Multiple sequence alignment - TraesCS5A01G093200

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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 TraesCS5A01G093200 chr5A 100.000 6759 0 0 1 6759 129605415 129598657 0.000000e+00 12482
1 TraesCS5A01G093200 chr5A 92.414 145 8 1 2798 2939 129602540 129602396 3.200000e-48 204
2 TraesCS5A01G093200 chr5A 92.414 145 8 1 2876 3020 129602618 129602477 3.200000e-48 204
3 TraesCS5A01G093200 chr5D 94.667 5982 224 50 818 6746 119489710 119483771 0.000000e+00 9191
4 TraesCS5A01G093200 chr5D 88.650 326 32 3 472 796 119490018 119489697 6.350000e-105 392
5 TraesCS5A01G093200 chr5D 90.698 215 18 2 31 243 119490302 119490088 1.110000e-72 285
6 TraesCS5A01G093200 chr5D 91.724 145 9 1 2876 3020 119487739 119487598 1.490000e-46 198
7 TraesCS5A01G093200 chr5B 96.920 5000 127 13 818 5797 132291083 132286091 0.000000e+00 8355
8 TraesCS5A01G093200 chr5B 95.665 1015 38 3 5745 6759 132286088 132285080 0.000000e+00 1626
9 TraesCS5A01G093200 chr5B 80.616 552 80 13 166 693 132292945 132292397 1.060000e-107 401
10 TraesCS5A01G093200 chr5B 90.148 203 12 5 11 207 132293144 132292944 2.420000e-64 257
11 TraesCS5A01G093200 chr5B 91.216 148 7 2 2876 3020 132289096 132288952 5.350000e-46 196
12 TraesCS5A01G093200 chr5B 90.244 123 11 1 216 337 57958187 57958065 7.020000e-35 159
13 TraesCS5A01G093200 chr2D 86.449 214 25 3 6546 6759 500811759 500811968 1.470000e-56 231
14 TraesCS5A01G093200 chr3A 85.000 220 24 5 6546 6759 25032143 25031927 1.480000e-51 215
15 TraesCS5A01G093200 chr2B 85.311 177 26 0 160 336 796178775 796178951 4.160000e-42 183
16 TraesCS5A01G093200 chr7A 85.897 156 21 1 181 336 228170085 228169931 1.510000e-36 165
17 TraesCS5A01G093200 chr7A 81.622 185 30 4 162 343 646840087 646840270 4.220000e-32 150
18 TraesCS5A01G093200 chr7A 86.923 130 15 2 208 336 721589702 721589830 1.960000e-30 145
19 TraesCS5A01G093200 chrUn 81.915 188 25 5 162 343 389438310 389438494 4.220000e-32 150
20 TraesCS5A01G093200 chrUn 81.915 188 25 5 162 343 415837373 415837557 4.220000e-32 150
21 TraesCS5A01G093200 chr7B 81.915 188 25 5 162 343 611262567 611262751 4.220000e-32 150
22 TraesCS5A01G093200 chr3D 81.921 177 28 4 162 336 606613616 606613790 5.460000e-31 147


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 TraesCS5A01G093200 chr5A 129598657 129605415 6758 True 4296.666667 12482 94.942667 1 6759 3 chr5A.!!$R1 6758
1 TraesCS5A01G093200 chr5D 119483771 119490302 6531 True 2516.500000 9191 91.434750 31 6746 4 chr5D.!!$R1 6715
2 TraesCS5A01G093200 chr5B 132285080 132293144 8064 True 2167.000000 8355 90.913000 11 6759 5 chr5B.!!$R2 6748


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
418 465 0.037590 TGGGACAAAAGCTATGCGGT 59.962 50.000 0.00 0.0 31.92 5.68 F
794 872 0.249322 CACAACTGACCGACGGAACT 60.249 55.000 23.38 0.0 0.00 3.01 F
1879 3192 0.108138 CGGCAGGAGAAACTTCCGAT 60.108 55.000 0.00 0.0 42.29 4.18 F
1957 3270 0.253207 CCTCCCCTCCCAAGTTAGGT 60.253 60.000 0.00 0.0 0.00 3.08 F
2849 4165 0.882042 AACAGAAGCTGTCACTGGCG 60.882 55.000 0.00 0.0 44.62 5.69 F
2850 4166 1.301244 CAGAAGCTGTCACTGGCGT 60.301 57.895 0.00 0.0 0.00 5.68 F
4464 5832 1.886777 GAAGCCTGAGCAGATCCGC 60.887 63.158 0.00 0.0 43.56 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1567 2880 0.034767 TGCTGAATTCAGGGGAGCTG 60.035 55.000 31.41 9.72 43.94 4.24 R
2065 3378 0.374758 CGGTGAATGCTCCAATGTCG 59.625 55.000 0.00 0.00 0.00 4.35 R
2849 4165 0.889306 ACTGTAGGAGGCTCAACGAC 59.111 55.000 17.69 6.94 0.00 4.34 R
3095 4411 0.976641 TCCTCAGTTACCACAGCAGG 59.023 55.000 0.00 0.00 0.00 4.85 R
4464 5832 0.876342 GGCCCTCGACAATCTTAGCG 60.876 60.000 0.00 0.00 0.00 4.26 R
4907 6275 7.993183 CCTGGAAACATAGGTATGTCAAGTTAT 59.007 37.037 3.12 0.00 45.55 1.89 R
6185 7607 1.004745 TCTCTTGGTGGGCAATCTTCC 59.995 52.381 0.00 0.00 0.00 3.46 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.