208 47.619 17.19 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2444 8593 4.097741 CAGGAATGAGTGGTTTTGTCACAA 59.902 41.667 0.0 0.0 37.58 3.33 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
402 6528 7.362802 AGTGGAGTATTCTTACAATAGGACC 57.637 40.000 0.00 0.00 0.00 4.46
688 6820 4.037446 GCAGTGTTTGTGTTTCTATTGGGA 59.963 41.667 0.00 0.00 0.00 4.37
699 6831 5.164233 GTTTCTATTGGGAAAAGCAAGAGC 58.836 41.667 0.00 0.00 37.02 4.09
743 6876 5.873732 ACGATACTACCAAACGAAGTCTAC 58.126 41.667 0.00 0.00 45.00 2.59
940 7073 1.792367 GTGGCGGCATTCTTGAAAAAC 59.208 47.619 17.19 0.00 0.00 2.43
1064 7197 9.699985 CTCTTTCTCAACGATTTCAATTATGAG 57.300 33.333 0.00 0.00 36.78 2.90
1119 7252 4.819105 ACTTGGAGGATTACGTGATTCA 57.181 40.909 0.00 0.00 0.00 2.57
1123 7256 5.351948 TGGAGGATTACGTGATTCATCAA 57.648 39.130 0.00 0.00 38.75 2.57
1330 7465 5.122711 ACGCCAAGTACTATTTTAACGCAAT 59.877 36.000 0.00 0.00 0.00 3.56
1371 7506 6.815142 GCCTTTTAACTGAAATGCATCAATCT 59.185 34.615 0.00 0.00 32.57 2.40
1375 7510 5.490139 AACTGAAATGCATCAATCTACGG 57.510 39.130 0.00 0.00 0.00 4.02
1456 7591 2.886523 AGCTATGCAACTCTTTTGTGCA 59.113 40.909 0.00 0.00 39.91 4.57
1458 7593 2.806608 ATGCAACTCTTTTGTGCAGG 57.193 45.000 3.77 0.00 38.95 4.85
1475 7610 2.224305 GCAGGTCCTTATTATCTGCCGT 60.224 50.000 0.00 0.00 43.36 5.68
1855 7994 7.638444 TCCACATTGGAAAGGTATGAATTCTA 58.362 34.615 7.05 0.00 45.00 2.10
2067 8207 5.886960 AGGGTTCTCAAAAATTCGAGATG 57.113 39.130 3.75 0.00 38.06 2.90
2122 8264 9.084164 TGCATTAATAGAGAAGACGAGTAAAAC 57.916 33.333 0.00 0.00 0.00 2.43
2127 8274 5.908916 AGAGAAGACGAGTAAAACAAAGC 57.091 39.130 0.00 0.00 0.00 3.51
2130 8277 6.315393 AGAGAAGACGAGTAAAACAAAGCAAA 59.685 34.615 0.00 0.00 0.00 3.68
2131 8278 7.012421 AGAGAAGACGAGTAAAACAAAGCAAAT 59.988 33.333 0.00 0.00 0.00 2.32
2541 8690 3.529319 GCATTGGGATAGATATTCCCCCT 59.471 47.826 8.26 0.00 42.91 4.79
2542 8691 4.726825 GCATTGGGATAGATATTCCCCCTA 59.273 45.833 8.26 0.58 42.91 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 7.693951 CGCTCGAAAATGATCTTGATTTTACTT 59.306 33.333 3.05 0.00 34.00 2.24
279 6405 5.699458 ACTTAGCACACAGTATACCAAACAC 59.301 40.000 0.00 0.00 0.00 3.32
402 6528 5.422331 TGGAGAAGATAGGTGGAAGTTGTAG 59.578 44.000 0.00 0.00 0.00 2.74
497 6625 9.416284 AGGATAAATATAAAAGGCTTTTTCGGA 57.584 29.630 28.33 12.48 37.64 4.55
634 6766 7.565680 AGAGTTGGAACTTCTTTTCTCTAACA 58.434 34.615 0.00 0.00 39.88 2.41
641 6773 6.473778 GCTTGAAAGAGTTGGAACTTCTTTTC 59.526 38.462 13.46 13.24 39.88 2.29
906 7039 1.079405 GCCACTCGGATTCGAACCA 60.079 57.895 0.00 0.00 45.47 3.67
966 7099 8.590204 AGGTCCCATTACGAAATTGTAAATTTT 58.410 29.630 0.00 0.00 37.81 1.82
1026 7159 7.708051 TCGTTGAGAAAGAGATATGAGTTAGG 58.292 38.462 0.00 0.00 0.00 2.69
1212 7345 8.557864 CATGAAAGGAAGATCAATGACTCATAC 58.442 37.037 0.00 0.00 0.00 2.39
1347 7482 9.294030 GTAGATTGATGCATTTCAGTTAAAAGG 57.706 33.333 0.00 0.00 0.00 3.11
1375 7510 6.766944 TGAGATTGTAGAGCAGGTACTAGTAC 59.233 42.308 22.53 22.53 36.02 2.73
1456 7591 6.270231 AGAATAACGGCAGATAATAAGGACCT 59.730 38.462 0.00 0.00 0.00 3.85
1458 7593 9.654663 ATTAGAATAACGGCAGATAATAAGGAC 57.345 33.333 0.00 0.00 0.00 3.85
1742 7881 4.729552 TCCCAATTCCAATAGGATCCAG 57.270 45.455 15.82 0.28 45.26 3.86
1743 7882 5.261040 GATCCCAATTCCAATAGGATCCA 57.739 43.478 15.82 0.00 44.81 3.41
1834 7973 8.511604 AGTGTAGAATTCATACCTTTCCAATG 57.488 34.615 8.44 0.00 0.00 2.82
1855 7994 8.184304 AGAAATCCTATCGAAGCTATAAGTGT 57.816 34.615 0.00 0.00 0.00 3.55
1936 8076 7.798596 TTAGGTGTTAATGTAAACGAACCAA 57.201 32.000 0.00 0.00 31.17 3.67
2109 8251 7.027778 AGATTTGCTTTGTTTTACTCGTCTT 57.972 32.000 0.00 0.00 0.00 3.01
2444 8593 4.097741 CAGGAATGAGTGGTTTTGTCACAA 59.902 41.667 0.00 0.00 37.58 3.33


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

AutoCloner maintained by Alex Coulton.