Multiple sequence alignment - TraesCS3A01G458900

Loading Multiple Alignment...

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 TraesCS3A01G458900 chr3A 100.000 2201 0 0 1 2201 695645711 695643511 0.000000e+00 4065
1 TraesCS3A01G458900 chr2A 98.457 2203 32 2 1 2201 726901127 726903329 0.000000e+00 3879
2 TraesCS3A01G458900 chr3B 98.139 2203 39 2 1 2201 201569459 201571661 0.000000e+00 3840
3 TraesCS3A01G458900 chr3B 97.911 2202 43 3 1 2201 201544845 201542646 0.000000e+00 3808
4 TraesCS3A01G458900 chr3B 97.001 1667 46 3 1 1664 757831129 757832794 0.000000e+00 2798
5 TraesCS3A01G458900 chr3B 96.680 482 16 0 1720 2201 757833037 757833518 0.000000e+00 802
6 TraesCS3A01G458900 chr3B 97.605 334 8 0 1512 1845 733064810 733064477 6.820000e-160 573
7 TraesCS3A01G458900 chr7B 98.093 2202 41 1 1 2201 662732241 662730040 0.000000e+00 3832
8 TraesCS3A01G458900 chr7B 98.002 2202 43 1 1 2201 663094098 663096299 0.000000e+00 3821
9 TraesCS3A01G458900 chr3D 98.003 2203 41 3 1 2201 589258200 589260401 0.000000e+00 3821
10 TraesCS3A01G458900 chr5D 97.957 2203 42 3 1 2201 503250598 503248397 0.000000e+00 3816
11 TraesCS3A01G458900 chr7A 97.867 2203 44 3 1 2201 258305486 258307687 0.000000e+00 3805


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 TraesCS3A01G458900 chr3A 695643511 695645711 2200 True 4065 4065 100.0000 1 2201 1 chr3A.!!$R1 2200
1 TraesCS3A01G458900 chr2A 726901127 726903329 2202 False 3879 3879 98.4570 1 2201 1 chr2A.!!$F1 2200
2 TraesCS3A01G458900 chr3B 201569459 201571661 2202 False 3840 3840 98.1390 1 2201 1 chr3B.!!$F1 2200
3 TraesCS3A01G458900 chr3B 201542646 201544845 2199 True 3808 3808 97.9110 1 2201 1 chr3B.!!$R1 2200
4 TraesCS3A01G458900 chr3B 757831129 757833518 2389 False 1800 2798 96.8405 1 2201 2 chr3B.!!$F2 2200
5 TraesCS3A01G458900 chr7B 662730040 662732241 2201 True 3832 3832 98.0930 1 2201 1 chr7B.!!$R1 2200
6 TraesCS3A01G458900 chr7B 663094098 663096299 2201 False 3821 3821 98.0020 1 2201 1 chr7B.!!$F1 2200
7 TraesCS3A01G458900 chr3D 589258200 589260401 2201 False 3821 3821 98.0030 1 2201 1 chr3D.!!$F1 2200
8 TraesCS3A01G458900 chr5D 503248397 503250598 2201 True 3816 3816 97.9570 1 2201 1 chr5D.!!$R1 2200
9 TraesCS3A01G458900 chr7A 258305486 258307687 2201 False 3805 3805 97.8670 1 2201 1 chr7A.!!$F1 2200

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
253 254 1.595357 GATTCGAACCCCCGACACT 59.405 57.895 0.0 0.0 38.39 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1575 1579 0.03716 GGCCTCCCAAAAGGTAACGA 59.963 55.0 0.0 0.0 46.39 3.85 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
86 87 9.981114 TTTCTATTGCATTCTATCTCATCGTAA 57.019 29.630 0.00 0.00 0.00 3.18
145 146 8.548877 AGGAAAGAGCATACCTAAGTTCAATAA 58.451 33.333 0.00 0.00 0.00 1.40
253 254 1.595357 GATTCGAACCCCCGACACT 59.405 57.895 0.00 0.00 38.39 3.55
444 445 8.514594 GTGATGATTGAGGTTTTGAATAAGACA 58.485 33.333 0.00 0.00 0.00 3.41
452 453 7.340743 TGAGGTTTTGAATAAGACAACCTTTGA 59.659 33.333 3.49 0.00 36.34 2.69
548 549 1.672363 CTGGCATCGAGCTATTTTGCA 59.328 47.619 7.17 0.00 44.79 4.08
666 668 2.297880 TCGAACCATGAACGAGGAAAGA 59.702 45.455 0.00 0.00 0.00 2.52
895 899 3.670055 TCAAATCGTTCGTTCGTTAGGAC 59.330 43.478 2.67 0.00 0.00 3.85
944 948 7.012894 CACTTCCACTTGACACCTATTTAAACA 59.987 37.037 0.00 0.00 0.00 2.83
1260 1264 0.526662 GGACCGAACTGTCTCACGAT 59.473 55.000 0.00 0.00 35.54 3.73
1278 1282 2.679059 CGATGTTCTGAACCCAGCTCAT 60.679 50.000 17.26 2.89 40.20 2.90
1487 1491 0.170561 GCCGACTTTCGTCTCTGCTA 59.829 55.000 0.00 0.00 38.40 3.49
1554 1558 2.185310 GACCAATGTCCGTCTGGCCT 62.185 60.000 3.32 0.00 35.34 5.19
1575 1579 1.620323 GAGGAAACCTTTGCATGCCTT 59.380 47.619 16.68 0.00 31.76 4.35
1673 1677 3.637769 AGGTTAGAATCCGAGCTCTTCT 58.362 45.455 17.76 17.76 33.91 2.85
1741 1932 1.480954 CTTCGCCTTCCACCTAAGCTA 59.519 52.381 0.00 0.00 0.00 3.32
2069 2260 1.289066 CGACTTTGCGGAGACCTGA 59.711 57.895 0.00 0.00 0.00 3.86
2091 2282 1.320507 TTTTGGTAAACAGTCGCCCC 58.679 50.000 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
145 146 0.383231 CGGGATAGCGGACGTAAAGT 59.617 55.000 0.00 0.00 0.00 2.66
191 192 0.033405 GGGGGAAGGGCCTTTACTTC 60.033 60.000 21.92 10.14 41.75 3.01
548 549 1.002274 CTGTAGGGGAGGTCCTGCT 59.998 63.158 10.60 0.00 39.76 4.24
841 845 0.652592 CACGGCCTGATCAAATCGAC 59.347 55.000 15.12 0.00 0.00 4.20
895 899 0.531311 TGATGTATGCAGCTGAGGCG 60.531 55.000 20.43 0.00 44.37 5.52
944 948 3.878519 GTAGCGGCGAGACGAGCT 61.879 66.667 12.98 15.40 42.51 4.09
1260 1264 1.421268 ACATGAGCTGGGTTCAGAACA 59.579 47.619 15.36 0.00 43.49 3.18
1278 1282 2.696566 CGCCCATTAATGCGGTACA 58.303 52.632 18.53 0.00 46.65 2.90
1487 1491 1.115930 ACTGCAAGACTCACCCGTCT 61.116 55.000 0.00 0.00 45.73 4.18
1554 1558 0.968405 GGCATGCAAAGGTTTCCTCA 59.032 50.000 21.36 0.00 30.89 3.86
1575 1579 0.037160 GGCCTCCCAAAAGGTAACGA 59.963 55.000 0.00 0.00 46.39 3.85
1644 1648 4.566004 CTCGGATTCTAACCTTGTGTCAA 58.434 43.478 0.00 0.00 0.00 3.18
1673 1677 3.891977 GCCATCAGTGAGATACCACTCTA 59.108 47.826 0.00 0.00 44.87 2.43
1741 1932 2.041153 CTTTGGGCCTTTCTTGCGT 58.959 52.632 4.53 0.00 0.00 5.24
2069 2260 2.359848 GGGCGACTGTTTACCAAAAACT 59.640 45.455 0.00 0.00 0.00 2.66
2161 2352 5.182380 CGAGACAACTCTCTCTAAGGAACTT 59.818 44.000 0.00 0.00 45.71 2.66


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

AutoCloner maintained by Alex Coulton.