Multiple sequence alignment - TraesCS5A01G416500

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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 TraesCS5A01G416500 chr5A 100.000 5217 0 0 376 5592 605157005 605162221 0.000000e+00 9635.0
1 TraesCS5A01G416500 chr5A 100.000 104 0 0 1 104 605156630 605156733 5.720000e-45 193.0
2 TraesCS5A01G416500 chr5B 87.245 2062 161 48 2358 4348 594907208 594909238 0.000000e+00 2257.0
3 TraesCS5A01G416500 chr5B 92.959 838 49 6 4471 5304 594909422 594910253 0.000000e+00 1212.0
4 TraesCS5A01G416500 chr5B 94.792 288 13 2 5305 5592 594910296 594910581 1.110000e-121 448.0
5 TraesCS5A01G416500 chr5B 84.635 384 20 12 1918 2282 594906804 594907167 4.150000e-91 346.0
6 TraesCS5A01G416500 chr5B 82.792 308 31 13 1210 1499 594906349 594906652 7.190000e-64 255.0
7 TraesCS5A01G416500 chr5B 87.940 199 24 0 583 781 294549178 294549376 9.370000e-58 235.0
8 TraesCS5A01G416500 chr5B 75.635 197 42 6 589 782 612629644 612629451 5.970000e-15 93.5
9 TraesCS5A01G416500 chr5D 89.766 1710 109 23 3925 5592 483703503 483705188 0.000000e+00 2128.0
10 TraesCS5A01G416500 chr5D 90.749 1535 105 19 2412 3926 483701824 483703341 0.000000e+00 2013.0
11 TraesCS5A01G416500 chr5D 84.921 378 24 13 869 1217 483700492 483700865 8.910000e-93 351.0
12 TraesCS5A01G416500 chr5D 86.640 247 15 8 2041 2282 483701407 483701640 2.000000e-64 257.0
13 TraesCS5A01G416500 chr5D 91.935 62 5 0 2361 2422 483701685 483701746 2.780000e-13 87.9
14 TraesCS5A01G416500 chr3D 91.288 528 31 10 2426 2941 7926736 7926212 0.000000e+00 706.0
15 TraesCS5A01G416500 chr3D 84.840 376 25 13 1952 2317 7927301 7926948 3.210000e-92 350.0
16 TraesCS5A01G416500 chr3D 93.467 199 12 1 583 781 586513908 586513711 1.520000e-75 294.0
17 TraesCS5A01G416500 chr2B 76.768 198 42 4 589 785 117106835 117107029 2.130000e-19 108.0


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 TraesCS5A01G416500 chr5A 605156630 605162221 5591 False 4914.00 9635 100.0000 1 5592 2 chr5A.!!$F1 5591
1 TraesCS5A01G416500 chr5B 594906349 594910581 4232 False 903.60 2257 88.4846 1210 5592 5 chr5B.!!$F2 4382
2 TraesCS5A01G416500 chr5D 483700492 483705188 4696 False 967.38 2128 88.8022 869 5592 5 chr5D.!!$F1 4723
3 TraesCS5A01G416500 chr3D 7926212 7927301 1089 True 528.00 706 88.0640 1952 2941 2 chr3D.!!$R2 989


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
843 844 0.033601 TTTGATAACCATGGGCCGCT 60.034 50.0 18.09 0.0 0.00 5.52 F
851 852 0.038166 CCATGGGCCGCTAATGGTAT 59.962 55.0 11.54 0.0 36.82 2.73 F
2200 2358 0.027586 CGGAAATTTTAGGCTCGGCG 59.972 55.0 0.00 0.0 0.00 6.46 F
3112 3522 0.035881 CTGGGGCAGCGATCATATGT 59.964 55.0 1.90 0.0 0.00 2.29 F
3566 3996 0.749454 GGACGCTGCCTTCATCCAAT 60.749 55.0 0.00 0.0 0.00 3.16 F
4268 4901 0.737219 GGGCATCAGAAGCACATGAC 59.263 55.0 0.00 0.0 34.91 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1949 0.036732 GGCATTGGTGTGAGGACTGA 59.963 55.0 0.00 0.00 0.00 3.41 R
2672 3071 0.041839 GTGCGTGTCAAGAACTGCAG 60.042 55.0 13.48 13.48 39.50 4.41 R
3566 3996 0.173481 AGCTGAGCTTCGCAACGATA 59.827 50.0 0.00 0.00 33.89 2.92 R
4230 4862 0.036010 CCAACTGGGCTGTAGACCTG 60.036 60.0 8.92 8.92 45.91 4.00 R
4504 5202 0.967380 AAAATGGCAAGAGAGGGCGG 60.967 55.0 0.00 0.00 0.00 6.13 R
5117 5830 1.347320 CGACGTCTTCTAAGCCAACC 58.653 55.0 14.70 0.00 0.00 3.77 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)



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

AutoCloner maintained by Alex Coulton.